diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index cfdefdb714..2e6d40ab70 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -10,7 +10,9 @@ on: pull_request: branches: [main, master] -name: R-CMD-check +name: R-CMD-check.yaml + +permissions: read-all jobs: R-CMD-check: @@ -25,15 +27,15 @@ jobs: - {os: macos-latest, r: 'release'} - {os: windows-latest, r: 'release'} - # use 4.1 to check with rtools40's older compiler - - {os: windows-latest, r: '4.1'} + # use 4.0 or 4.1 to check with rtools40's older compiler + - {os: windows-latest, r: 'oldrel-4'} - - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} - - {os: ubuntu-latest, r: 'release'} - - {os: ubuntu-latest, r: 'oldrel-1'} - - {os: ubuntu-latest, r: 'oldrel-2'} - - {os: ubuntu-latest, r: 'oldrel-3'} - - {os: ubuntu-latest, r: 'oldrel-4'} + - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} + - {os: ubuntu-latest, r: 'release'} + - {os: ubuntu-latest, r: 'oldrel-1'} + - {os: ubuntu-latest, r: 'oldrel-2'} + - {os: ubuntu-latest, r: 'oldrel-3'} + - {os: ubuntu-latest, r: 'oldrel-4'} env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} @@ -46,7 +48,7 @@ jobs: VDIFFR_LOG_PATH: "../vdiffr.Rout.fail" steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-pandoc@v2 @@ -62,9 +64,10 @@ jobs: extra-packages: > any::rcmdcheck, Hmisc=?ignore-before-r=4.1.0, - quantreg=?ignore-before-r=4.3.0, + quantreg=?ignore-before-r=4.3.0 needs: check - uses: r-lib/actions/check-r-package@v2 with: upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 087f0b05fc..4bbce75080 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -9,7 +9,9 @@ on: types: [published] workflow_dispatch: -name: pkgdown +name: pkgdown.yaml + +permissions: read-all jobs: pkgdown: @@ -19,8 +21,10 @@ jobs: group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + permissions: + contents: write steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-pandoc@v2 @@ -39,7 +43,7 @@ jobs: - name: Deploy to GitHub pages 🚀 if: github.event_name != 'pull_request' - uses: JamesIves/github-pages-deploy-action@v4.4.1 + uses: JamesIves/github-pages-deploy-action@v4.5.0 with: clean: false branch: gh-pages diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml index 71f335b3ea..2edd93f27e 100644 --- a/.github/workflows/pr-commands.yaml +++ b/.github/workflows/pr-commands.yaml @@ -4,7 +4,9 @@ on: issue_comment: types: [created] -name: Commands +name: pr-commands.yaml + +permissions: read-all jobs: document: @@ -13,8 +15,10 @@ jobs: runs-on: ubuntu-latest env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + permissions: + contents: write steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/pr-fetch@v2 with: @@ -50,8 +54,10 @@ jobs: runs-on: ubuntu-latest env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + permissions: + contents: write steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/pr-fetch@v2 with: diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 2c5bb50294..988226098e 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -6,7 +6,9 @@ on: pull_request: branches: [main, master] -name: test-coverage +name: test-coverage.yaml + +permissions: read-all jobs: test-coverage: @@ -15,7 +17,7 @@ jobs: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-r@v2 with: @@ -23,28 +25,37 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::covr + extra-packages: any::covr, any::xml2 needs: coverage - name: Test coverage run: | - covr::codecov( + cov <- covr::package_coverage( quiet = FALSE, clean = FALSE, - install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package") + install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") ) + covr::to_cobertura(cov) shell: Rscript {0} + - uses: codecov/codecov-action@v4 + with: + fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }} + file: ./cobertura.xml + plugin: noop + disable_search: true + token: ${{ secrets.CODECOV_TOKEN }} + - name: Show testthat output if: always() run: | ## -------------------------------------------------------------------- - find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true + find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true shell: bash - name: Upload test results if: failure() - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: coverage-test-failures path: ${{ runner.temp }}/package diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 8796efb5d8..77553769db 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -61,20 +61,19 @@ Each of these steps are described in more detail below. This might feel overwhelming the first time you get set up, but it gets easier with practice. If you get stuck at any point, please reach out for help on the [ggplot2-dev](https://groups.google.com/forum/#!forum/ggplot2-dev) mailing list. -If you're not familiar with git or github, please start by reading +If you're not familiar with git or github, please start by reading Pull requests will be evaluated against a seven point checklist: @@ -100,20 +99,16 @@ Pull requests will be evaluated against a seven point checklist: and don't submit any others until the first one has been processed. 1. __Use ggplot2 coding style__. Please follow the - [official tidyverse style](http://style.tidyverse.org). Maintaining + [official tidyverse style](https://style.tidyverse.org). Maintaining a consistent style across the whole code base makes it much easier to jump into the code. If you're modifying existing ggplot2 code that doesn't follow the style guide, a separate pull request to fix the style would be greatly appreciated. 1. If you're adding new parameters or a new function, you'll also need - to document them with [roxygen](https://github.com/klutometis/roxygen). + to document them with [roxygen2](https://github.com/r-lib/roxygen2). Make sure to re-run `devtools::document()` on the code before submitting. - Currently, ggplot2 uses the development version of roxygen2, which you - can get with `install_github("klutometis/roxygen")`. This will be - available on CRAN in the near future. - 1. If fixing a bug or adding a new feature to a non-graphical function, please add a [testthat](https://github.com/r-lib/testthat) unit test. diff --git a/DESCRIPTION b/DESCRIPTION index 3f34454b36..b4cd9ec950 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -39,11 +39,9 @@ Imports: isoband, lifecycle (> 1.0.1), MASS, - mgcv, rlang (>= 1.1.0), scales (>= 1.3.0), stats, - tibble, vctrs (>= 0.6.0), withr (>= 2.5.0) Suggests: @@ -55,6 +53,7 @@ Suggests: knitr, mapproj, maps, + mgcv, multcomp, munsell, nlme, @@ -67,6 +66,7 @@ Suggests: sf (>= 0.7-3), svglite (>= 2.1.2), testthat (>= 3.1.5), + tibble, vdiffr (>= 1.0.6), xml2 Enhances: @@ -78,7 +78,7 @@ Config/testthat/edition: 3 Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.2 Collate: 'ggproto.R' 'ggplot-global.R' diff --git a/NAMESPACE b/NAMESPACE index 6a57c5132d..f0ccf3bec1 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -344,6 +344,7 @@ export(draw_key_vpath) export(dup_axis) export(el_def) export(element_blank) +export(element_geom) export(element_grob) export(element_line) export(element_rect) @@ -367,6 +368,7 @@ export(find_panel) export(flip_data) export(flipped_names) export(fortify) +export(from_theme) export(geom_abline) export(geom_area) export(geom_bar) @@ -422,6 +424,7 @@ export(geom_violin) export(geom_vline) export(get_alt_text) export(get_element_tree) +export(get_geom_defaults) export(get_guide_data) export(get_last_plot) export(get_layer_data) @@ -513,6 +516,8 @@ export(remove_missing) export(render_axes) export(render_strips) export(replace_theme) +export(reset_geom_defaults) +export(reset_stat_defaults) export(reset_theme_settings) export(resolution) export(scale_alpha) @@ -733,7 +738,6 @@ importFrom(grid,unit) importFrom(lifecycle,deprecated) importFrom(scales,alpha) importFrom(stats,setNames) -importFrom(tibble,tibble) importFrom(utils,.DollarNames) importFrom(utils,head) importFrom(utils,tail) diff --git a/NEWS.md b/NEWS.md index c1d1ae252b..c527454cdd 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,7 +1,33 @@ # ggplot2 (development version) -* The ellipsis argument is now checked in `fortify()`, `get_alt_text()`, - `labs()` and several guides (@teunbrand, #3196). +* (Breaking) The defaults for all geoms can be set at one in the theme. + (@teunbrand based on pioneering work by @dpseidel, #2239) + * A new `theme(geom)` argument is used to track these defaults. + * The `element_geom()` function can be used to populate that argument. + * The `from_theme()` function allows access to the theme default fields from + inside the `aes()` function. +* Passing empty unmapped aesthetics to layers raises a warning instead of + throwing an error (@teunbrand, #6009). +* Moved {mgcv} from Imports to Suggests (@teunbrand, #5986) +* New `reset_geom_defaults()` and `reset_stat_defaults()` to restore all geom or + stat default aesthetics at once (@teunbrand, #5975). +* `facet_wrap()` can have `space = "free_x"` with 1-row layouts and + `space = "free_y"` with 1-column layouts (@teunbrand) +* Secondary axes respect `n.breaks` setting in continuous scales (@teunbrand, #4483). +* Layers can have names (@teunbrand, #4066). +* (internal) improvements to `pal_qualitative()` (@teunbrand, #5013) +* `coord_radial(clip = "on")` clips to the panel area when the graphics device + supports clipping paths (@teunbrand, #5952). +* (internal) Panel clipping responsibility moved from Facet class to Coord + class through new `Coord$draw_panel()` method. +* `theme(strip.clip)` now defaults to `"on"` and is independent of Coord + clipping (@teunbrand, 5952). +* (internal) rearranged the code of `Facet$draw_paensl()` method (@teunbrand). +* Axis labels are now justified across facet panels (@teunbrand, #5820) +* Fixed bug in `stat_function()` so x-axis title now produced automatically + when no data added. (@phispu, #5647). +* geom_sf now accepts shape names (@sierrajohnson, #5808) +* Added `gg` class to `labs()` (@phispu, #5553). * Missing values from discrete palettes are no longer translated (@teunbrand, #5929). * Fixed bug in `facet_grid(margins = TRUE)` when using expresssions @@ -135,6 +161,15 @@ (@teunbrand, #5938, #4327). * Fixed bug where empty discrete scales weren't recognised as such (@teunbrand, #5945). +* (internal) The summary function of `stat_summary()` and `stat_summary_bin()` + is setup once in total instead of once per group (@teunbrand, #5971) +* `facet_grid(space = "free")` can now be combined with `coord_fixed()` + (@teunbrand, #4584). +* `theme_classic()` now has black ticks and text instead of dark gray. In + addition, `theme_classic()`'s axis line end is `"square"` (@teunbrand, #5978). +* {tibble} is now suggested instead of imported (@teunbrand, #5986) +* The ellipsis argument is now checked in `fortify()`, `get_alt_text()`, + `labs()` and several guides (@teunbrand, #3196). # ggplot2 3.5.1 diff --git a/R/aes-evaluation.R b/R/aes-evaluation.R index 4c682e3f63..5554b54772 100644 --- a/R/aes-evaluation.R +++ b/R/aes-evaluation.R @@ -109,6 +109,13 @@ #' fun.data = ~ round(data.frame(mean = mean(.x), sd = sd(.x)), 2) #' ) #' ``` +#' +#' ## Theme access +#' The `from_theme()` function can be used to acces the [`element_geom()`] +#' fields of the `theme(geom)` argument. Using `aes(colour = from_theme(ink))` +#' and `aes(colour = from_theme(accent))` allows swapping between foreground and +#' accent colours. +#' #' @rdname aes_eval #' @name aes_eval #' @@ -192,6 +199,13 @@ stat <- function(x) { after_scale <- function(x) { x } + +#' @rdname aes_eval +#' @export +from_theme <- function(x) { + x +} + #' @rdname aes_eval #' @export stage <- function(start = NULL, after_stat = NULL, after_scale = NULL) { @@ -221,6 +235,9 @@ is_scaled_aes <- function(aesthetics) { is_staged_aes <- function(aesthetics) { vapply(aesthetics, is_staged, logical(1), USE.NAMES = FALSE) } +is_themed_aes <- function(aesthetics) { + vapply(aesthetics, is_themed, logical(1), USE.NAMES = FALSE) +} is_calculated <- function(x, warn = FALSE) { if (is_call(get_expr(x), "after_stat")) { return(TRUE) @@ -263,6 +280,9 @@ is_scaled <- function(x) { is_staged <- function(x) { is_call(get_expr(x), "stage") } +is_themed <- function(x) { + is_call(get_expr(x), "from_theme") +} # Strip dots from expressions strip_dots <- function(expr, env, strip_pronoun = FALSE) { diff --git a/R/annotation-logticks.R b/R/annotation-logticks.R index 33f0a952a4..aa03d472cf 100644 --- a/R/annotation-logticks.R +++ b/R/annotation-logticks.R @@ -165,7 +165,7 @@ GeomLogticks <- ggproto("GeomLogticks", Geom, names(xticks)[names(xticks) == "value"] <- x_name # Rename to 'x' for coordinates$transform xticks <- coord$transform(xticks, panel_params) - xticks = xticks[xticks$x <= 1 & xticks$x >= 0,] + xticks <- xticks[xticks$x <= 1 & xticks$x >= 0,] if (outside) xticks$end = -xticks$end @@ -203,7 +203,7 @@ GeomLogticks <- ggproto("GeomLogticks", Geom, names(yticks)[names(yticks) == "value"] <- y_name # Rename to 'y' for coordinates$transform yticks <- coord$transform(yticks, panel_params) - yticks = yticks[yticks$y <= 1 & yticks$y >= 0,] + yticks <- yticks[yticks$y <= 1 & yticks$y >= 0,] if (outside) yticks$end = -yticks$end @@ -228,7 +228,12 @@ GeomLogticks <- ggproto("GeomLogticks", Geom, gTree(children = inject(gList(!!!ticks))) }, - default_aes = aes(colour = "black", linewidth = 0.5, linetype = 1, alpha = 1) + default_aes = aes( + colour = from_theme(ink), + linewidth = from_theme(linewidth), + linetype = from_theme(linetype), + alpha = 1 + ) ) @@ -238,7 +243,7 @@ GeomLogticks <- ggproto("GeomLogticks", Geom, # - start: on the other axis, start position of the line (usually 0) # - end: on the other axis, end position of the line (for example, .1, .2, or .3) calc_logticks <- function(base = 10, ticks_per_base = base - 1, - minpow = 0, maxpow = minpow + 1, start = 0, shortend = .1, midend = .2, longend = .3) { + minpow = 0, maxpow = minpow + 1, start = 0, shortend = 0.1, midend = 0.2, longend = 0.3) { # Number of blocks of tick marks reps <- maxpow - minpow diff --git a/R/axis-secondary.R b/R/axis-secondary.R index e535b1a95a..2999bd79b5 100644 --- a/R/axis-secondary.R +++ b/R/axis-secondary.R @@ -188,7 +188,13 @@ AxisSecondary <- ggproto("AxisSecondary", NULL, if (scale$is_discrete()) { self$breaks <- scale$get_breaks() } else { - self$breaks <- scale$get_transformation()$breaks + breaks <- scale$get_transformation()$breaks + n_breaks <- scale$n.breaks + if (!is.null(n_breaks) && "n" %in% fn_fmls_names(breaks)) { + self$breaks <- function(x) breaks(x, n = n_breaks) + } else { + self$breaks <- breaks + } } } if (is.derived(self$labels)) self$labels <- scale$labels diff --git a/R/bin.R b/R/bin.R index 856568f08c..a7784d02e5 100644 --- a/R/bin.R +++ b/R/bin.R @@ -165,7 +165,7 @@ bin_vector <- function(x, bins, weight = NULL, pad = FALSE) { } # Add row for missings - if (any(is.na(bins))) { + if (anyNA(bins)) { bin_count <- c(bin_count, sum(is.na(bins))) bin_widths <- c(bin_widths, NA) bin_x <- c(bin_x, NA) diff --git a/R/compat-plyr.R b/R/compat-plyr.R index 95c317a02c..efc2865a0c 100644 --- a/R/compat-plyr.R +++ b/R/compat-plyr.R @@ -54,13 +54,13 @@ rename <- function(x, replace) { id_var <- function(x, drop = FALSE) { if (length(x) == 0) { id <- integer() - n = 0L + n <- 0L } else if (!is.null(attr(x, "n")) && !drop) { return(x) } else if (is.factor(x) && !drop) { x <- addNA(x, ifany = TRUE) id <- as.integer(x) - n <- length(levels(x)) + n <- nlevels(x) } else { levels <- sort(unique0(x), na.last = TRUE) id <- match(x, levels) diff --git a/R/coord-.R b/R/coord-.R index 6736059fbc..57cf351f92 100644 --- a/R/coord-.R +++ b/R/coord-.R @@ -208,6 +208,20 @@ Coord <- ggproto("Coord", # used as a fudge for CoordFlip and CoordPolar modify_scales = function(scales_x, scales_y) { invisible() + }, + + draw_panel = function(self, panel, params, theme) { + fg <- self$render_fg(params, theme) + bg <- self$render_bg(params, theme) + if (isTRUE(theme$panel.ontop)) { + panel <- list2(!!!panel, bg, fg) + } else { + panel <- list2(bg, !!!panel, fg) + } + gTree( + children = inject(gList(!!!panel)), + vp = viewport(clip = self$clip) + ) } ) diff --git a/R/coord-polar.R b/R/coord-polar.R index e0712760fb..f1c8108ddf 100644 --- a/R/coord-polar.R +++ b/R/coord-polar.R @@ -137,7 +137,7 @@ CoordPolar <- ggproto("CoordPolar", Coord, ret[[n]]$sec.labels <- out$sec.labels } - details = list( + details <- list( x.range = ret$x$range, y.range = ret$y$range, x.major = ret$x$major, y.major = ret$y$major, x.minor = ret$x$minor, y.minor = ret$y$minor, diff --git a/R/coord-radial.R b/R/coord-radial.R index c47d55bb56..2f44e1ae4b 100644 --- a/R/coord-radial.R +++ b/R/coord-radial.R @@ -409,6 +409,27 @@ CoordRadial <- ggproto("CoordRadial", Coord, ) }, + + draw_panel = function(self, panel, params, theme) { + clip_support <- check_device("clippingPaths", "test", maybe = TRUE) + if (self$clip == "on" && !isFALSE(clip_support)) { + clip_path <- data_frame0( + x = c(Inf, Inf, -Inf, -Inf), + y = c(Inf, -Inf, -Inf, Inf) + ) + clip_path <- coord_munch(self, clip_path, params, is_closed = TRUE) + clip_path <- polygonGrob(clip_path$x, clip_path$y) + # Note that clipping path is applied to panel without coord + # foreground/background (added in parent method). + # These may contain decorations that needn't be clipped + panel <- list(gTree( + children = inject(gList(!!!panel)), + vp = viewport(clip = clip_path) + )) + } + ggproto_parent(Coord, self)$draw_panel(panel, params, theme) + }, + labels = function(self, labels, panel_params) { # `Layout$resolve_label()` doesn't know to look for theta/r/r.sec guides, # so we'll handle title propagation here. diff --git a/R/coord-sf.R b/R/coord-sf.R index f861ae2d28..a14b3c718c 100644 --- a/R/coord-sf.R +++ b/R/coord-sf.R @@ -416,7 +416,7 @@ sf_rescale01 <- function(x, x_range, y_range) { # different limits methods calc_limits_bbox <- function(method, xlim, ylim, crs, default_crs) { - if (any(!is.finite(c(xlim, ylim))) && method != "geometry_bbox") { + if (!all(is.finite(c(xlim, ylim))) && method != "geometry_bbox") { cli::cli_abort(c( "Scale limits cannot be mapped onto spatial coordinates in {.fn coord_sf}.", "i" = "Consider setting {.code lims_method = \"geometry_bbox\"} or {.code default_crs = NULL}." @@ -585,7 +585,7 @@ coord_sf <- function(xlim = NULL, ylim = NULL, expand = TRUE, } parse_axes_labeling <- function(x) { - labs = unlist(strsplit(x, "")) + labs <- unlist(strsplit(x, "")) list(top = labs[1], right = labs[2], bottom = labs[3], left = labs[4]) } diff --git a/R/facet-.R b/R/facet-.R index 96c96dc6fd..2e349f6f97 100644 --- a/R/facet-.R +++ b/R/facet-.R @@ -139,22 +139,25 @@ Facet <- ggproto("Facet", NULL, free <- params$free %||% list(x = FALSE, y = FALSE) space <- params$space_free %||% list(x = FALSE, y = FALSE) - if ((free$x || free$y) && !coord$is_free()) { - cli::cli_abort( - "{.fn {snake_class(self)}} can't use free scales with \\ - {.fn {snake_class(coord)}}." - ) - } - aspect_ratio <- theme$aspect.ratio if (!is.null(aspect_ratio) && (space$x || space$y)) { cli::cli_abort("Free scales cannot be mixed with a fixed aspect ratio.") } + if (!coord$is_free()) { + if (space$x && space$y) { + aspect_ratio <- aspect_ratio %||% coord$ratio + } else if (free$x || free$y) { + cli::cli_abort( + "{.fn {snake_class(self)}} can't use free scales with \\ + {.fn {snake_class(coord)}}." + ) + } + } + table <- self$init_gtable( panels, layout, theme, ranges, params, - aspect_ratio = aspect_ratio %||% coord$aspect(ranges[[1]]), - clip = coord$clip + aspect_ratio = aspect_ratio %||% coord$aspect(ranges[[1]]) ) table <- self$attach_axes(table, layout, ranges, coord, theme, params) @@ -198,7 +201,7 @@ Facet <- ggproto("Facet", NULL, data }, init_gtable = function(panels, layout, theme, ranges, params, - aspect_ratio = NULL, clip = "on") { + aspect_ratio = NULL) { # Initialise matrix of panels dim <- c(max(layout$ROW), max(layout$COL)) @@ -220,7 +223,7 @@ Facet <- ggproto("Facet", NULL, if (space$y) { idx <- layout$PANEL[layout$COL == 1] heights <- vapply(idx, function(i) diff(ranges[[i]]$y.range), numeric(1)) - heights <- unit(heights, "null") + heights <- unit(heights * abs(aspect_ratio %||% 1), "null") } # Build gtable @@ -228,7 +231,7 @@ Facet <- ggproto("Facet", NULL, "layout", table, widths = widths, heights = heights, respect = !is.null(aspect_ratio), - clip = clip, z = matrix(1, dim[1], dim[2]) + clip = "off", z = matrix(1, dim[1], dim[2]) ) # Set panel names @@ -561,7 +564,7 @@ is_facets <- function(x) { # but that seems like a reasonable tradeoff. eval_facets <- function(facets, data, possible_columns = NULL) { vars <- compact(lapply(facets, eval_facet, data, possible_columns = possible_columns)) - data_frame0(tibble::as_tibble(vars)) + data_frame0(!!!vars) } eval_facet <- function(facet, data, possible_columns = NULL) { # Treat the case when `facet` is a quosure of a symbol specifically @@ -678,7 +681,7 @@ find_panel <- function(table) { } #' @rdname find_panel #' @export -panel_cols = function(table) { +panel_cols <- function(table) { panels <- table$layout[grepl("^panel", table$layout$name), , drop = FALSE] unique0(panels[, c('l', 'r')]) } diff --git a/R/facet-grid-.R b/R/facet-grid-.R index 7bfb30dd6e..a0b6e31931 100644 --- a/R/facet-grid-.R +++ b/R/facet-grid-.R @@ -319,8 +319,8 @@ FacetGrid <- ggproto("FacetGrid", Facet, if (length(missing_facets) > 0) { to_add <- unique0(layout[missing_facets]) - data_rep <- rep.int(1:nrow(data), nrow(to_add)) - facet_rep <- rep(1:nrow(to_add), each = nrow(data)) + data_rep <- rep.int(seq_len(nrow(data)), nrow(to_add)) + facet_rep <- rep(seq_len(nrow(to_add)), each = nrow(data)) data <- unrowname(data[data_rep, , drop = FALSE]) facet_vals <- unrowname(vec_cbind( @@ -404,13 +404,13 @@ FacetGrid <- ggproto("FacetGrid", Facet, space <- if (!inside_x & table_has_grob(table, "axis-b")) padding table <- seam_table( table, strips$x$bottom, side = "bottom", name = "strip-b", - shift = shift_x, z = 2, clip = "on", spacing = space + shift = shift_x, z = 2, clip = "off", spacing = space ) } else { space <- if (!inside_x & table_has_grob(table, "axis-t")) padding table <- seam_table( table, strips$x$top, side = "top", name = "strip-t", - shift = shift_x, z = 2, clip = "on", spacing = space + shift = shift_x, z = 2, clip = "off", spacing = space ) } @@ -422,13 +422,13 @@ FacetGrid <- ggproto("FacetGrid", Facet, space <- if (!inside_y & table_has_grob(table, "axis-l")) padding table <- seam_table( table, strips$y$left, side = "left", name = "strip-l", - shift = shift_y, z = 2, clip = "on", spacing = space + shift = shift_y, z = 2, clip = "off", spacing = space ) } else { space <- if (!inside_y & table_has_grob(table, "axis-r")) padding table <- seam_table( table, strips$y$right, side = "right", name = "strip-r", - shift = shift_y, z = 2, clip = "on", spacing = space + shift = shift_y, z = 2, clip = "off", spacing = space ) } table diff --git a/R/facet-null.R b/R/facet-null.R index bc95141fde..c66f39fa03 100644 --- a/R/facet-null.R +++ b/R/facet-null.R @@ -63,11 +63,10 @@ FacetNull <- ggproto("FacetNull", Facet, grob_widths <- unit.c(grobWidth(axis_v$left), unit(1, "null"), grobWidth(axis_v$right)) grob_heights <- unit.c(grobHeight(axis_h$top), unit(abs(aspect_ratio), "null"), grobHeight(axis_h$bottom)) grob_names <- c("spacer", "axis-l", "spacer", "axis-t", "panel", "axis-b", "spacer", "axis-r", "spacer") - grob_clip <- c("off", "off", "off", "off", coord$clip, "off", "off", "off", "off") layout <- gtable_matrix("layout", all, widths = grob_widths, heights = grob_heights, - respect = respect, clip = grob_clip, + respect = respect, clip = "off", z = z_matrix ) layout$layout$name <- grob_names diff --git a/R/facet-wrap.R b/R/facet-wrap.R index 68c02f0b21..8564f319b7 100644 --- a/R/facet-wrap.R +++ b/R/facet-wrap.R @@ -18,6 +18,12 @@ NULL #' @param scales Should scales be fixed (`"fixed"`, the default), #' free (`"free"`), or free in one dimension (`"free_x"`, #' `"free_y"`)? +#' @param space If `"fixed"` (default), all panels have the same size and +#' the number of rows and columns in the layout can be arbitrary. If +#' `"free_x"`, panels have widths proportional to the length of the x-scale, +#' but the layout is constrained to one row. If `"free_y"`, panels have +#' heights proportional to the length of the y-scale, but the layout is +#' constrained to one column. #' @param strip.position By default, the labels are displayed on the top of #' the plot. Using `strip.position` it is possible to place the labels on #' either of the four sides by setting \code{strip.position = c("top", @@ -109,9 +115,9 @@ NULL #' geom_point() + #' facet_wrap(vars(class), dir = "tr") facet_wrap <- function(facets, nrow = NULL, ncol = NULL, scales = "fixed", - shrink = TRUE, labeller = "label_value", as.table = TRUE, - switch = deprecated(), drop = TRUE, dir = "h", - strip.position = 'top', axes = "margins", + space = "fixed", shrink = TRUE, labeller = "label_value", + as.table = TRUE, switch = deprecated(), drop = TRUE, + dir = "h", strip.position = 'top', axes = "margins", axis.labels = "all") { scales <- arg_match0(scales %||% "fixed", c("fixed", "free_x", "free_y", "free")) dir <- arg_match0(dir, c("h", "v", "lt", "tl", "lb", "bl", "rt", "tr", "rb", "br")) @@ -128,6 +134,30 @@ facet_wrap <- function(facets, nrow = NULL, ncol = NULL, scales = "fixed", y = any(scales %in% c("free_y", "free")) ) + # We cannot have free space in both directions + space <- arg_match0(space, c("free_x", "free_y", "fixed")) + space_free <- list(x = space == "free_x", y = space == "free_y") + if (space_free$x) { + if ((nrow %||% 1) != 1 || !is.null(ncol)) { + cli::cli_warn( + "Cannot use {.code space = \"free_x\"} with custom \\ + {.arg nrow} or {.arg ncol}." + ) + } + ncol <- NULL + nrow <- 1L + } + if (space_free$y) { + if ((ncol %||% 1) != 1 || !is.null(nrow)) { + cli::cli_warn( + "Cannot use {.code space= \"free_y\"} with custom \\ + {.arg nrow} or {.arg ncol}." + ) + } + ncol <- 1L + nrow <- NULL + } + # If scales are free, always draw the axes draw_axes <- arg_match0(axes, c("margins", "all_x", "all_y", "all")) draw_axes <- list( @@ -174,6 +204,7 @@ facet_wrap <- function(facets, nrow = NULL, ncol = NULL, scales = "fixed", drop = drop, ncol = ncol, nrow = nrow, + space_free = space_free, labeller = labeller, dir = dir, draw_axes = draw_axes, @@ -242,8 +273,8 @@ FacetWrap <- ggproto("FacetWrap", Facet, to_add <- unique0(layout[missing_facets]) - data_rep <- rep.int(1:nrow(data), nrow(to_add)) - facet_rep <- rep(1:nrow(to_add), each = nrow(data)) + data_rep <- rep.int(seq_len(nrow(data)), nrow(to_add)) + facet_rep <- rep(seq_len(nrow(to_add)), each = nrow(data)) data <- data[data_rep, , drop = FALSE] facet_vals <- vec_cbind( @@ -405,7 +436,7 @@ FacetWrap <- ggproto("FacetWrap", Facet, shift <- if (inside) shift[1] else shift[2] size <- unit(size, "cm") - table <- weave(table, mat, shift, size, name = prefix, z = 2, clip = "on") + table <- weave(table, mat, shift, size, name = prefix, z = 2, clip = "off") if (!inside) { axes <- grepl(paste0("axis-", pos), table$layout$name) diff --git a/R/fortify-spatial.R b/R/fortify-spatial.R index 6fe7392a37..0e9f37d046 100644 --- a/R/fortify-spatial.R +++ b/R/fortify-spatial.R @@ -71,7 +71,7 @@ fortify.Polygons <- function(model, data, ...) { }) pieces <- vec_rbind0(!!!pieces) - pieces$order <- 1:nrow(pieces) + pieces$order <- seq_len(nrow(pieces)) pieces$id <- model@ID pieces$piece <- factor(pieces$piece) pieces$group <- interaction(pieces$id, pieces$piece) @@ -89,7 +89,7 @@ fortify.Polygon <- function(model, data, ...) { df <- as.data.frame(model@coords) names(df) <- c("long", "lat") - df$order <- 1:nrow(df) + df$order <- seq_len(nrow(df)) df$hole <- model@hole df } @@ -124,7 +124,7 @@ fortify.Lines <- function(model, data, ...) { }) pieces <- vec_rbind0(!!!pieces) - pieces$order <- 1:nrow(pieces) + pieces$order <- seq_len(nrow(pieces)) pieces$id <- model@ID pieces$piece <- factor(pieces$piece) pieces$group <- interaction(pieces$id, pieces$piece) @@ -142,7 +142,7 @@ fortify.Line <- function(model, data, ...) { df <- as.data.frame(model@coords) names(df) <- c("long", "lat") - df$order <- 1:nrow(df) + df$order <- seq_len(nrow(df)) df } diff --git a/R/geom-.R b/R/geom-.R index c3da9be244..5b6a2af09d 100644 --- a/R/geom-.R +++ b/R/geom-.R @@ -114,7 +114,8 @@ Geom <- ggproto("Geom", setup_data = function(data, params) data, # Combine data with defaults and set aesthetics from parameters - use_defaults = function(self, data, params = list(), modifiers = aes(), default_aes = NULL, ...) { + use_defaults = function(self, data, params = list(), modifiers = aes(), + default_aes = NULL, theme = NULL, ...) { default_aes <- default_aes %||% self$default_aes # Inherit size as linewidth if no linewidth aesthetic and param exist @@ -131,8 +132,11 @@ Geom <- ggproto("Geom", # Fill in missing aesthetics with their defaults missing_aes <- setdiff(names(default_aes), names(data)) + default_aes <- default_aes[missing_aes] + themed_defaults <- eval_from_theme(default_aes, theme) + default_aes[names(themed_defaults)] <- themed_defaults - missing_eval <- lapply(default_aes[missing_aes], eval_tidy) + missing_eval <- lapply(default_aes, eval_tidy) # Needed for geoms with defaults set to NULL (e.g. GeomSf) missing_eval <- compact(missing_eval) @@ -142,6 +146,13 @@ Geom <- ggproto("Geom", data[names(missing_eval)] <- missing_eval } + themed <- is_themed_aes(modifiers) + if (any(themed)) { + themed <- eval_from_theme(modifiers[themed], theme) + modifiers <- modifiers[setdiff(names(modifiers), names(themed))] + data[names(themed)] <- themed + } + # If any after_scale mappings are detected they will be resolved here # This order means that they will have access to all default aesthetics if (length(modifiers) != 0) { @@ -226,6 +237,15 @@ Geom <- ggproto("Geom", ) +eval_from_theme <- function(aesthetics, theme) { + themed <- is_themed_aes(aesthetics) + if (!any(themed)) { + return(aesthetics) + } + settings <- calc_element("geom", theme) %||% .default_geom_element + lapply(aesthetics[themed], eval_tidy, data = settings) +} + #' Graphical units #' #' Multiply size in mm by these constants in order to convert to the units diff --git a/R/geom-abline.R b/R/geom-abline.R index da65483635..e9775e33fb 100644 --- a/R/geom-abline.R +++ b/R/geom-abline.R @@ -142,7 +142,13 @@ GeomAbline <- ggproto("GeomAbline", Geom, GeomSegment$draw_panel(unique0(data), panel_params, coord, lineend = lineend) }, - default_aes = aes(colour = "black", linewidth = 0.5, linetype = 1, alpha = NA), + default_aes = aes( + colour = from_theme(ink), + linewidth = from_theme(linewidth), + linetype = from_theme(linetype), + alpha = NA + ), + required_aes = c("slope", "intercept"), draw_key = draw_key_abline, diff --git a/R/geom-boxplot.R b/R/geom-boxplot.R index 399f92d7a8..1ac23ba80f 100644 --- a/R/geom-boxplot.R +++ b/R/geom-boxplot.R @@ -117,8 +117,8 @@ geom_boxplot <- function(mapping = NULL, data = NULL, outlier.colour = NULL, outlier.color = NULL, outlier.fill = NULL, - outlier.shape = 19, - outlier.size = 1.5, + outlier.shape = NULL, + outlier.size = NULL, outlier.stroke = 0.5, outlier.alpha = NULL, notch = FALSE, @@ -223,8 +223,8 @@ GeomBoxplot <- ggproto("GeomBoxplot", Geom, draw_group = function(self, data, panel_params, coord, lineend = "butt", linejoin = "mitre", fatten = 2, outlier.colour = NULL, - outlier.fill = NULL, outlier.shape = 19, - outlier.size = 1.5, outlier.stroke = 0.5, + outlier.fill = NULL, outlier.shape = NULL, + outlier.size = NULL, outlier.stroke = 0.5, outlier.alpha = NULL, notch = FALSE, notchwidth = 0.5, staplewidth = 0, varwidth = FALSE, flipped_aes = FALSE) { data <- check_linewidth(data, snake_class(self)) @@ -327,8 +327,12 @@ GeomBoxplot <- ggproto("GeomBoxplot", Geom, draw_key = draw_key_boxplot, - default_aes = aes(weight = 1, colour = "grey20", fill = "white", size = NULL, - alpha = NA, shape = 19, linetype = "solid", linewidth = 0.5), + default_aes = aes( + weight = 1, colour = from_theme(col_mix(ink, paper, 0.2)), + fill = from_theme(paper), size = from_theme(pointsize), + alpha = NA, shape = from_theme(pointshape), linetype = from_theme(bordertype), + linewidth = from_theme(borderwidth) + ), required_aes = c("x|y", "lower|xlower", "upper|xupper", "middle|xmiddle", "ymin|xmin", "ymax|xmax"), diff --git a/R/geom-contour.R b/R/geom-contour.R index 7dfe9fb228..a73bc3a135 100644 --- a/R/geom-contour.R +++ b/R/geom-contour.R @@ -126,9 +126,9 @@ geom_contour_filled <- function(mapping = NULL, data = NULL, GeomContour <- ggproto("GeomContour", GeomPath, default_aes = aes( weight = 1, - colour = "#3366FF", - linewidth = 0.5, - linetype = 1, + colour = from_theme(accent), + linewidth = from_theme(linewidth), + linetype = from_theme(linetype), alpha = NA ) ) diff --git a/R/geom-crossbar.R b/R/geom-crossbar.R index 36c3d4b9ff..1f7c66f832 100644 --- a/R/geom-crossbar.R +++ b/R/geom-crossbar.R @@ -40,8 +40,13 @@ GeomCrossbar <- ggproto("GeomCrossbar", Geom, GeomErrorbar$setup_data(data, params) }, - default_aes = aes(colour = "black", fill = NA, linewidth = 0.5, linetype = 1, - alpha = NA), + default_aes = aes( + colour = from_theme(ink), + fill = NA, + linewidth = from_theme(borderwidth), + linetype = from_theme(bordertype), + alpha = NA + ), required_aes = c("x", "y", "ymin|xmin", "ymax|xmax"), diff --git a/R/geom-curve.R b/R/geom-curve.R index 4c5b60e2c5..e1c38d1cd4 100644 --- a/R/geom-curve.R +++ b/R/geom-curve.R @@ -40,7 +40,14 @@ geom_curve <- function(mapping = NULL, data = NULL, #' @usage NULL #' @export GeomCurve <- ggproto("GeomCurve", GeomSegment, - default_aes = aes(colour = "black", linewidth = 0.5, linetype = 1, alpha = NA), + + default_aes = aes( + colour = from_theme(ink), + linewidth = from_theme(linewidth), + linetype = from_theme(linetype), + alpha = NA + ), + draw_panel = function(data, panel_params, coord, curvature = 0.5, angle = 90, ncp = 5, arrow = NULL, arrow.fill = NULL, lineend = "butt", na.rm = FALSE) { diff --git a/R/geom-defaults.R b/R/geom-defaults.R index 8b81eeef94..65974f841a 100644 --- a/R/geom-defaults.R +++ b/R/geom-defaults.R @@ -1,5 +1,7 @@ #' Modify geom/stat aesthetic defaults for future plots #' +#' Functions to update or reset the default aesthetics of geoms and stats. +#' #' @param stat,geom Name of geom/stat to modify (like `"point"` or #' `"bin"`), or a Geom/Stat object (like `GeomPoint` or #' `StatBin`). @@ -7,6 +9,9 @@ #' * A named list of aesthetics to serve as new defaults. #' * `NULL` to reset the defaults. #' @keywords internal +#' @note +#' Please note that geom defaults can be set *en masse* via the `theme(geom)` +#' argument. #' @export #' @examples #' @@ -17,9 +22,11 @@ #' GeomPoint$default_aes #' ggplot(mtcars, aes(mpg, wt)) + geom_point() #' -#' # reset default +#' # reset single default #' update_geom_defaults("point", NULL) #' +#' # reset all defaults +#' reset_geom_defaults() #' #' # updating a stat's default aesthetic settings #' # example: change stat_bin()'s default y-axis to the density scale @@ -30,9 +37,12 @@ #' geom_histogram() + #' geom_function(fun = dnorm, color = "red") #' -#' # reset default +#' # reset single default #' update_stat_defaults("bin", NULL) #' +#' # reset all defaults +#' reset_stat_defaults() +#' #' @rdname update_defaults update_geom_defaults <- function(geom, new) { update_defaults(geom, "Geom", new, env = parent.frame()) @@ -44,6 +54,65 @@ update_stat_defaults <- function(stat, new) { update_defaults(stat, "Stat", new, env = parent.frame()) } +#' Resolve and get geom defaults +#' +#' @param geom Some definition of a geom: +#' * A `function` that creates a layer, e.g. `geom_path()`. +#' * A layer created by such function +#' * A string naming a geom class in snake case without the `geom_`-prefix, +#' e.g. `"contour_filled"`. +#' * A geom class object. +#' @param theme A [`theme`] object. Defaults to the current global theme. +#' +#' @return A list of aesthetics +#' @export +#' @keywords internal +#' +#' @examples +#' # Using a function +#' get_geom_defaults(geom_raster) +#' +#' # Using a layer includes static aesthetics as default +#' get_geom_defaults(geom_tile(fill = "white")) +#' +#' # Using a class name +#' get_geom_defaults("density_2d") +#' +#' # Using a class +#' get_geom_defaults(GeomPoint) +#' +#' # Changed theme +#' get_geom_defaults("point", theme(geom = element_geom(ink = "purple"))) +get_geom_defaults <- function(geom, theme = theme_get()) { + theme <- theme %||% list(geom = .default_geom_element) + + if (is.function(geom)) { + geom <- geom() + } + if (is.layer(geom)) { + data <- data_frame0(.id = 1L) + data <- geom$compute_geom_2(data = data, theme = theme) + data$.id <- NULL + return(data) + } + if (is.character(geom)) { + geom <- check_subclass(geom, "Geom") + } + if (inherits(geom, "Geom")) { + out <- geom$use_defaults(data = NULL, theme = theme) + return(out) + } + stop_input_type(geom, as_cli("a layer function, string or {.cls Geom} object")) +} + +#' @rdname update_defaults +#' @export +reset_geom_defaults <- function() reset_defaults("geom") + +#' @rdname update_defaults +#' @export +reset_stat_defaults <- function() reset_defaults("stat") + cache_defaults <- new_environment() update_defaults <- function(name, subclass, new, env = parent.frame()) { @@ -73,3 +142,20 @@ update_defaults <- function(name, subclass, new, env = parent.frame()) { } } + +reset_defaults <- function(type) { + # Lookup matching names in cache + prefix <- paste0("^", type, "_") + full_names <- grep(prefix, ls(cache_defaults), value = TRUE) + # Early exit if there is nothing to reset + if (length(full_names) < 1) { + return(invisible()) + } + # Format names without prefix + short_names <- gsub(prefix, "", full_names) + names(short_names) <- full_names + + # Run updates + update <- switch(type, geom = update_geom_defaults, update_stat_defaults) + invisible(lapply(short_names, update, new = NULL)) +} diff --git a/R/geom-density.R b/R/geom-density.R index c71a9f98eb..a4a7754f2e 100644 --- a/R/geom-density.R +++ b/R/geom-density.R @@ -93,7 +93,7 @@ geom_density <- function(mapping = NULL, data = NULL, #' @include geom-ribbon.R GeomDensity <- ggproto("GeomDensity", GeomArea, default_aes = defaults( - aes(fill = NA, weight = 1, colour = "black", alpha = NA), + aes(fill = NA, weight = 1, colour = from_theme(ink), alpha = NA), GeomArea$default_aes ) ) diff --git a/R/geom-density2d.R b/R/geom-density2d.R index e95a8b2c31..832546b563 100644 --- a/R/geom-density2d.R +++ b/R/geom-density2d.R @@ -106,7 +106,12 @@ geom_density2d <- geom_density_2d #' @usage NULL #' @export GeomDensity2d <- ggproto("GeomDensity2d", GeomPath, - default_aes = aes(colour = "#3366FF", linewidth = 0.5, linetype = 1, alpha = NA) + default_aes = aes( + colour = from_theme(accent), + linewidth = from_theme(linewidth), + linetype = from_theme(linetype), + alpha = NA + ) ) #' @export diff --git a/R/geom-dotplot.R b/R/geom-dotplot.R index e163fb272b..54b7ce1f57 100644 --- a/R/geom-dotplot.R +++ b/R/geom-dotplot.R @@ -188,8 +188,14 @@ GeomDotplot <- ggproto("GeomDotplot", Geom, required_aes = c("x", "y"), non_missing_aes = c("size", "shape"), - default_aes = aes(colour = "black", fill = "black", alpha = NA, - stroke = 1, linetype = "solid", weight = 1), + default_aes = aes( + colour = from_theme(ink), + fill = from_theme(ink), + alpha = NA, + stroke = from_theme(borderwidth * 2), + linetype = from_theme(linetype), + weight = 1 + ), setup_data = function(data, params) { data$width <- data$width %||% @@ -197,25 +203,25 @@ GeomDotplot <- ggproto("GeomDotplot", Geom, # Set up the stacking function and range if (is.null(params$stackdir) || params$stackdir == "up") { - stackdots <- function(a) a - .5 + stackdots <- function(a) a - 0.5 stackaxismin <- 0 stackaxismax <- 1 } else if (params$stackdir == "down") { - stackdots <- function(a) -a + .5 + stackdots <- function(a) -a + 0.5 stackaxismin <- -1 stackaxismax <- 0 } else if (params$stackdir == "center") { stackdots <- function(a) a - 1 - max(a - 1) / 2 - stackaxismin <- -.5 - stackaxismax <- .5 + stackaxismin <- -0.5 + stackaxismax <- 0.5 } else if (params$stackdir == "centerwhole") { stackdots <- function(a) a - 1 - floor(max(a - 1) / 2) - stackaxismin <- -.5 - stackaxismax <- .5 + stackaxismin <- -0.5 + stackaxismax <- 0.5 } # Fill the bins: at a given x (or y), if count=3, make 3 entries at that x - data <- data[rep(1:nrow(data), data$count), ] + data <- data[rep(seq_len(nrow(data)), data$count), ] # Next part will set the position of each dot within each stack # If stackgroups=TRUE, split only on x (or y) and panel; if not stacking, also split by group @@ -231,7 +237,7 @@ GeomDotplot <- ggproto("GeomDotplot", Geom, # Within each x, or x+group, set countidx=1,2,3, and set stackpos according to stack function data <- dapply(data, plyvars, function(xx) { - xx$countidx <- 1:nrow(xx) + xx$countidx <- seq_len(nrow(xx)) xx$stackpos <- stackdots(xx$countidx) xx }) @@ -281,11 +287,11 @@ GeomDotplot <- ggproto("GeomDotplot", Geom, binaxis <- ifelse(binaxis == "x", "y", "x") if (binaxis == "x") { - stackaxis = "y" + stackaxis <- "y" dotdianpc <- dotsize * tdata$binwidth[1] / (max(panel_params$x.range) - min(panel_params$x.range)) } else if (binaxis == "y") { - stackaxis = "x" + stackaxis <- "x" dotdianpc <- dotsize * tdata$binwidth[1] / (max(panel_params$y.range) - min(panel_params$y.range)) } diff --git a/R/geom-errorbar.R b/R/geom-errorbar.R index c02ab16ed9..3e40b20318 100644 --- a/R/geom-errorbar.R +++ b/R/geom-errorbar.R @@ -28,8 +28,14 @@ geom_errorbar <- function(mapping = NULL, data = NULL, #' @usage NULL #' @export GeomErrorbar <- ggproto("GeomErrorbar", Geom, - default_aes = aes(colour = "black", linewidth = 0.5, linetype = 1, width = 0.5, - alpha = NA), + + default_aes = aes( + colour = from_theme(ink), + linewidth = from_theme(linewidth), + linetype = from_theme(linetype), + width = 0.5, + alpha = NA + ), draw_key = draw_key_path, diff --git a/R/geom-errorbarh.R b/R/geom-errorbarh.R index b23d125da4..c38b9b7cd6 100644 --- a/R/geom-errorbarh.R +++ b/R/geom-errorbarh.R @@ -51,8 +51,14 @@ geom_errorbarh <- function(mapping = NULL, data = NULL, #' @usage NULL #' @export GeomErrorbarh <- ggproto("GeomErrorbarh", Geom, - default_aes = aes(colour = "black", linewidth = 0.5, linetype = 1, height = 0.5, - alpha = NA), + + default_aes = aes( + colour = from_theme(ink), + linewidth = from_theme(linewidth), + linetype = from_theme(linetype), + height = 0.5, + alpha = NA + ), draw_key = draw_key_path, diff --git a/R/geom-hex.R b/R/geom-hex.R index 8573d6d8ba..0eb777b808 100644 --- a/R/geom-hex.R +++ b/R/geom-hex.R @@ -107,9 +107,9 @@ GeomHex <- ggproto("GeomHex", Geom, default_aes = aes( colour = NA, - fill = "grey50", - linewidth = 0.5, - linetype = 1, + fill = from_theme(col_mix(ink, paper)), + linewidth = from_theme(borderwidth), + linetype = from_theme(bordertype), alpha = NA ), diff --git a/R/geom-hline.R b/R/geom-hline.R index 6b80d0bb08..2650066183 100644 --- a/R/geom-hline.R +++ b/R/geom-hline.R @@ -56,7 +56,12 @@ GeomHline <- ggproto("GeomHline", Geom, GeomSegment$draw_panel(unique0(data), panel_params, coord, lineend = lineend) }, - default_aes = aes(colour = "black", linewidth = 0.5, linetype = 1, alpha = NA), + default_aes = aes( + colour = from_theme(ink), + linewidth = from_theme(linewidth), + linetype = from_theme(linetype), + alpha = NA + ), required_aes = "yintercept", draw_key = draw_key_path, diff --git a/R/geom-label.R b/R/geom-label.R index e8a4605b54..4168c98d94 100644 --- a/R/geom-label.R +++ b/R/geom-label.R @@ -56,8 +56,11 @@ GeomLabel <- ggproto("GeomLabel", Geom, required_aes = c("x", "y", "label"), default_aes = aes( - colour = "black", fill = "white", size = 3.88, angle = 0, - hjust = 0.5, vjust = 0.5, alpha = NA, family = "", fontface = 1, + colour = from_theme(ink), fill = from_theme(paper), + family = from_theme(family), + size = from_theme(fontsize), + angle = 0, + hjust = 0.5, vjust = 0.5, alpha = NA, fontface = 1, lineheight = 1.2 ), @@ -81,7 +84,7 @@ GeomLabel <- ggproto("GeomLabel", Geom, size.unit <- resolve_text_unit(size.unit) - grobs <- lapply(1:nrow(data), function(i) { + grobs <- lapply(seq_len(nrow(data)), function(i) { row <- data[i, , drop = FALSE] labelGrob(lab[i], x = unit(row$x, "native"), diff --git a/R/geom-linerange.R b/R/geom-linerange.R index 7144d0084a..83360800e2 100644 --- a/R/geom-linerange.R +++ b/R/geom-linerange.R @@ -91,7 +91,13 @@ geom_linerange <- function(mapping = NULL, data = NULL, #' @usage NULL #' @export GeomLinerange <- ggproto("GeomLinerange", Geom, - default_aes = aes(colour = "black", linewidth = 0.5, linetype = 1, alpha = NA), + + default_aes = aes( + colour = from_theme(ink), + linewidth = from_theme(linewidth), + linetype = from_theme(linetype), + alpha = NA + ), draw_key = draw_key_linerange, diff --git a/R/geom-path.R b/R/geom-path.R index 9b737267ca..72c4f7154e 100644 --- a/R/geom-path.R +++ b/R/geom-path.R @@ -36,8 +36,9 @@ #' @examples #' # geom_line() is suitable for time series #' ggplot(economics, aes(date, unemploy)) + geom_line() +#' # separate by colour and use "timeseries" legend key glyph #' ggplot(economics_long, aes(date, value01, colour = variable)) + -#' geom_line() +#' geom_line(key_glyph = "timeseries") #' #' # You can get a timeseries that run vertically by setting the orientation #' ggplot(economics, aes(unemploy, date)) + geom_line(orientation = "y") @@ -134,7 +135,12 @@ geom_path <- function(mapping = NULL, data = NULL, GeomPath <- ggproto("GeomPath", Geom, required_aes = c("x", "y"), - default_aes = aes(colour = "black", linewidth = 0.5, linetype = 1, alpha = NA), + default_aes = aes( + colour = from_theme(ink), + linewidth = from_theme(linewidth), + linetype = from_theme(linetype), + alpha = NA + ), non_missing_aes = c("linewidth", "colour", "linetype"), @@ -180,7 +186,7 @@ GeomPath <- ggproto("GeomPath", Geom, attr <- dapply(munched, "group", function(df) { linetype <- unique0(df$linetype) data_frame0( - solid = identical(linetype, 1) || identical(linetype, "solid"), + solid = length(linetype) == 1 && (identical(linetype, "solid") || linetype == 1), constant = nrow(unique0(df[, names(df) %in% c("alpha", "colour", "linewidth", "linetype")])) == 1, .size = 1 ) diff --git a/R/geom-point.R b/R/geom-point.R index 26e6705398..3efa394c31 100644 --- a/R/geom-point.R +++ b/R/geom-point.R @@ -135,8 +135,9 @@ GeomPoint <- ggproto("GeomPoint", Geom, required_aes = c("x", "y"), non_missing_aes = c("size", "shape", "colour"), default_aes = aes( - shape = 19, colour = "black", size = 1.5, fill = NA, - alpha = NA, stroke = 0.5 + shape = from_theme(pointshape), + colour = from_theme(ink), size = from_theme(pointsize), fill = NA, + alpha = NA, stroke = from_theme(borderwidth) ), draw_panel = function(self, data, panel_params, coord, na.rm = FALSE) { diff --git a/R/geom-pointrange.R b/R/geom-pointrange.R index ccecfc0d95..d0e5194311 100644 --- a/R/geom-pointrange.R +++ b/R/geom-pointrange.R @@ -30,8 +30,12 @@ geom_pointrange <- function(mapping = NULL, data = NULL, #' @usage NULL #' @export GeomPointrange <- ggproto("GeomPointrange", Geom, - default_aes = aes(colour = "black", size = 0.5, linewidth = 0.5, linetype = 1, - shape = 19, fill = NA, alpha = NA, stroke = 1), + default_aes = aes( + colour = from_theme(ink), size = from_theme(pointsize / 3), + linewidth = from_theme(linewidth), linetype = from_theme(linetype), + shape = from_theme(pointshape), fill = NA, alpha = NA, + stroke = from_theme(borderwidth * 2) + ), draw_key = draw_key_pointrange, diff --git a/R/geom-polygon.R b/R/geom-polygon.R index 8e812e2737..a271ef5011 100644 --- a/R/geom-polygon.R +++ b/R/geom-polygon.R @@ -175,8 +175,13 @@ GeomPolygon <- ggproto("GeomPolygon", Geom, } }, - default_aes = aes(colour = NA, fill = "grey20", linewidth = 0.5, linetype = 1, - alpha = NA, subgroup = NULL), + default_aes = aes( + colour = NA, + fill = from_theme(col_mix(ink, paper, 0.2)), + linewidth = from_theme(borderwidth), + linetype = from_theme(bordertype), + alpha = NA, subgroup = NULL + ), handle_na = function(data, params) { data diff --git a/R/geom-quantile.R b/R/geom-quantile.R index bb3ff581ab..732ab62f8a 100644 --- a/R/geom-quantile.R +++ b/R/geom-quantile.R @@ -66,7 +66,7 @@ geom_quantile <- function(mapping = NULL, data = NULL, #' @include geom-path.R GeomQuantile <- ggproto("GeomQuantile", GeomPath, default_aes = defaults( - aes(weight = 1, colour = "#3366FF", linewidth = 0.5), + aes(weight = 1, colour = from_theme(accent)), GeomPath$default_aes ) ) diff --git a/R/geom-raster.R b/R/geom-raster.R index 2d4ecd85d2..94b1775373 100644 --- a/R/geom-raster.R +++ b/R/geom-raster.R @@ -44,7 +44,7 @@ geom_raster <- function(mapping = NULL, data = NULL, #' @usage NULL #' @export GeomRaster <- ggproto("GeomRaster", Geom, - default_aes = aes(fill = "grey20", alpha = NA), + default_aes = aes(fill = from_theme(col_mix(ink, paper, 0.2)), alpha = NA), non_missing_aes = c("fill", "xmin", "xmax", "ymin", "ymax"), required_aes = c("x", "y"), diff --git a/R/geom-rect.R b/R/geom-rect.R index 0a9d4bdeed..8473474525 100644 --- a/R/geom-rect.R +++ b/R/geom-rect.R @@ -28,8 +28,11 @@ geom_rect <- function(mapping = NULL, data = NULL, #' @usage NULL #' @export GeomRect <- ggproto("GeomRect", Geom, - default_aes = aes(colour = NA, fill = "grey35", linewidth = 0.5, linetype = 1, - alpha = NA), + default_aes = aes( + colour = NA, fill = from_theme(col_mix(ink, paper, 0.35)), + linewidth = from_theme(borderwidth), linetype = from_theme(bordertype), + alpha = NA + ), required_aes = c("x|width|xmin|xmax", "y|height|ymin|ymax"), diff --git a/R/geom-ribbon.R b/R/geom-ribbon.R index 549320deb9..470c013eee 100644 --- a/R/geom-ribbon.R +++ b/R/geom-ribbon.R @@ -96,7 +96,11 @@ geom_ribbon <- function(mapping = NULL, data = NULL, #' @usage NULL #' @export GeomRibbon <- ggproto("GeomRibbon", Geom, - default_aes = aes(colour = NA, fill = "grey20", linewidth = 0.5, linetype = 1, + default_aes = aes( + colour = NA, + fill = from_theme(col_mix(ink, paper, 0.799)), + linewidth = from_theme(borderwidth), + linetype = from_theme(bordertype), alpha = NA), required_aes = c("x|y", "ymin|xmin", "ymax|xmax"), @@ -292,8 +296,14 @@ geom_area <- function(mapping = NULL, data = NULL, stat = "align", #' @usage NULL #' @export GeomArea <- ggproto("GeomArea", GeomRibbon, - default_aes = aes(colour = NA, fill = "grey20", linewidth = 0.5, linetype = 1, - alpha = NA), + + default_aes = aes( + colour = NA, + fill = from_theme(col_mix(ink, paper, 0.2)), + linewidth = from_theme(borderwidth), + linetype = from_theme(bordertype), + alpha = NA + ), required_aes = c("x", "y"), diff --git a/R/geom-rug.R b/R/geom-rug.R index eca79951d8..d675474f43 100644 --- a/R/geom-rug.R +++ b/R/geom-rug.R @@ -153,7 +153,12 @@ GeomRug <- ggproto("GeomRug", Geom, gTree(children = inject(gList(!!!rugs))) }, - default_aes = aes(colour = "black", linewidth = 0.5, linetype = 1, alpha = NA), + default_aes = aes( + colour = from_theme(ink), + linewidth = from_theme(linewidth), + linetype = from_theme(linetype), + alpha = NA + ), draw_key = draw_key_path, diff --git a/R/geom-segment.R b/R/geom-segment.R index be3492bb56..00d9eff87a 100644 --- a/R/geom-segment.R +++ b/R/geom-segment.R @@ -104,7 +104,14 @@ geom_segment <- function(mapping = NULL, data = NULL, GeomSegment <- ggproto("GeomSegment", Geom, required_aes = c("x", "y", "xend|yend"), non_missing_aes = c("linetype", "linewidth"), - default_aes = aes(colour = "black", linewidth = 0.5, linetype = 1, alpha = NA), + + default_aes = aes( + colour = from_theme(ink), + linewidth = from_theme(linewidth), + linetype = from_theme(linetype), + alpha = NA + ), + draw_panel = function(self, data, panel_params, coord, arrow = NULL, arrow.fill = NULL, lineend = "butt", linejoin = "round", na.rm = FALSE) { data$xend <- data$xend %||% data$x @@ -134,7 +141,7 @@ GeomSegment <- ggproto("GeomSegment", Geom, )) } - data$group <- 1:nrow(data) + data$group <- seq_len(nrow(data)) starts <- subset(data, select = c(-xend, -yend)) ends <- rename(subset(data, select = c(-x, -y)), c("xend" = "x", "yend" = "y")) diff --git a/R/geom-sf.R b/R/geom-sf.R index c6298e4b3a..2e9aee78b8 100644 --- a/R/geom-sf.R +++ b/R/geom-sf.R @@ -126,14 +126,17 @@ GeomSf <- ggproto("GeomSf", Geom, fill = NULL, size = NULL, linewidth = NULL, - linetype = 1, + linetype = from_theme(linetype), alpha = NA, stroke = 0.5 ), use_defaults = function(self, data, params = list(), modifiers = aes(), - default_aes = NULL, ...) { - data <- ggproto_parent(Geom, self)$use_defaults(data, params, modifiers, default_aes) + default_aes = NULL, theme = NULL, ...) { + data <- ggproto_parent(Geom, self)$use_defaults( + data, params, modifiers, default_aes, theme = theme, ... + ) + # Early exit for e.g. legend data that don't have geometry columns if (!"geometry" %in% names(data)) { return(data) } @@ -156,24 +159,29 @@ GeomSf <- ggproto("GeomSf", Geom, if (length(index$point) > 0) { points <- GeomPoint$use_defaults( vec_slice(data, index$point), - params, modifiers + params, modifiers, theme = theme ) } if (length(index$line) > 0) { lines <- GeomLine$use_defaults( vec_slice(data, index$line), - params, modifiers + params, modifiers, theme = theme ) } other_default <- modify_list( GeomPolygon$default_aes, - list(fill = "grey90", colour = "grey35", linewidth = 0.2) + aes( + fill = from_theme(col_mix(ink, paper, 0.9)), + colour = from_theme(col_mix(ink, paper, 0.35)), + linewidth = from_theme(0.4 * borderwidth) + ) ) if (length(index$other) > 0) { others <- GeomPolygon$use_defaults( vec_slice(data, index$other), params, modifiers, - default_aes = other_default + default_aes = other_default, + theme = theme ) } if (length(index$collection) > 0) { @@ -185,7 +193,8 @@ GeomSf <- ggproto("GeomSf", Geom, collections <- Geom$use_defaults( vec_slice(data, index$collection), params, modifiers, - default_aes = modified + default_aes = modified, + theme = theme ) } @@ -200,6 +209,9 @@ GeomSf <- ggproto("GeomSf", Geom, if (!inherits(coord, "CoordSf")) { cli::cli_abort("{.fn {snake_class(self)}} can only be used with {.fn coord_sf}.") } + if (is.character(data$shape)) { + data$shape <- translate_shape_string(data$shape) + } data <- coord$transform(data, panel_params) diff --git a/R/geom-smooth.R b/R/geom-smooth.R index 0c3432620c..08e1099df0 100644 --- a/R/geom-smooth.R +++ b/R/geom-smooth.R @@ -9,7 +9,7 @@ #' `predictdf()` generic and its methods. For most methods the standard #' error bounds are computed using the [predict()] method -- the #' exceptions are `loess()`, which uses a t-based approximation, and -#' `glm()`, where the normal confidence interval is constructed on the link +#' `glm()`, where the normal confidence band is constructed on the link #' scale and then back-transformed to the response scale. #' #' @eval rd_orientation() @@ -153,8 +153,8 @@ GeomSmooth <- ggproto("GeomSmooth", Geom, ribbon <- transform(data, colour = NA) path <- transform(data, alpha = NA) - ymin = flipped_names(flipped_aes)$ymin - ymax = flipped_names(flipped_aes)$ymax + ymin <- flipped_names(flipped_aes)$ymin + ymax <- flipped_names(flipped_aes)$ymax has_ribbon <- se && !is.null(data[[ymax]]) && !is.null(data[[ymin]]) gList( @@ -168,8 +168,13 @@ GeomSmooth <- ggproto("GeomSmooth", Geom, required_aes = c("x", "y"), optional_aes = c("ymin", "ymax"), - default_aes = aes(colour = "#3366FF", fill = "grey60", linewidth = 1, - linetype = 1, weight = 1, alpha = 0.4), + default_aes = aes( + colour = from_theme(accent), + fill = from_theme(col_mix(ink, paper, 0.6)), + linewidth = from_theme(2 * linewidth), + linetype = from_theme(linetype), + weight = 1, alpha = 0.4 + ), rename_size = TRUE ) diff --git a/R/geom-text.R b/R/geom-text.R index d0f33a12ff..b7f0d3f320 100644 --- a/R/geom-text.R +++ b/R/geom-text.R @@ -49,7 +49,7 @@ #' can be used in various ways, including to prevent overplotting and #' improving the display. The `position` argument accepts the following: #' * The result of calling a position function, such as `position_jitter()`. -#' * A string nameing the position adjustment. To give the position as a +#' * A string naming the position adjustment. To give the position as a #' string, strip the function name of the `position_` prefix. For example, #' to use `position_jitter()`, give the position as `"jitter"`. #' * For more information and other ways to specify the position, see the @@ -98,10 +98,11 @@ #' scale_colour_discrete(l = 40) #' p + geom_label(aes(fill = factor(cyl)), colour = "white", fontface = "bold") #' -#' p + geom_text(aes(size = wt)) +#' # Scale size of text, and change legend key glyph from a to point +#' p + geom_text(aes(size = wt), key_glyph = "point") #' # Scale height of text, rather than sqrt(height) #' p + -#' geom_text(aes(size = wt)) + +#' geom_text(aes(size = wt), key_glyph = "point") + #' scale_radius(range = c(3,6)) #' #' # You can display expressions by setting parse = TRUE. The @@ -215,8 +216,11 @@ GeomText <- ggproto("GeomText", Geom, non_missing_aes = "angle", default_aes = aes( - colour = "black", size = 3.88, angle = 0, hjust = 0.5, - vjust = 0.5, alpha = NA, family = "", fontface = 1, lineheight = 1.2 + colour = from_theme(ink), + family = from_theme(family), + size = from_theme(fontsize), + angle = 0, hjust = 0.5, + vjust = 0.5, alpha = NA, fontface = 1, lineheight = 1.2 ), draw_panel = function(data, panel_params, coord, parse = FALSE, diff --git a/R/geom-tile.R b/R/geom-tile.R index a5e3232080..e7bb6bc9e3 100644 --- a/R/geom-tile.R +++ b/R/geom-tile.R @@ -110,7 +110,7 @@ GeomTile <- ggproto("GeomTile", GeomRect, extra_params = c("na.rm"), setup_data = function(data, params) { - + data$width <- data$width %||% params$width %||% stats::ave(data$x, data$PANEL, FUN = function(x) resolution(x, FALSE, TRUE)) data$height <- data$height %||% params$height %||% @@ -122,8 +122,13 @@ GeomTile <- ggproto("GeomTile", GeomRect, ) }, - default_aes = aes(fill = "grey20", colour = NA, linewidth = 0.1, linetype = 1, - alpha = NA, width = NA, height = NA), + default_aes = aes( + fill = from_theme(col_mix(ink, paper, 0.2)), + colour = NA, + linewidth = from_theme(0.4 * borderwidth), + linetype = from_theme(bordertype), + alpha = NA, width = NA, height = NA + ), required_aes = c("x", "y"), diff --git a/R/geom-violin.R b/R/geom-violin.R index 0ac6cd29df..17a2d40e94 100644 --- a/R/geom-violin.R +++ b/R/geom-violin.R @@ -197,8 +197,14 @@ GeomViolin <- ggproto("GeomViolin", Geom, draw_key = draw_key_polygon, - default_aes = aes(weight = 1, colour = "grey20", fill = "white", linewidth = 0.5, - alpha = NA, linetype = "solid"), + default_aes = aes( + weight = 1, + colour = from_theme(col_mix(ink, paper, 0.2)), + fill = from_theme(paper), + linewidth = from_theme(borderwidth), + linetype = from_theme(bordertype), + alpha = NA + ), required_aes = c("x", "y"), diff --git a/R/geom-vline.R b/R/geom-vline.R index 85cacf3e63..a9a50e6ff3 100644 --- a/R/geom-vline.R +++ b/R/geom-vline.R @@ -56,7 +56,13 @@ GeomVline <- ggproto("GeomVline", Geom, GeomSegment$draw_panel(unique0(data), panel_params, coord, lineend = lineend) }, - default_aes = aes(colour = "black", linewidth = 0.5, linetype = 1, alpha = NA), + default_aes = aes( + colour = from_theme(ink), + linewidth = from_theme(linewidth), + linetype = from_theme(linetype), + alpha = NA + ), + required_aes = "xintercept", draw_key = draw_key_vline, diff --git a/R/guide-.R b/R/guide-.R index 0a334c4580..4cb77ee7bb 100644 --- a/R/guide-.R +++ b/R/guide-.R @@ -265,11 +265,11 @@ Guide <- ggproto( # Function for extracting information from the layers. # Mostly applies to `guide_legend()` and `guide_binned()` - process_layers = function(self, params, layers, data = NULL) { - self$get_layer_key(params, layers, data) + process_layers = function(self, params, layers, data = NULL, theme = NULL) { + self$get_layer_key(params, layers, data, theme) }, - get_layer_key = function(params, layers, data = NULL) { + get_layer_key = function(params, layers, data = NULL, theme = NULL) { return(params) }, @@ -487,7 +487,7 @@ Guide <- ggproto( # Helper function that may facilitate flipping theme elements by # swapping x/y related arguments to `element_grob()` -flip_element_grob = function(..., flip = FALSE) { +flip_element_grob <- function(..., flip = FALSE) { if (!flip) { ans <- element_grob(...) return(ans) @@ -499,7 +499,7 @@ flip_element_grob = function(..., flip = FALSE) { } # The flippable arguments for `flip_element_grob()`. -flip_names = c( +flip_names <- c( "x" = "y", "y" = "x", "width" = "height", diff --git a/R/guide-axis-stack.R b/R/guide-axis-stack.R index c645c29d99..74fe2b2b3a 100644 --- a/R/guide-axis-stack.R +++ b/R/guide-axis-stack.R @@ -41,7 +41,7 @@ guide_axis_stack <- function(first = "axis", ..., title = waiver(), theme = NULL # Check available aesthetics available <- lapply(axes, `[[`, name = "available_aes") available <- vapply(available, function(x) all(c("x", "y") %in% x), logical(1)) - if (all(!available)) { + if (!any(available)) { cli::cli_abort(paste0( "{.fn guide_axis_stack} can only use guides that handle {.field x} and ", "{.field y} aesthetics." @@ -49,7 +49,7 @@ guide_axis_stack <- function(first = "axis", ..., title = waiver(), theme = NULL } # Remove guides that don't support x/y aesthetics - if (any(!available)) { + if (!all(available)) { remove <- which(!available) removed <- vapply(axes[remove], snake_class, character(1)) axes[remove] <- NULL @@ -134,7 +134,7 @@ GuideAxisStack <- ggproto( }, # Just loops through guides - get_layer_key = function(params, layers) { + get_layer_key = function(params, layers, ...) { for (i in seq_along(params$guides)) { params$guide_params[[i]] <- params$guides[[i]]$get_layer_key( params = params$guide_params[[i]], diff --git a/R/guide-axis.R b/R/guide-axis.R index dc57ffd23e..8280219f3d 100644 --- a/R/guide-axis.R +++ b/R/guide-axis.R @@ -424,6 +424,7 @@ GuideAxis <- ggproto( # Unlist the 'label' grobs z <- if (params$position == "left") c(2, 1, 3) else 1:3 z <- rep(z, c(1, length(grobs$labels), 1)) + has_labels <- !is.zero(grobs$labels[[1]]) grobs <- c(list(grobs$ticks), grobs$labels, list(grobs$title)) # Initialise empty gtable @@ -445,10 +446,25 @@ GuideAxis <- ggproto( vp <- exec( viewport, !!params$orth_aes := unit(params$orth_side, "npc"), - !!params$orth_size := params$measure_gtable(gt), + !!params$orth_size := max(params$measure_gtable(gt), unit(1, "npc")), just = params$opposite ) + # Add null-unit padding to justify based on eventual gtable cell shape + # rather than dimensions of this axis alone. + if (has_labels && params$position %in% c("left", "right")) { + where <- layout$l[-c(1, length(layout$l))] + just <- with(elements$text, rotate_just(angle, hjust, vjust))$hjust %||% 0.5 + gt <- gtable_add_cols(gt, unit(just, "null"), pos = min(where) - 1) + gt <- gtable_add_cols(gt, unit(1 - just, "null"), pos = max(where) + 1) + } + if (has_labels && params$position %in% c("top", "bottom")) { + where <- layout$t[-c(1, length(layout$t))] + just <- with(elements$text, rotate_just(angle, hjust, vjust))$vjust %||% 0.5 + gt <- gtable_add_rows(gt, unit(1 - just, "null"), pos = min(where) - 1) + gt <- gtable_add_rows(gt, unit(just, "null"), pos = max(where) + 1) + } + # Assemble with axis line absoluteGrob( gList(axis_line, gt), @@ -592,23 +608,23 @@ axis_label_element_overrides <- function(axis_position, angle = NULL) { if (axis_position == "bottom") { - hjust = if (angle %in% c(0, 180)) 0.5 else if (angle < 180) 1 else 0 - vjust = if (angle %in% c(90, 270)) 0.5 else if (angle > 90 & angle < 270) 0 else 1 + hjust <- if (angle %in% c(0, 180)) 0.5 else if (angle < 180) 1 else 0 + vjust <- if (angle %in% c(90, 270)) 0.5 else if (angle > 90 & angle < 270) 0 else 1 } else if (axis_position == "left") { - hjust = if (angle %in% c(90, 270)) 0.5 else if (angle > 90 & angle < 270) 0 else 1 - vjust = if (angle %in% c(0, 180)) 0.5 else if (angle < 180) 0 else 1 + hjust <- if (angle %in% c(90, 270)) 0.5 else if (angle > 90 & angle < 270) 0 else 1 + vjust <- if (angle %in% c(0, 180)) 0.5 else if (angle < 180) 0 else 1 } else if (axis_position == "top") { - hjust = if (angle %in% c(0, 180)) 0.5 else if (angle < 180) 0 else 1 - vjust = if (angle %in% c(90, 270)) 0.5 else if (angle > 90 & angle < 270) 1 else 0 + hjust <- if (angle %in% c(0, 180)) 0.5 else if (angle < 180) 0 else 1 + vjust <- if (angle %in% c(90, 270)) 0.5 else if (angle > 90 & angle < 270) 1 else 0 } else if (axis_position == "right") { - hjust = if (angle %in% c(90, 270)) 0.5 else if (angle > 90 & angle < 270) 1 else 0 - vjust = if (angle %in% c(0, 180)) 0.5 else if (angle < 180) 1 else 0 + hjust <- if (angle %in% c(90, 270)) 0.5 else if (angle > 90 & angle < 270) 1 else 0 + vjust <- if (angle %in% c(0, 180)) 0.5 else if (angle < 180) 1 else 0 } diff --git a/R/guide-bins.R b/R/guide-bins.R index e2bd0db428..518655cbba 100644 --- a/R/guide-bins.R +++ b/R/guide-bins.R @@ -326,7 +326,7 @@ GuideBins <- ggproto( } ) -parse_binned_breaks = function(scale, breaks = scale$get_breaks()) { +parse_binned_breaks <- function(scale, breaks = scale$get_breaks()) { breaks <- breaks[!is.na(breaks)] if (length(breaks) == 0) { diff --git a/R/guide-colorbar.R b/R/guide-colorbar.R index ca63f29b54..d03484edae 100644 --- a/R/guide-colorbar.R +++ b/R/guide-colorbar.R @@ -269,7 +269,7 @@ GuideColourbar <- ggproto( return(list(guide = self, params = params)) }, - get_layer_key = function(params, layers, data = NULL) { + get_layer_key = function(params, layers, data = NULL, theme = NULL) { params }, @@ -366,12 +366,12 @@ GuideColourbar <- ggproto( if (params$direction == "horizontal") { width <- 1 / nrow(decor) height <- 1 - x <- (seq(nrow(decor)) - 1) * width + x <- (seq_len(nrow(decor)) - 1) * width y <- 0 } else { width <- 1 height <- 1 / nrow(decor) - y <- (seq(nrow(decor)) - 1) * height + y <- (seq_len(nrow(decor)) - 1) * height x <- 0 } grob <- rectGrob( diff --git a/R/guide-legend.R b/R/guide-legend.R index c35e432230..4dd088f358 100644 --- a/R/guide-legend.R +++ b/R/guide-legend.R @@ -209,7 +209,7 @@ GuideLegend <- ggproto( }, # Arrange common data for vertical and horizontal legends - process_layers = function(self, params, layers, data = NULL) { + process_layers = function(self, params, layers, data = NULL, theme = NULL) { include <- vapply(layers, function(layer) { aes <- matched_aes(layer, params) @@ -220,10 +220,10 @@ GuideLegend <- ggproto( return(NULL) } - self$get_layer_key(params, layers[include], data[include]) + self$get_layer_key(params, layers[include], data[include], theme) }, - get_layer_key = function(params, layers, data) { + get_layer_key = function(params, layers, data, theme = NULL) { # Return empty guides as-is if (nrow(params$key) < 1) { @@ -242,7 +242,7 @@ GuideLegend <- ggproto( single_params <- layer$aes_params[single_params] # Use layer to populate defaults - key <- layer$compute_geom_2(key, single_params) + key <- layer$compute_geom_2(key, single_params, theme) # Filter non-existing levels if (length(matched_aes) > 0) { @@ -631,7 +631,7 @@ keep_key_data <- function(key, data, aes, show) { if (isTRUE(any(show)) || length(show) == 0) { return(TRUE) } - if (isTRUE(all(!show))) { + if (isTRUE(!any(show))) { return(FALSE) } # Second, we go find if the value is actually present in the data. diff --git a/R/guide-old.R b/R/guide-old.R index b2a137fffd..de870965fd 100644 --- a/R/guide-old.R +++ b/R/guide-old.R @@ -103,7 +103,7 @@ GuideOld <- ggproto( guide_transform(params, coord, panel_params) }, - process_layers = function(self, params, layers, data = NULL) { + process_layers = function(self, params, layers, data = NULL, theme = NULL) { guide_geom(params, layers, default_mapping = NULL) }, diff --git a/R/guides-.R b/R/guides-.R index fc9d6e2b3c..fcd65bb94a 100644 --- a/R/guides-.R +++ b/R/guides-.R @@ -194,7 +194,7 @@ Guides <- ggproto( if (is.character(index)) { index <- match(index, self$aesthetics) } - if (any(is.na(index)) || length(index) == 0) { + if (anyNA(index) || length(index) == 0) { return(NULL) } if (length(index) == 1) { @@ -209,7 +209,7 @@ Guides <- ggproto( if (is.character(index)) { index <- match(index, self$aesthetics) } - if (any(is.na(index)) || length(index) == 0) { + if (anyNA(index) || length(index) == 0) { return(NULL) } if (length(index) == 1) { @@ -285,7 +285,7 @@ Guides <- ggproto( # # The resulting guide is then drawn in ggplot_gtable - build = function(self, scales, layers, labels, layer_data) { + build = function(self, scales, layers, labels, layer_data, theme) { # Empty guides list custom <- self$get_custom() @@ -312,7 +312,7 @@ Guides <- ggproto( # Merge and process layers guides$merge() - guides$process_layers(layers, layer_data) + guides$process_layers(layers, layer_data, theme) if (length(guides$guides) == 0) { return(no_guides) } @@ -460,9 +460,9 @@ Guides <- ggproto( }, # Loop over guides to let them extract information from layers - process_layers = function(self, layers, data = NULL) { + process_layers = function(self, layers, data = NULL, theme = NULL) { self$params <- Map( - function(guide, param) guide$process_layers(param, layers, data), + function(guide, param) guide$process_layers(param, layers, data, theme), guide = self$guides, param = self$params ) diff --git a/R/labeller.R b/R/labeller.R index 442f05d496..f23f22b459 100644 --- a/R/labeller.R +++ b/R/labeller.R @@ -83,6 +83,9 @@ #' # Interpreting the labels as plotmath expressions #' p + facet_grid(. ~ cyl2) #' p + facet_grid(. ~ cyl2, labeller = label_parsed) +#' +#' # Include optional argument in label function +#' p + facet_grid(. ~ cyl, labeller = function(x) label_both(x, sep = "=")) #' } #' @name labellers NULL @@ -320,7 +323,7 @@ as_labeller <- function(x, default = label_value, multi_line = TRUE) { #' #' This function makes it easy to assign different labellers to #' different factors. The labeller can be a function or it can be a -#' named character vectors that will serve as a lookup table. +#' named character vector that will serve as a lookup table. #' #' In case of functions, if the labeller has class `labeller`, it #' is directly applied on the data frame of labels. Otherwise, it is diff --git a/R/labels.R b/R/labels.R index aa04732095..20cc929d37 100644 --- a/R/labels.R +++ b/R/labels.R @@ -24,9 +24,11 @@ setup_plot_labels <- function(plot, layers, data) { # Find labels from every layer for (i in seq_along(layers)) { layer <- layers[[i]] + exclude <- names(layer$aes_params) mapping <- layer$computed_mapping mapping <- strip_stage(mapping) mapping <- strip_dots(mapping, strip_pronoun = TRUE) + mapping <- mapping[setdiff(names(mapping), exclude)] # Acquire default labels mapping_default <- make_labels(mapping) @@ -156,7 +158,7 @@ labs <- function(..., title = waiver(), subtitle = waiver(), caption = waiver(), args <- args[!duplicated(names(args))] args <- rename_aes(args) - structure(args, class = "labels") + structure(args, class = c("labels", "gg")) } #' @rdname labs diff --git a/R/layer-sf.R b/R/layer-sf.R index 437ecef3df..3a282e734f 100644 --- a/R/layer-sf.R +++ b/R/layer-sf.R @@ -72,6 +72,7 @@ LayerSf <- ggproto("LayerSf", Layer, }, compute_geom_2 = function(self, data, params = self$aes_params, ...) { + if (empty(data)) return(data) data$geometry <- data$geometry %||% self$computed_geom_params$legend ggproto_parent(Layer, self)$compute_geom_2(data, params, ...) } diff --git a/R/layer.R b/R/layer.R index 8b4621bde2..8acb438c9e 100644 --- a/R/layer.R +++ b/R/layer.R @@ -36,7 +36,7 @@ #' [layer geom][layer_geoms] documentation. #' @param stat The statistical transformation to use on the data for this layer. #' When using a `geom_*()` function to construct a layer, the `stat` -#' argument can be used the override the default coupling between geoms and +#' argument can be used to override the default coupling between geoms and #' stats. The `stat` argument accepts the following: #' * A `Stat` ggproto subclass, for example `StatCount`. #' * A string naming the stat. To give the stat as a string, strip the @@ -58,7 +58,9 @@ #' `NA`, the default, includes if any aesthetics are mapped. #' `FALSE` never includes, and `TRUE` always includes. #' It can also be a named logical vector to finely select the aesthetics to -#' display. +#' display. To include legend keys for all levels, even +#' when no data exists, use `TRUE`. If `NA`, all levels are shown in legend, +#' but unobserved levels are omitted. #' @param inherit.aes If `FALSE`, overrides the default aesthetics, #' rather than combining with them. This is most useful for helper functions #' that define both data and aesthetics and shouldn't inherit behaviour from @@ -128,16 +130,7 @@ layer <- function(geom = NULL, stat = NULL, position <- check_subclass(position, "Position", env = parent.frame(), call = call_env) # Special case for na.rm parameter needed by all layers - if (is.null(params$na.rm)) { - params$na.rm <- FALSE - } - - # Special case for key_glyph parameter which is handed in through - # params since all geoms/stats forward ... to params - if (!is.null(params$key_glyph)) { - key_glyph <- params$key_glyph - params$key_glyph <- NULL # remove to avoid warning about unknown parameter - } + params$na.rm <- params$na.rm %||% FALSE # Split up params between aesthetics, geom, and stat params <- rename_aes(params) @@ -145,13 +138,23 @@ layer <- function(geom = NULL, stat = NULL, geom_params <- params[intersect(names(params), geom$parameters(TRUE))] stat_params <- params[intersect(names(params), stat$parameters(TRUE))] - all <- c(geom$parameters(TRUE), stat$parameters(TRUE), geom$aesthetics()) + ignore <- c("key_glyph", "name") + all <- c(geom$parameters(TRUE), stat$parameters(TRUE), geom$aesthetics(), ignore) # Take care of plain patterns provided as aesthetic pattern <- vapply(aes_params, is_pattern, logical(1)) if (any(pattern)) { aes_params[pattern] <- lapply(aes_params[pattern], list) } + # Drop empty aesthetics + empty_aes <- names(aes_params)[lengths(aes_params) == 0] + if (length(empty_aes) > 0) { + cli::cli_warn( + "Ignoring empty aesthetic{?s}: {.arg {empty_aes}}.", + call = call_env + ) + aes_params <- aes_params[setdiff(names(aes_params), empty_aes)] + } # Warn about extra params and aesthetics extra_param <- setdiff(names(params), all) @@ -179,9 +182,9 @@ layer <- function(geom = NULL, stat = NULL, } # adjust the legend draw key if requested - geom <- set_draw_key(geom, key_glyph) + geom <- set_draw_key(geom, key_glyph %||% params$key_glyph) - fr_call <- layer_class$constructor %||% frame_call(call_env) + fr_call <- layer_class$constructor %||% frame_call(call_env) %||% current_call() ggproto("LayerInstance", layer_class, constructor = fr_call, @@ -194,7 +197,8 @@ layer <- function(geom = NULL, stat = NULL, aes_params = aes_params, position = position, inherit.aes = inherit.aes, - show.legend = show.legend + show.legend = show.legend, + name = params$name ) } @@ -289,8 +293,9 @@ Layer <- ggproto("Layer", NULL, set <- names(aesthetics) %in% names(self$aes_params) calculated <- is_calculated_aes(aesthetics, warn = TRUE) modifiers <- is_scaled_aes(aesthetics) + themed <- is_themed_aes(aesthetics) - aesthetics <- aesthetics[!set & !calculated & !modifiers] + aesthetics <- aesthetics[!set & !calculated & !modifiers & !themed] # Override grouping if set in layer if (!is.null(self$geom_params$group)) { @@ -438,14 +443,14 @@ Layer <- ggproto("Layer", NULL, self$position$compute_layer(data, params, layout) }, - compute_geom_2 = function(self, data, params = self$aes_params, ...) { + compute_geom_2 = function(self, data, params = self$aes_params, theme = NULL, ...) { # Combine aesthetics, defaults, & params if (empty(data)) return(data) aesthetics <- self$computed_mapping - modifiers <- aesthetics[is_scaled_aes(aesthetics) | is_staged_aes(aesthetics)] + modifiers <- aesthetics[is_scaled_aes(aesthetics) | is_staged_aes(aesthetics) | is_themed_aes(aesthetics)] - self$geom$use_defaults(data, params, modifiers, ...) + self$geom$use_defaults(data, params, modifiers, theme = theme, ...) }, finish_statistics = function(self, data) { diff --git a/R/layout.R b/R/layout.R index f6e04f9b9c..1b578111b2 100644 --- a/R/layout.R +++ b/R/layout.R @@ -80,19 +80,8 @@ Layout <- ggproto("Layout", NULL, panels <- lapply(seq_along(panels[[1]]), function(i) { panel <- lapply(panels, `[[`, i) panel <- c(facet_bg[i], panel, facet_fg[i]) - - coord_fg <- self$coord$render_fg(self$panel_params[[i]], theme) - coord_bg <- self$coord$render_bg(self$panel_params[[i]], theme) - if (isTRUE(theme$panel.ontop)) { - panel <- c(panel, list(coord_bg), list(coord_fg)) - } else { - panel <- c(list(coord_bg), panel, list(coord_fg)) - } - - ggname( - paste("panel", i, sep = "-"), - gTree(children = inject(gList(!!!panel))) - ) + panel <- self$coord$draw_panel(panel, self$panel_params[[i]], theme) + ggname(paste("panel", i, sep = "-"), panel) }) plot_table <- self$facet$draw_panels( panels, diff --git a/R/legend-draw.R b/R/legend-draw.R index 9bfd1d9d93..ccfb035872 100644 --- a/R/legend-draw.R +++ b/R/legend-draw.R @@ -207,7 +207,7 @@ draw_key_vpath <- function(data, params, size) { #' @export #' @rdname draw_key draw_key_dotplot <- function(data, params, size) { - pointsGrob(0.5, 0.5, size = unit(.5, "npc"), + pointsGrob(0.5, 0.5, size = unit(0.5, "npc"), pch = 21, gp = gg_par( col = alpha(data$colour %||% "black", data$alpha), diff --git a/R/limits.R b/R/limits.R index 26528ee7ff..087c4c11d0 100644 --- a/R/limits.R +++ b/R/limits.R @@ -116,7 +116,7 @@ limits.numeric <- function(lims, var, call = caller_env()) { if (length(lims) != 2) { cli::cli_abort("{.arg {var}} must be a two-element vector.", call = call) } - if (!any(is.na(lims)) && lims[1] > lims[2]) { + if (!anyNA(lims) && lims[1] > lims[2]) { trans <- "reverse" } else { trans <- "identity" diff --git a/R/margins.R b/R/margins.R index 0fee3ca0ab..176072b4de 100644 --- a/R/margins.R +++ b/R/margins.R @@ -198,7 +198,7 @@ justify_grobs <- function(grobs, x = NULL, y = NULL, hjust = 0.5, vjust = 0.5, ) } else { - children = gList(grobs) + children <- gList(grobs) } diff --git a/R/plot-build.R b/R/plot-build.R index 2a68dd550f..36f33616fd 100644 --- a/R/plot-build.R +++ b/R/plot-build.R @@ -100,11 +100,14 @@ ggplot_build.ggplot <- function(plot) { # Hand off position guides to layout layout$setup_panel_guides(plot$guides, plot$layers) + # Complete the plot's theme + plot$theme <- plot_theme(plot) + # Train and map non-position scales and guides npscales <- scales$non_position_scales() if (npscales$n() > 0) { lapply(data, npscales$train_df) - plot$guides <- plot$guides$build(npscales, plot$layers, plot$labels, data) + plot$guides <- plot$guides$build(npscales, plot$layers, plot$labels, data, plot$theme) data <- lapply(data, npscales$map_df) } else { # Only keep custom guides if there are no non-position scales @@ -113,7 +116,10 @@ ggplot_build.ggplot <- function(plot) { data <- .expose_data(data) # Fill in defaults etc. - data <- by_layer(function(l, d) l$compute_geom_2(d), layers, data, "setting up geom aesthetics") + data <- by_layer( + function(l, d) l$compute_geom_2(d, theme = plot$theme), + layers, data, "setting up geom aesthetics" + ) # Let layer stat have a final say before rendering data <- by_layer(function(l, d) l$finish_statistics(d), layers, data, "finishing layer stat") @@ -199,7 +205,7 @@ ggplot_gtable.ggplot_built <- function(data) { plot <- data$plot layout <- data$layout data <- data$data - theme <- plot_theme(plot) + theme <- plot$theme geom_grobs <- by_layer(function(l, d) l$draw_geom(d, layout), plot$layers, data, "converting geom to grob") @@ -250,18 +256,18 @@ ggplot_gtable.ggplot_built <- function(data) { pans <- plot_table$layout[grepl("^panel", plot_table$layout$name), , drop = FALSE] if (title_pos == "panel") { - title_l = min(pans$l) - title_r = max(pans$r) + title_l <- min(pans$l) + title_r <- max(pans$r) } else { - title_l = 1 - title_r = ncol(plot_table) + title_l <- 1 + title_r <- ncol(plot_table) } if (caption_pos == "panel") { - caption_l = min(pans$l) - caption_r = max(pans$r) + caption_l <- min(pans$l) + caption_r <- max(pans$r) } else { - caption_l = 1 - caption_r = ncol(plot_table) + caption_l <- 1 + caption_r <- ncol(plot_table) } plot_table <- gtable_add_rows(plot_table, subtitle_height, pos = 0) diff --git a/R/plot-construction.R b/R/plot-construction.R index de1306098f..14f2badaed 100644 --- a/R/plot-construction.R +++ b/R/plot-construction.R @@ -84,9 +84,32 @@ add_ggplot <- function(p, object, objectname) { #' @param object_name The name of the object to add #' #' @return A modified ggplot object +#' @details +#' Custom methods for `ggplot_add()` are intended to update the `plot` variable +#' using information from a custom `object`. This can become convenient when +#' writing extensions that don't build on the pre-existing grammar like +#' layers, facets, coords and themes. The `ggplot_add()` function is never +#' intended to be used directly, but it is triggered when an object is added +#' to a plot via the `+` operator. Please note that the full `plot` object is +#' exposed at this point, which comes with the responsibility of returning +#' the plot intact. #' #' @keywords internal #' @export +#' @examples +#' # making a new method for the generic +#' # in this example, we apply a text element to the text theme setting +#' ggplot_add.element_text <- function(object, plot, object_name) { +#' plot + theme(text = object) +#' } +#' +#' # we can now use `+` to add our object to a plot +#' ggplot(mpg, aes(displ, cty)) + +#' geom_point() + +#' element_text(colour = "red") +#' +#' # clean-up +#' rm(ggplot_add.element_text) ggplot_add <- function(object, plot, object_name) { UseMethod("ggplot_add") } @@ -152,7 +175,7 @@ ggplot_add.Facet <- function(object, plot, object_name) { #' @export ggplot_add.list <- function(object, plot, object_name) { for (o in object) { - plot <- plot %+% o + plot <- ggplot_add(o, plot, object_name) } plot } @@ -163,6 +186,25 @@ ggplot_add.by <- function(object, plot, object_name) { #' @export ggplot_add.Layer <- function(object, plot, object_name) { + layers_names <- new_layer_names(object, names(plot$layers)) plot$layers <- append(plot$layers, object) + names(plot$layers) <- layers_names plot } + +new_layer_names <- function(layer, existing) { + new_name <- layer$name + if (is.null(new_name)) { + # Construct a name from the layer's call + new_name <- call_name(layer$constructor) + + if (new_name %in% existing) { + names <- c(existing, new_name) + names <- vec_as_names(names, repair = "unique", quiet = TRUE) + new_name <- names[length(names)] + } + } + + names <- c(existing, new_name) + vec_as_names(names, repair = "check_unique") +} diff --git a/R/position-dodge.R b/R/position-dodge.R index b3818cf08c..ec4b64cdad 100644 --- a/R/position-dodge.R +++ b/R/position-dodge.R @@ -175,7 +175,7 @@ pos_dodge <- function(df, width, n = NULL) { groupidx <- match(df$group, unique0(df$group)) # Find the center for each group, then use that to calculate xmin and xmax - df$x <- df$x + width * ((groupidx - 0.5) / n - .5) + df$x <- df$x + width * ((groupidx - 0.5) / n - 0.5) df$xmin <- df$x - d_width / n / 2 df$xmax <- df$x + d_width / n / 2 diff --git a/R/position-dodge2.R b/R/position-dodge2.R index e8e291c62c..a670ffc349 100644 --- a/R/position-dodge2.R +++ b/R/position-dodge2.R @@ -113,7 +113,7 @@ pos_dodge2 <- function(df, width, n = NULL, padding = 0.1) { df$x <- (df$xmin + df$xmax) / 2 # If no elements occupy the same position, there is no need to add padding - if (!any(duplicated(df$xid))) { + if (!anyDuplicated(df$xid) > 0) { return(df) } diff --git a/R/position-jitter.R b/R/position-jitter.R index 99d807fbe3..ddf59d090b 100644 --- a/R/position-jitter.R +++ b/R/position-jitter.R @@ -41,7 +41,7 @@ #' geom_jitter(position = position_jitter(width = 0.1, height = 0.1)) #' #' # Create a jitter object for reproducible jitter: -#' jitter <- position_jitter(width = 0.1, height = 0.1) +#' jitter <- position_jitter(width = 0.1, height = 0.1, seed = 0) #' ggplot(mtcars, aes(am, vs)) + #' geom_point(position = jitter) + #' geom_point(position = jitter, color = "red", aes(am + 0.2, vs + 0.2)) diff --git a/R/position-stack.R b/R/position-stack.R index 2da5c91ef6..6d77269a1f 100644 --- a/R/position-stack.R +++ b/R/position-stack.R @@ -116,14 +116,12 @@ #' #' # Negative values ----------------------------------------------------------- #' -#' df <- tibble::tribble( -#' ~x, ~y, ~grp, -#' "a", 1, "x", -#' "a", 2, "y", -#' "b", 1, "x", -#' "b", 3, "y", -#' "b", -1, "y" +#' df <- data.frame( +#' x = rep(c("a", "b"), 2:3), +#' y = c(1, 2, 1, 3, -1), +#' grp = c("x", "y", "x", "y", "y") #' ) +#' #' ggplot(data = df, aes(x, y, group = grp)) + #' geom_col(aes(fill = grp), position = position_stack(reverse = TRUE)) + #' geom_hline(yintercept = 0) diff --git a/R/save.R b/R/save.R index 2f28c49418..acc4176162 100644 --- a/R/save.R +++ b/R/save.R @@ -197,7 +197,7 @@ plot_dim <- function(dim = c(NA, NA), scale = 1, units = "in", dim <- to_inches(dim) * scale - if (any(is.na(dim))) { + if (anyNA(dim)) { if (length(grDevices::dev.list()) == 0) { default_dim <- c(7, 7) } else { diff --git a/R/scale-.R b/R/scale-.R index 1773f15142..fd0bbd444f 100644 --- a/R/scale-.R +++ b/R/scale-.R @@ -123,7 +123,7 @@ continuous_scale <- function(aesthetics, scale_name = deprecated(), palette, nam position <- arg_match0(position, c("left", "right", "top", "bottom")) # If the scale is non-positional, break = NULL means removing the guide - if (is.null(breaks) && all(!is_position_aes(aesthetics))) { + if (is.null(breaks) && !any(is_position_aes(aesthetics))) { guide <- "none" } diff --git a/R/scale-binned.R b/R/scale-binned.R index d84080fdef..4db4f1a916 100644 --- a/R/scale-binned.R +++ b/R/scale-binned.R @@ -92,7 +92,7 @@ ScaleBinnedPosition <- ggproto("ScaleBinnedPosition", ScaleBinned, include.lowest = TRUE, right = self$right ) - (x - x_binned + .5) * diff(all_breaks)[x_binned] + all_breaks[x_binned] + (x - x_binned + 0.5) * diff(all_breaks)[x_binned] + all_breaks[x_binned] } else { x <- as.numeric(self$oob(x, limits)) x <- ifelse(!is.na(x), x, self$na.value) diff --git a/R/scale-expansion.R b/R/scale-expansion.R index 8ec72c2a78..e3392fc5bf 100644 --- a/R/scale-expansion.R +++ b/R/scale-expansion.R @@ -69,7 +69,7 @@ expand_range4 <- function(limits, expand) { cli::cli_abort("{.arg expand} must be a numeric vector with 2 or 4 elements.") } - if (all(!is.finite(limits))) { + if (!any(is.finite(limits))) { return(c(-Inf, Inf)) } diff --git a/R/scale-gradient.R b/R/scale-gradient.R index 788ee3e9f0..32f61a2e8e 100644 --- a/R/scale-gradient.R +++ b/R/scale-gradient.R @@ -16,7 +16,7 @@ #' @param low,high Colours for low and high ends of the gradient. #' @param guide Type of legend. Use `"colourbar"` for continuous #' colour bar, or `"legend"` for discrete colour legend. -#' @inheritDotParams continuous_scale -na.value -guide -aesthetics -expand -position +#' @inheritDotParams continuous_scale -na.value -guide -aesthetics -expand -position -palette #' @seealso [scales::pal_seq_gradient()] for details on underlying #' palette, [scale_colour_steps()] for binned variants of these scales. #' diff --git a/R/scale-grey.R b/R/scale-grey.R index b3683295f7..cc6a88033e 100644 --- a/R/scale-grey.R +++ b/R/scale-grey.R @@ -5,7 +5,7 @@ #' #' @inheritParams scales::pal_grey #' @inheritParams scale_colour_hue -#' @inheritDotParams discrete_scale -expand -position -scale_name +#' @inheritDotParams discrete_scale -expand -position -scale_name -palette #' @family colour scales #' @seealso #' The documentation on [colour aesthetics][aes_colour_fill_alpha]. diff --git a/R/scale-hue.R b/R/scale-hue.R index ba50f81dc2..414f10864e 100644 --- a/R/scale-hue.R +++ b/R/scale-hue.R @@ -4,7 +4,7 @@ #' It does not generate colour-blind safe palettes. #' #' @param na.value Colour to use for missing values -#' @inheritDotParams discrete_scale -aesthetics -expand -position -scale_name +#' @inheritDotParams discrete_scale -aesthetics -expand -position -scale_name -palette #' @param aesthetics Character string or vector of character strings listing the #' name(s) of the aesthetic(s) that this scale works with. This can be useful, for #' example, to apply colour settings to the `colour` and `fill` aesthetics at the @@ -205,22 +205,22 @@ scale_fill_qualitative <- function(name = waiver(), ..., type = NULL, #' @param type a character vector or a list of character vectors #' @noRd pal_qualitative <- function(type, h, c, l, h.start, direction) { + type_list <- type + if (!is.list(type_list)) { + type_list <- list(type_list) + } + if (!all(vapply(type_list, is.character, logical(1)))) { + stop_input_type(type, "a character vector or list of character vectors") + } + type_lengths <- lengths(type_list) function(n) { - type_list <- if (!is.list(type)) list(type) else type - if (!all(vapply(type_list, is.character, logical(1)))) { - cli::cli_abort("{.arg type} must be a character vector or a list of character vectors.") - } - type_lengths <- lengths(type_list) # If there are more levels than color codes default to pal_hue() if (max(type_lengths) < n) { return(scales::pal_hue(h, c, l, h.start, direction)(n)) } # Use the minimum length vector that exceeds the number of levels (n) - type_list <- type_list[order(type_lengths)] - i <- 1 - while (length(type_list[[i]]) < n) { - i <- i + 1 - } - type_list[[i]][seq_len(n)] + i <- which(type_lengths >= n) + i <- i[which.min(type_lengths[i])] + type_list[[i]] } } diff --git a/R/scale-linetype.R b/R/scale-linetype.R index a1b983b23d..bc4fa0ce71 100644 --- a/R/scale-linetype.R +++ b/R/scale-linetype.R @@ -6,7 +6,7 @@ #' no inherent order, this use is not advised. #' #' @inheritParams scale_x_discrete -#' @inheritDotParams discrete_scale -expand -position -na.value -scale_name +#' @inheritDotParams discrete_scale -expand -position -na.value -scale_name -palette #' @param na.value The linetype to use for `NA` values. #' @rdname scale_linetype #' @seealso diff --git a/R/scale-manual.R b/R/scale-manual.R index 6e96a54c3b..bcd0624094 100644 --- a/R/scale-manual.R +++ b/R/scale-manual.R @@ -176,7 +176,7 @@ manual_scale <- function(aesthetic, values = NULL, breaks = waiver(), if (length(breaks) <= length(values)) { names(values) <- breaks } else { - names(values) <- breaks[1:length(values)] + names(values) <- breaks[seq_along(values)] } } diff --git a/R/scale-shape.R b/R/scale-shape.R index 7c4c750519..ecb8a2a2a1 100644 --- a/R/scale-shape.R +++ b/R/scale-shape.R @@ -10,7 +10,7 @@ #' @param solid Should the shapes be solid, `TRUE`, or hollow, #' `FALSE`? #' @inheritParams scale_x_discrete -#' @inheritDotParams discrete_scale -expand -position -scale_name +#' @inheritDotParams discrete_scale -expand -position -scale_name -palette #' @rdname scale_shape #' @seealso #' The documentation for [differentiation related aesthetics][aes_linetype_size_shape]. diff --git a/R/stat-bin.R b/R/stat-bin.R index 4c00b2e3ab..c085f818a2 100644 --- a/R/stat-bin.R +++ b/R/stat-bin.R @@ -1,8 +1,7 @@ #' @param binwidth The width of the bins. Can be specified as a numeric value -#' or as a function that calculates width from unscaled x. Here, "unscaled x" -#' refers to the original x values in the data, before application of any -#' scale transformation. When specifying a function along with a grouping -#' structure, the function will be called once per group. +#' or as a function that takes x after scale transformation as input and +#' returns a single numeric value. When specifying a function along with a +#' grouping structure, the function will be called once per group. #' The default is to use the number of bins in `bins`, #' covering the range of the data. You should always override #' this value, exploring multiple widths to find the best to illustrate the diff --git a/R/stat-bindot.R b/R/stat-bindot.R index 66e40ce6cb..85eecc4d54 100644 --- a/R/stat-bindot.R +++ b/R/stat-bindot.R @@ -143,14 +143,14 @@ densitybin <- function(x, weight = NULL, binwidth = NULL, method = method, range # Sort weight and x, by x weight <- weight[order(x)] - x <- x[order(x)] + x <- sort(x, na.last = TRUE) cbin <- 0 # Current bin ID bin <- rep.int(NA, length(x)) # The bin ID for each observation binend <- -Inf # End position of current bin (scan left to right) # Scan list and put dots in bins - for (i in 1:length(x)) { + for (i in seq_along(x)) { # If past end of bin, start a new bin at this point if (x[i] >= binend) { binend <- x[i] + binwidth diff --git a/R/stat-contour.R b/R/stat-contour.R index 882879430d..e0590f2ec9 100644 --- a/R/stat-contour.R +++ b/R/stat-contour.R @@ -108,7 +108,7 @@ StatContour <- ggproto("StatContour", Stat, breaks <- contour_breaks(z.range, bins, binwidth, breaks) isolines <- withr::with_options(list(OutDec = "."), xyz_to_isolines(data, breaks)) - path_df <- iso_to_path(isolines, data$group[1]) + path_df <- iso_to_geom(isolines, data$group[1], geom = "path") path_df$level <- as.numeric(path_df$level) path_df$nlevel <- rescale_max(path_df$level) @@ -142,7 +142,7 @@ StatContourFilled <- ggproto("StatContourFilled", Stat, isobands <- withr::with_options(list(OutDec = "."), xyz_to_isobands(data, breaks)) names(isobands) <- pretty_isoband_levels(names(isobands)) - path_df <- iso_to_polygon(isobands, data$group[1]) + path_df <- iso_to_geom(isobands, data$group[1], geom = "polygon") path_df$level <- ordered(path_df$level, levels = names(isobands)) path_df$level_low <- breaks[as.numeric(path_df$level)] @@ -259,51 +259,17 @@ isoband_z_matrix <- function(data) { raster } -#' Convert the output of isolines functions -#' -#' @param iso the output of [isoband::isolines()] -#' @param group the name of the group -#' -#' @return A data frame that can be passed to [geom_path()]. -#' @noRd -#' -iso_to_path <- function(iso, group = 1) { - lengths <- vapply(iso, function(x) length(x$x), integer(1)) - - if (all(lengths == 0)) { - cli::cli_warn("{.fn stat_contour}: Zero contours were generated") - return(data_frame0()) - } - - levels <- names(iso) - xs <- unlist(lapply(iso, "[[", "x"), use.names = FALSE) - ys <- unlist(lapply(iso, "[[", "y"), use.names = FALSE) - ids <- unlist(lapply(iso, "[[", "id"), use.names = FALSE) - item_id <- rep(seq_along(iso), lengths) - - # Add leading zeros so that groups can be properly sorted - groups <- paste(group, sprintf("%03d", item_id), sprintf("%03d", ids), sep = "-") - groups <- factor(groups) - - data_frame0( - level = rep(levels, lengths), - x = xs, - y = ys, - piece = as.integer(groups), - group = groups, - .size = length(xs) - ) -} - #' Convert the output of isoband functions #' -#' @param iso the output of [isoband::isobands()] +#' @param iso the output of [isoband::isobands()] or [isoband::isolines()] #' @param group the name of the group +#' @param geom The type of geometry to return. Either `"path"` or `"polygon"` +#' for isolines and isobands respectively. #' -#' @return A data frame that can be passed to [geom_polygon()]. +#' @return A data frame that can be passed to [geom_polygon()] or [geom_path()]. #' @noRd #' -iso_to_polygon <- function(iso, group = 1) { +iso_to_geom <- function(iso, group = 1, geom = "path") { lengths <- vapply(iso, function(x) length(x$x), integer(1)) if (all(lengths == 0)) { @@ -319,6 +285,11 @@ iso_to_polygon <- function(iso, group = 1) { # Add leading zeros so that groups can be properly sorted groups <- paste(group, sprintf("%03d", item_id), sep = "-") + if (geom == "path") { + groups <- paste(groups, sprintf("%03d", ids), sep = "-") + ids <- NULL + } + groups <- factor(groups) data_frame0( diff --git a/R/stat-density.R b/R/stat-density.R index 27cafd4b6d..5b948f5d88 100644 --- a/R/stat-density.R +++ b/R/stat-density.R @@ -239,9 +239,10 @@ reflect_density <- function(dens, bounds, from, to) { # Similar to stats::density.default # Once R4.3.0 is the lowest supported version, this function can be replaced by # using `density(..., warnWbw = FALSE)`. -precompute_bw = function(x, bw = "nrd0") { +precompute_bw <- function(x, bw = "nrd0") { bw <- bw[1] if (is.character(bw)) { + bw <- to_lower_ascii(bw) bw <- arg_match0(bw, c("nrd0", "nrd", "ucv", "bcv", "sj", "sj-ste", "sj-dpi")) bw <- switch( to_lower_ascii(bw), diff --git a/R/stat-ecdf.R b/R/stat-ecdf.R index 85287b9130..96430b1e32 100644 --- a/R/stat-ecdf.R +++ b/R/stat-ecdf.R @@ -147,7 +147,7 @@ wecdf <- function(x, weights = NULL) { x <- x[ord] weights <- weights[ord] - if (any(!is.finite(weights))) { + if (!all(is.finite(weights))) { cli::cli_warn(c(paste0( "The {.field weight} aesthetic does not support non-finite or ", "{.code NA} values." diff --git a/R/stat-function.R b/R/stat-function.R index 8f31b8daba..bf6d2e4b74 100644 --- a/R/stat-function.R +++ b/R/stat-function.R @@ -50,7 +50,7 @@ stat_function <- function(mapping = NULL, data = NULL, #' @usage NULL #' @export StatFunction <- ggproto("StatFunction", Stat, - default_aes = aes(y = after_scale(y)), + default_aes = aes(x = NULL, y = after_scale(y)), compute_group = function(data, scales, fun, xlim = NULL, n = 101, args = list()) { if (is.null(scales$x)) { diff --git a/R/stat-qq-line.R b/R/stat-qq-line.R index 67b0da407d..8133216779 100644 --- a/R/stat-qq-line.R +++ b/R/stat-qq-line.R @@ -11,7 +11,7 @@ geom_qq_line <- function(mapping = NULL, ..., distribution = stats::qnorm, dparams = list(), - line.p = c(.25, .75), + line.p = c(0.25, 0.75), fullrange = FALSE, na.rm = FALSE, show.legend = NA, @@ -56,7 +56,7 @@ StatQqLine <- ggproto("StatQqLine", Stat, distribution = stats::qnorm, dparams = list(), na.rm = FALSE, - line.p = c(.25, .75), + line.p = c(0.25, 0.75), fullrange = FALSE) { sample <- sort(data$sample) diff --git a/R/stat-smooth-methods.R b/R/stat-smooth-methods.R index 77d50cdff3..dc90e3c457 100644 --- a/R/stat-smooth-methods.R +++ b/R/stat-smooth-methods.R @@ -60,7 +60,7 @@ predictdf.loess <- function(model, xseq, se, level) { if (se) { y <- pred$fit - ci <- pred$se.fit * stats::qt(level / 2 + .5, pred$df) + ci <- pred$se.fit * stats::qt(level / 2 + 0.5, pred$df) ymin <- y - ci ymax <- y + ci base::data.frame(x = xseq, y, ymin, ymax, se = pred$se.fit) @@ -79,7 +79,7 @@ predictdf.locfit <- function(model, xseq, se, level) { if (se) { y <- pred$fit - ci <- pred$se.fit * stats::qt(level / 2 + .5, model$dp["df2"]) + ci <- pred$se.fit * stats::qt(level / 2 + 0.5, model$dp["df2"]) ymin <- y - ci ymax <- y + ci base::data.frame(x = xseq, y, ymin, ymax, se = pred$se.fit) diff --git a/R/stat-smooth.R b/R/stat-smooth.R index 864e229edf..147bd06e41 100644 --- a/R/stat-smooth.R +++ b/R/stat-smooth.R @@ -18,7 +18,7 @@ #' `y ~ poly(x, 2)`, `y ~ log(x)`. `NULL` by default, in which case #' `method = NULL` implies `formula = y ~ x` when there are fewer than 1,000 #' observations and `formula = y ~ s(x, bs = "cs")` otherwise. -#' @param se Display confidence interval around smooth? (`TRUE` by default, see +#' @param se Display confidence band around smooth? (`TRUE` by default, see #' `level` to control.) #' @param fullrange If `TRUE`, the smoothing line gets expanded to the range of the plot, #' potentially beyond the data. This does not extend the line into any additional padding @@ -26,7 +26,7 @@ #' @param xseq A numeric vector of values at which the smoother is evaluated. #' When `NULL` (default), `xseq` is internally evaluated as a sequence of `n` #' equally spaced points for continuous data. -#' @param level Level of confidence interval to use (0.95 by default). +#' @param level Level of confidence band to use (0.95 by default). #' @param span Controls the amount of smoothing for the default loess smoother. #' Smaller numbers produce wigglier lines, larger numbers produce smoother #' lines. Only used with loess, i.e. when `method = "loess"`, @@ -40,8 +40,8 @@ #' .details = "`stat_smooth()` provides the following variables, some of #' which depend on the orientation:", #' "y|x" = "Predicted value.", -#' "ymin|xmin" = "Lower pointwise confidence interval around the mean.", -#' "ymax|xmax" = "Upper pointwise confidence interval around the mean.", +#' "ymin|xmin" = "Lower pointwise confidence band around the mean.", +#' "ymax|xmax" = "Upper pointwise confidence band around the mean.", #' "se" = "Standard error." #' ) #' @export @@ -95,36 +95,63 @@ StatSmooth <- ggproto("StatSmooth", Stat, setup_params = function(data, params) { params$flipped_aes <- has_flipped_aes(data, params, ambiguous = TRUE) msg <- character() - if (is.null(params$method) || identical(params$method, "auto")) { + method <- params$method + if (is.null(method) || identical(method, "auto")) { # Use loess for small datasets, gam with a cubic regression basis for # larger. Based on size of the _largest_ group to avoid bad memory # behaviour of loess max_group <- max(table(interaction(data$group, data$PANEL, drop = TRUE))) if (max_group < 1000) { - params$method <- "loess" + method <- "loess" } else { - params$method <- "gam" + method <- "gam" } - msg <- c(msg, paste0("method = '", params$method, "'")) + msg <- c(msg, paste0("method = '", method, "'")) + } + + if (identical(method, "gam") && + !prompt_install("mgcv", "for using {.code method = \"gam\"}")) { + cli::cli_inform(c( + "The {.arg method} was set to {.val gam}, but {.pkg mgcv} is not installed.", + "!" = "Falling back to {.code method = \"lm\"}.", + i = "Install {.pkg mgcv} or change the {.arg method} argument to \\ + resolve this issue." + )) + method <- "lm" } if (is.null(params$formula)) { - if (identical(params$method, "gam")) { + if (identical(method, "gam")) { params$formula <- y ~ s(x, bs = "cs") } else { params$formula <- y ~ x } msg <- c(msg, paste0("formula = '", deparse(params$formula), "'")) } - if (identical(params$method, "gam")) { - params$method <- gam_method() + + # Special case span because it's the most commonly used model argument + if (identical(method, "loess")) { + params$method.args$span <- params$span %||% 0.75 + } + + if (is.character(method)) { + if (identical(method, "gam")) { + method <- gam_method() + } else { + method <- match.fun(method) + } + } + # If gam and gam's method is not specified by the user then use REML + if (identical(method, gam_method())) { + params$method.args$method <- params$method.args$method %||% "REML" } if (length(msg) > 0) { cli::cli_inform("{.fn geom_smooth} using {msg}") } + params$method <- method params }, @@ -159,23 +186,6 @@ StatSmooth <- ggproto("StatSmooth", Stat, } } - # Special case span because it's the most commonly used model argument - if (identical(method, "loess")) { - method.args$span <- span - } - - if (is.character(method)) { - if (identical(method, "gam")) { - method <- gam_method() - } else { - method <- match.fun(method) - } - } - # If gam and gam's method is not specified by the user then use REML - if (identical(method, gam_method()) && is.null(method.args$method)) { - method.args$method <- "REML" - } - prediction <- try_fetch( { model <- inject(method( @@ -205,4 +215,10 @@ StatSmooth <- ggproto("StatSmooth", Stat, ) # This function exists to silence an undeclared import warning -gam_method <- function() mgcv::gam +gam_method <- function() { + if (is_installed("mgcv")) { + mgcv::gam + } else { + NA + } +} diff --git a/R/stat-summary-bin.R b/R/stat-summary-bin.R index ce57b6def9..3a4fea585e 100644 --- a/R/stat-summary-bin.R +++ b/R/stat-summary-bin.R @@ -23,15 +23,15 @@ stat_summary_bin <- function(mapping = NULL, data = NULL, fun.ymax = deprecated()) { if (lifecycle::is_present(fun.y)) { deprecate_warn0("3.3.0", "stat_summary_bin(fun.y)", "stat_summary_bin(fun)") - fun = fun %||% fun.y + fun <- fun %||% fun.y } if (lifecycle::is_present(fun.ymin)) { deprecate_warn0("3.3.0", "stat_summary_bin(fun.ymin)", "stat_summary_bin(fun.min)") - fun.min = fun.min %||% fun.ymin + fun.min <- fun.min %||% fun.ymin } if (lifecycle::is_present(fun.ymax)) { deprecate_warn0("3.3.0", "stat_summary_bin(fun.ymax)", "stat_summary_bin(fun.max)") - fun.max = fun.max %||% fun.ymax + fun.max <- fun.max %||% fun.ymax } layer( data = data, @@ -64,24 +64,28 @@ stat_summary_bin <- function(mapping = NULL, data = NULL, StatSummaryBin <- ggproto("StatSummaryBin", Stat, required_aes = c("x", "y"), - extra_params = c("na.rm", "orientation"), + extra_params = c("na.rm", "orientation", "fun.data", "fun.max", "fun.min", "fun.args"), + setup_params = function(data, params) { - params$flipped_aes <- has_flipped_aes(data, params, ambiguous = TRUE) + params$flipped_aes <- has_flipped_aes(data, params) + params$fun <- make_summary_fun( + params$fun.data, params$fun, + params$fun.max, params$fun.min, + params$fun.args %||% list() + ) params }, - compute_group = function(data, scales, fun.data = NULL, fun = NULL, - fun.max = NULL, fun.min = NULL, fun.args = list(), + compute_group = function(data, scales, fun = NULL, bins = 30, binwidth = NULL, breaks = NULL, origin = NULL, right = FALSE, na.rm = FALSE, flipped_aes = FALSE) { data <- flip_data(data, flipped_aes) - fun <- make_summary_fun(fun.data, fun, fun.max, fun.min, fun.args) x <- flipped_names(flipped_aes)$x breaks <- bin2d_breaks(scales[[x]], breaks, origin, binwidth, bins, right = right) data$bin <- cut(data$x, breaks, include.lowest = TRUE, labels = FALSE) - out <- dapply(data, "bin", fun) + out <- dapply(data, "bin", fun %||% function(df) mean_se(df$y)) locs <- bin_loc(breaks, out$bin) out$x <- locs$mid diff --git a/R/stat-summary.R b/R/stat-summary.R index ddcb7b5ae3..6476021fc5 100644 --- a/R/stat-summary.R +++ b/R/stat-summary.R @@ -143,15 +143,15 @@ stat_summary <- function(mapping = NULL, data = NULL, fun.ymax = deprecated()) { if (lifecycle::is_present(fun.y)) { deprecate_warn0("3.3.0", "stat_summary(fun.y)", "stat_summary(fun)") - fun = fun %||% fun.y + fun <- fun %||% fun.y } if (lifecycle::is_present(fun.ymin)) { deprecate_warn0("3.3.0", "stat_summary(fun.ymin)", "stat_summary(fun.min)") - fun.min = fun.min %||% fun.ymin + fun.min <- fun.min %||% fun.ymin } if (lifecycle::is_present(fun.ymax)) { deprecate_warn0("3.3.0", "stat_summary(fun.ymax)", "stat_summary(fun.max)") - fun.max = fun.max %||% fun.ymax + fun.max <- fun.max %||% fun.ymax } layer( data = data, @@ -181,18 +181,22 @@ stat_summary <- function(mapping = NULL, data = NULL, StatSummary <- ggproto("StatSummary", Stat, required_aes = c("x", "y"), - extra_params = c("na.rm", "orientation"), + extra_params = c("na.rm", "orientation", "fun.data", "fun.max", "fun.min", "fun.args"), + setup_params = function(data, params) { params$flipped_aes <- has_flipped_aes(data, params) + params$fun <- make_summary_fun( + params$fun.data, params$fun, + params$fun.max, params$fun.min, + params$fun.args %||% list() + ) params }, - compute_panel = function(data, scales, fun.data = NULL, fun = NULL, - fun.max = NULL, fun.min = NULL, fun.args = list(), - na.rm = FALSE, flipped_aes = FALSE) { + compute_panel = function(data, scales, fun = NULL, + na.rm = FALSE, flipped_aes = FALSE) { data <- flip_data(data, flipped_aes) - fun <- make_summary_fun(fun.data, fun, fun.max, fun.min, fun.args) - summarised <- summarise_by_x(data, fun) + summarised <- summarise_by_x(data, fun %||% function(df) mean_se(df$y)) summarised$flipped_aes <- flipped_aes flip_data(summarised, flipped_aes) } diff --git a/R/summarise-plot.R b/R/summarise-plot.R index 9411c1c586..9ab046cb8c 100644 --- a/R/summarise-plot.R +++ b/R/summarise-plot.R @@ -61,12 +61,12 @@ NULL #' @rdname summarise_plot #' @export -summarise_layout = function(p) { +summarise_layout <- function(p) { check_inherits(p, "ggplot_built") l <- p$layout layout <- l$layout - layout <- tibble( + layout <- data_frame0( panel = l$layout$PANEL, row = l$layout$ROW, col = l$layout$COL @@ -98,7 +98,7 @@ summarise_layout = function(p) { #' @rdname summarise_plot #' @export -summarise_coord = function(p) { +summarise_coord <- function(p) { check_inherits(p, "ggplot_built") # Given a transform object, find the log base; if the transform object is @@ -134,7 +134,7 @@ summarise_layers <- function(p) { # This currently only returns the mappings, but in the future, other # information could be added. - tibble( + data_frame0( mapping = layer_mappings ) } diff --git a/R/theme-defaults.R b/R/theme-defaults.R index 951f20a01c..77b36e243e 100644 --- a/R/theme-defaults.R +++ b/R/theme-defaults.R @@ -143,6 +143,14 @@ theme_grey <- function(base_size = 11, base_family = "", spacing = unit(half_line, "pt"), margins = margin(half_line, half_line, half_line, half_line), + geom = element_geom( + ink = "black", paper = "white", accent = "#3366FF", + linewidth = base_line_size, borderwidth = base_line_size, + linetype = 1L, bordertype = 1L, + family = base_family, fontsize = base_size, + pointsize = (base_size / 11) * 1.5, pointshape = 19 + ), + axis.line = element_blank(), axis.line.x = NULL, axis.line.y = NULL, @@ -212,7 +220,7 @@ theme_grey <- function(base_size = 11, base_family = "", panel.ontop = FALSE, strip.background = element_rect(fill = "grey85", colour = NA), - strip.clip = "inherit", + strip.clip = "on", strip.text = element_text( colour = "grey10", size = rel(0.8), @@ -460,10 +468,12 @@ theme_classic <- function(base_size = 11, base_family = "", panel.grid.minor = element_blank(), # show axes - axis.line = element_line(colour = "black", linewidth = rel(1)), + axis.text = element_text(size = rel(0.8)), + axis.line = element_line(lineend = "square"), + axis.ticks = element_line(), # simple, black and white strips - strip.background = element_rect(fill = "white", colour = "black", linewidth = rel(2)), + strip.background = element_rect(linewidth = rel(2)), # NB: size is 1 but clipped, it looks like the 0.5 of the axes complete = TRUE @@ -511,7 +521,7 @@ theme_void <- function(base_size = 11, base_family = "", legend.box.margin = rel(0), legend.box.spacing = unit(0.2, "cm"), legend.ticks.length = rel(0.2), - strip.clip = "inherit", + strip.clip = "on", strip.text = element_text(size = rel(0.8)), strip.switch.pad.grid = rel(0.5), strip.switch.pad.wrap = rel(0.5), @@ -574,6 +584,14 @@ theme_test <- function(base_size = 11, base_family = "", title = element_text(family = header_family), spacing = unit(half_line, "pt"), margins = margin(half_line, half_line, half_line, half_line), + geom = element_geom( + ink = "black", paper = "white", accent = "#3366FF", + linewidth = base_line_size, borderwidth = base_line_size, + family = base_family, fontsize = base_size, + linetype = 1L, + pointsize = (base_size / 11) * 1.5, pointshape = 19 + ), + axis.line = element_blank(), axis.line.x = NULL, axis.line.y = NULL, @@ -643,7 +661,7 @@ theme_test <- function(base_size = 11, base_family = "", panel.ontop = FALSE, strip.background = element_rect(fill = "grey85", colour = "grey20"), - strip.clip = "inherit", + strip.clip = "on", strip.text = element_text( colour = "grey10", size = rel(0.8), diff --git a/R/theme-elements.R b/R/theme-elements.R index 4a0bfce774..747bb0cf78 100644 --- a/R/theme-elements.R +++ b/R/theme-elements.R @@ -8,14 +8,15 @@ #' - `element_rect()`: borders and backgrounds. #' - `element_line()`: lines. #' - `element_text()`: text. +#' - `element_geom()`: defaults for drawing layers. #' #' `rel()` is used to specify sizes relative to the parent, #' `margin()` is used to specify the margins of elements. #' #' @param fill Fill colour. #' @param colour,color Line/border colour. Color is an alias for colour. -#' @param linewidth Line/border size in mm. -#' @param size text size in pts. +#' @param linewidth,borderwidth Line/border size in mm. +#' @param size,fontsize text size in pts. #' @param arrow.fill Fill colour for arrows. #' @param inherit.blank Should this element inherit the existence of an #' `element_blank` among its parents? If `TRUE` the existence of @@ -48,6 +49,14 @@ #' linewidth = 1 #' ) #' ) +#' +#' ggplot(mpg, aes(displ, hwy)) + +#' geom_point() + +#' geom_smooth(formula = y ~ x, method = "lm") + +#' theme(geom = element_geom( +#' ink = "red", accent = "black", +#' pointsize = 1, linewidth = 2 +#' )) #' @name element #' @aliases NULL NULL @@ -81,10 +90,10 @@ element_rect <- function(fill = NULL, colour = NULL, linewidth = NULL, #' @export #' @rdname element -#' @param linetype Line type. An integer (0:8), a name (blank, solid, -#' dashed, dotted, dotdash, longdash, twodash), or a string with -#' an even number (up to eight) of hexadecimal digits which give the -#' lengths in consecutive positions in the string. +#' @param linetype,bordertype Line type for lines and borders respectively. An +#' integer (0:8), a name (blank, solid, dashed, dotted, dotdash, longdash, +#' twodash), or a string with an even number (up to eight) of hexadecimal +#' digits which give the lengths in consecutive positions in the string. #' @param lineend Line end Line end style (round, butt, square) #' @param arrow Arrow specification, as created by [grid::arrow()] element_line <- function(colour = NULL, linewidth = NULL, linetype = NULL, @@ -148,6 +157,50 @@ element_text <- function(family = NULL, face = NULL, colour = NULL, ) } +#' @param ink Foreground colour. +#' @param paper Background colour. +#' @param accent Accent colour. +#' @param pointsize Size for points in mm. +#' @param pointshape Shape for points (1-25). +#' @export +#' @rdname element +element_geom <- function( + # colours + ink = NULL, paper = NULL, accent = NULL, + # linewidth + linewidth = NULL, borderwidth = NULL, + # linetype + linetype = NULL, bordertype = NULL, + # text + family = NULL, fontsize = NULL, + # points + pointsize = NULL, pointshape = NULL) { + + if (!is.null(fontsize)) { + fontsize <- fontsize / .pt + } + + structure( + list( + ink = ink, + paper = paper, + accent = accent, + linewidth = linewidth, borderwidth = borderwidth, + linetype = linetype, bordertype = bordertype, + family = family, fontsize = fontsize, + pointsize = pointsize, pointshape = pointshape + ), + class = c("element_geom", "element") + ) +} + +.default_geom_element <- element_geom( + ink = "black", paper = "white", accent = "#3366FF", + linewidth = 0.5, borderwidth = 0.5, + linetype = 1L, bordertype = 1L, + family = "", fontsize = 11, + pointsize = 1.5, pointshape = 19 +) #' @export print.element <- function(x, ...) utils::str(x) @@ -429,6 +482,7 @@ el_def <- function(class = NULL, inherit = NULL, description = NULL) { line = el_def("element_line"), rect = el_def("element_rect"), text = el_def("element_text"), + geom = el_def("element_geom"), title = el_def("element_text", "text"), spacing = el_def("unit"), margins = el_def(c("margin", "unit")), diff --git a/R/theme.R b/R/theme.R index 7e8a794a11..43c379f9b6 100644 --- a/R/theme.R +++ b/R/theme.R @@ -25,6 +25,7 @@ #' @param text all text elements ([element_text()]) #' @param title all title elements: plot, axes, legends ([element_text()]; #' inherits from `text`) +#' @param geom defaults for geoms ([element_geom()]) #' @param spacing all spacings ([`unit()`][grid::unit]) #' @param margins all margins ([margin()]) #' @param aspect.ratio aspect ratio of the panel @@ -315,6 +316,7 @@ theme <- function(..., rect, text, title, + geom, spacing, margins, aspect.ratio, diff --git a/R/utilities-break.R b/R/utilities-break.R index 1bcce62ec3..0ed711ad7a 100644 --- a/R/utilities-break.R +++ b/R/utilities-break.R @@ -24,6 +24,9 @@ #' table(cut_width(runif(1000), 0.1, center = 0)) #' table(cut_width(runif(1000), 0.1, labels = FALSE)) cut_interval <- function(x, n = NULL, length = NULL, ...) { + if ((!is.null(n) && !is.null(length)) || (is.null(n) && is.null(length))) { + cli::cli_abort("Specify exactly one of {.var n} and {.var length}.") + } cut(x, breaks(x, "width", n, length), include.lowest = TRUE, ...) } diff --git a/R/utilities-checks.R b/R/utilities-checks.R index db5fee2353..a1ed1b5091 100644 --- a/R/utilities-checks.R +++ b/R/utilities-checks.R @@ -182,7 +182,7 @@ check_inherits <- function(x, #' #' # Possibly throw an error #' try(check_device("glyphs", action = "abort")) -check_device = function(feature, action = "warn", op = NULL, maybe = FALSE, +check_device <- function(feature, action = "warn", op = NULL, maybe = FALSE, call = caller_env()) { check_bool(maybe, allow_na = TRUE) diff --git a/R/utilities.R b/R/utilities.R index f69c2de52b..56325e83d9 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -371,10 +371,6 @@ seq_asc <- function(to, from) { } } -# Needed to trigger package loading -#' @importFrom tibble tibble -NULL - # Wrapping vctrs data_frame constructor with no name repair data_frame0 <- function(...) data_frame(..., .name_repair = "minimal") @@ -858,3 +854,50 @@ warn_dots_used <- function(env = caller_env(), call = caller_env()) { } ) } + +# Shim for scales/#424 +col_mix <- function(a, b, amount = 0.5) { + input <- vec_recycle_common(a = a, b = b, amount = amount) + a <- grDevices::col2rgb(input$a, TRUE) + b <- grDevices::col2rgb(input$b, TRUE) + new <- (a * (1 - input$amount) + b * input$amount) + grDevices::rgb( + new["red", ], new["green", ], new["blue", ], + alpha = new["alpha", ], maxColorValue = 255 + ) +} + +on_load({ + if ("col_mix" %in% getNamespaceExports("scales")) { + col_mix <- scales::col_mix + } +}) + +# TODO: Replace me if rlang/#1730 gets implemented +# Similar to `rlang::check_installed()` but returns boolean and misses +# features such as versions, comparisons and using {pak}. +prompt_install <- function(pkg, reason = NULL) { + if (length(pkg) < 1 || is_installed(pkg)) { + return(TRUE) + } + if (!interactive()) { + return(FALSE) + } + + pkg <- pkg[!vapply(pkg, is_installed, logical(1))] + + message <- "The {.pkg {pkg}} package{?s} {?is/are} required" + if (is.null(reason)) { + message <- paste0(message, ".") + } else { + message <- paste0(message, " ", reason) + } + question <- "Would you like to install {cli::qty(pkg)}{?it/them}?" + + cli::cli_bullets(c("!" = message, "i" = question)) + if (utils::menu(c("Yes", "No")) != 1) { + return(FALSE) + } + utils::install.packages(pkg) + is_installed(pkg) +} diff --git a/man/aes_eval.Rd b/man/aes_eval.Rd index 827bc6a876..11b8d2f1bd 100644 --- a/man/aes_eval.Rd +++ b/man/aes_eval.Rd @@ -5,6 +5,7 @@ \alias{after_stat} \alias{stat} \alias{after_scale} +\alias{from_theme} \alias{stage} \title{Control aesthetic evaluation} \usage{ @@ -16,6 +17,8 @@ after_stat(x) after_scale(x) +from_theme(x) + stage(start = NULL, after_stat = NULL, after_scale = NULL) } \arguments{ @@ -127,6 +130,14 @@ ggplot(mpg, aes(class, displ)) + ) }\if{html}{\out{}} } + +\subsection{Theme access}{ + +The \code{from_theme()} function can be used to acces the \code{\link[=element_geom]{element_geom()}} +fields of the \code{theme(geom)} argument. Using \code{aes(colour = from_theme(ink))} +and \code{aes(colour = from_theme(accent))} allows swapping between foreground and +accent colours. +} } \examples{ diff --git a/man/borders.Rd b/man/borders.Rd index 1fcb3f2630..2f5e9f6841 100644 --- a/man/borders.Rd +++ b/man/borders.Rd @@ -53,7 +53,7 @@ will be used as the layer data. A \code{function} can be created from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{\code{stat}}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. @@ -79,7 +79,9 @@ to use \code{position_jitter()}, give the position as \code{"jitter"}. \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{\code{inherit.aes}}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from diff --git a/man/element.Rd b/man/element.Rd index 2a4f68e2eb..adb1b7eb22 100644 --- a/man/element.Rd +++ b/man/element.Rd @@ -5,6 +5,7 @@ \alias{element_rect} \alias{element_line} \alias{element_text} +\alias{element_geom} \alias{rel} \alias{margin} \title{Theme elements} @@ -48,6 +49,20 @@ element_text( inherit.blank = FALSE ) +element_geom( + ink = NULL, + paper = NULL, + accent = NULL, + linewidth = NULL, + borderwidth = NULL, + linetype = NULL, + bordertype = NULL, + family = NULL, + fontsize = NULL, + pointsize = NULL, + pointshape = NULL +) + rel(x) margin(t = 0, r = 0, b = 0, l = 0, unit = "pt") @@ -57,12 +72,12 @@ margin(t = 0, r = 0, b = 0, l = 0, unit = "pt") \item{colour, color}{Line/border colour. Color is an alias for colour.} -\item{linewidth}{Line/border size in mm.} +\item{linewidth, borderwidth}{Line/border size in mm.} -\item{linetype}{Line type. An integer (0:8), a name (blank, solid, -dashed, dotted, dotdash, longdash, twodash), or a string with -an even number (up to eight) of hexadecimal digits which give the -lengths in consecutive positions in the string.} +\item{linetype, bordertype}{Line type for lines and borders respectively. An +integer (0:8), a name (blank, solid, dashed, dotted, dotdash, longdash, +twodash), or a string with an even number (up to eight) of hexadecimal +digits which give the lengths in consecutive positions in the string.} \item{inherit.blank}{Should this element inherit the existence of an \code{element_blank} among its parents? If \code{TRUE} the existence of @@ -70,7 +85,7 @@ a blank element among its parents will cause this element to be blank as well. If \code{FALSE} any blank parent element will be ignored when calculating final element state.} -\item{size}{text size in pts.} +\item{size, fontsize}{text size in pts.} \item{lineend}{Line end Line end style (round, butt, square)} @@ -98,6 +113,16 @@ side of the text facing towards the center of the plot.} rectangle behind the complete text area, and a point where each label is anchored.} +\item{ink}{Foreground colour.} + +\item{paper}{Background colour.} + +\item{accent}{Accent colour.} + +\item{pointsize}{Size for points in mm.} + +\item{pointshape}{Shape for points (1-25).} + \item{x}{A single number specifying size relative to parent element.} \item{t, r, b, l}{Dimensions of each margin. (To remember order, think trouble).} @@ -116,6 +141,7 @@ specify the display of how non-data components of the plot are drawn. \item \code{element_rect()}: borders and backgrounds. \item \code{element_line()}: lines. \item \code{element_text()}: text. +\item \code{element_geom()}: defaults for drawing layers. } \code{rel()} is used to specify sizes relative to the parent, @@ -146,4 +172,12 @@ plot + theme( linewidth = 1 ) ) + +ggplot(mpg, aes(displ, hwy)) + + geom_point() + + geom_smooth(formula = y ~ x, method = "lm") + + theme(geom = element_geom( + ink = "red", accent = "black", + pointsize = 1, linewidth = 2 + )) } diff --git a/man/facet_wrap.Rd b/man/facet_wrap.Rd index d431f0098a..66716f5c5f 100644 --- a/man/facet_wrap.Rd +++ b/man/facet_wrap.Rd @@ -9,6 +9,7 @@ facet_wrap( nrow = NULL, ncol = NULL, scales = "fixed", + space = "fixed", shrink = TRUE, labeller = "label_value", as.table = TRUE, @@ -35,6 +36,13 @@ or a character vector, \code{c("a", "b")}.} free (\code{"free"}), or free in one dimension (\code{"free_x"}, \code{"free_y"})?} +\item{space}{If \code{"fixed"} (default), all panels have the same size and +the number of rows and columns in the layout can be arbitrary. If +\code{"free_x"}, panels have widths proportional to the length of the x-scale, +but the layout is constrained to one row. If \code{"free_y"}, panels have +heights proportional to the length of the y-scale, but the layout is +constrained to one column.} + \item{shrink}{If \code{TRUE}, will shrink scales to fit output of statistics, not raw data. If \code{FALSE}, will be range of raw data before statistical summary.} diff --git a/man/geom_abline.Rd b/man/geom_abline.Rd index 8fd63ae8e0..0c3bd12b24 100644 --- a/man/geom_abline.Rd +++ b/man/geom_abline.Rd @@ -89,7 +89,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{position}{A position adjustment to use on the data for this layer. This can be used in various ways, including to prevent overplotting and diff --git a/man/geom_bar.Rd b/man/geom_bar.Rd index 4f8196b4c1..6c8c67cc19 100644 --- a/man/geom_bar.Rd +++ b/man/geom_bar.Rd @@ -122,7 +122,9 @@ to either \code{"x"} or \code{"y"}. See the \emph{Orientation} section for more \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_bin_2d.Rd b/man/geom_bin_2d.Rd index 38341bf063..fa3b32b4ce 100644 --- a/man/geom_bin_2d.Rd +++ b/man/geom_bin_2d.Rd @@ -101,7 +101,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_blank.Rd b/man/geom_blank.Rd index c547845953..a8d4a2613d 100644 --- a/man/geom_blank.Rd +++ b/man/geom_blank.Rd @@ -37,7 +37,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. @@ -93,7 +93,9 @@ lists which parameters it can accept. \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_boxplot.Rd b/man/geom_boxplot.Rd index e995aa6635..3fc39d212b 100644 --- a/man/geom_boxplot.Rd +++ b/man/geom_boxplot.Rd @@ -15,8 +15,8 @@ geom_boxplot( outlier.colour = NULL, outlier.color = NULL, outlier.fill = NULL, - outlier.shape = 19, - outlier.size = 1.5, + outlier.shape = NULL, + outlier.size = NULL, outlier.stroke = 0.5, outlier.alpha = NULL, notch = FALSE, @@ -145,7 +145,9 @@ to either \code{"x"} or \code{"y"}. See the \emph{Orientation} section for more \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_contour.Rd b/man/geom_contour.Rd index d53e300a79..c42aec41c9 100644 --- a/man/geom_contour.Rd +++ b/man/geom_contour.Rd @@ -89,7 +89,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. @@ -169,7 +169,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_count.Rd b/man/geom_count.Rd index 370db388ed..1b925e7450 100644 --- a/man/geom_count.Rd +++ b/man/geom_count.Rd @@ -96,7 +96,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_density.Rd b/man/geom_density.Rd index 86bf57d6e9..58f6dae9e2 100644 --- a/man/geom_density.Rd +++ b/man/geom_density.Rd @@ -110,7 +110,9 @@ to either \code{"x"} or \code{"y"}. See the \emph{Orientation} section for more \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_density_2d.Rd b/man/geom_density_2d.Rd index 68f1353262..f063cfdd4a 100644 --- a/man/geom_density_2d.Rd +++ b/man/geom_density_2d.Rd @@ -138,7 +138,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_dotplot.Rd b/man/geom_dotplot.Rd index 1a57df3233..ff7f30a4fc 100644 --- a/man/geom_dotplot.Rd +++ b/man/geom_dotplot.Rd @@ -131,7 +131,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_errorbarh.Rd b/man/geom_errorbarh.Rd index f72ccd5a2a..4e6fb3aae9 100644 --- a/man/geom_errorbarh.Rd +++ b/man/geom_errorbarh.Rd @@ -38,7 +38,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. @@ -97,7 +97,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_function.Rd b/man/geom_function.Rd index 529f552d11..faf9d8552e 100644 --- a/man/geom_function.Rd +++ b/man/geom_function.Rd @@ -41,7 +41,7 @@ mapping.} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. @@ -100,7 +100,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_hex.Rd b/man/geom_hex.Rd index 1876bf19fe..11dbdb1f87 100644 --- a/man/geom_hex.Rd +++ b/man/geom_hex.Rd @@ -99,7 +99,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_histogram.Rd b/man/geom_histogram.Rd index f60ec4b1f5..1f290dbcdc 100644 --- a/man/geom_histogram.Rd +++ b/man/geom_histogram.Rd @@ -120,7 +120,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions @@ -128,10 +130,9 @@ that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. \code{\link[=borders]{borders()}}.} \item{binwidth}{The width of the bins. Can be specified as a numeric value -or as a function that calculates width from unscaled x. Here, "unscaled x" -refers to the original x values in the data, before application of any -scale transformation. When specifying a function along with a grouping -structure, the function will be called once per group. +or as a function that takes x after scale transformation as input and +returns a single numeric value. When specifying a function along with a +grouping structure, the function will be called once per group. The default is to use the number of bins in \code{bins}, covering the range of the data. You should always override this value, exploring multiple widths to find the best to illustrate the diff --git a/man/geom_jitter.Rd b/man/geom_jitter.Rd index 4ca3577792..03ad3e8490 100644 --- a/man/geom_jitter.Rd +++ b/man/geom_jitter.Rd @@ -40,7 +40,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. @@ -108,7 +108,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_linerange.Rd b/man/geom_linerange.Rd index 03eb82f896..87bc5c8e75 100644 --- a/man/geom_linerange.Rd +++ b/man/geom_linerange.Rd @@ -81,7 +81,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. @@ -149,7 +149,9 @@ to either \code{"x"} or \code{"y"}. See the \emph{Orientation} section for more \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_map.Rd b/man/geom_map.Rd index f6aaf69dca..58e83adad4 100644 --- a/man/geom_map.Rd +++ b/man/geom_map.Rd @@ -38,7 +38,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. @@ -89,7 +89,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_path.Rd b/man/geom_path.Rd index 239b7dc0c6..88913a5a7b 100644 --- a/man/geom_path.Rd +++ b/man/geom_path.Rd @@ -70,7 +70,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. @@ -140,7 +140,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions @@ -203,8 +205,9 @@ the \code{NA} is removed silently, without warning. \examples{ # geom_line() is suitable for time series ggplot(economics, aes(date, unemploy)) + geom_line() +# separate by colour and use "timeseries" legend key glyph ggplot(economics_long, aes(date, value01, colour = variable)) + - geom_line() + geom_line(key_glyph = "timeseries") # You can get a timeseries that run vertically by setting the orientation ggplot(economics, aes(unemploy, date)) + geom_line(orientation = "y") diff --git a/man/geom_point.Rd b/man/geom_point.Rd index b7e6a0d5d2..56264c0a36 100644 --- a/man/geom_point.Rd +++ b/man/geom_point.Rd @@ -38,7 +38,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. @@ -97,7 +97,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_polygon.Rd b/man/geom_polygon.Rd index 5e69742056..241490284a 100644 --- a/man/geom_polygon.Rd +++ b/man/geom_polygon.Rd @@ -39,7 +39,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. @@ -103,7 +103,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_qq.Rd b/man/geom_qq.Rd index 62ff813561..d450b3d948 100644 --- a/man/geom_qq.Rd +++ b/man/geom_qq.Rd @@ -156,7 +156,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_quantile.Rd b/man/geom_quantile.Rd index a3aa6ac3c0..568c33e970 100644 --- a/man/geom_quantile.Rd +++ b/man/geom_quantile.Rd @@ -109,7 +109,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_ribbon.Rd b/man/geom_ribbon.Rd index 418c759f8c..d4f5a707e1 100644 --- a/man/geom_ribbon.Rd +++ b/man/geom_ribbon.Rd @@ -66,7 +66,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. @@ -130,7 +130,9 @@ to either \code{"x"} or \code{"y"}. See the \emph{Orientation} section for more \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_rug.Rd b/man/geom_rug.Rd index db5b200b76..1cc10e785a 100644 --- a/man/geom_rug.Rd +++ b/man/geom_rug.Rd @@ -41,7 +41,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. @@ -108,7 +108,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_segment.Rd b/man/geom_segment.Rd index 05ecf827e8..392ba20669 100644 --- a/man/geom_segment.Rd +++ b/man/geom_segment.Rd @@ -60,7 +60,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. @@ -128,7 +128,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_smooth.Rd b/man/geom_smooth.Rd index ece17611a4..6d89a61782 100644 --- a/man/geom_smooth.Rd +++ b/man/geom_smooth.Rd @@ -125,7 +125,7 @@ model that \code{method = NULL} would use, then set \code{method = NULL} implies \code{formula = y ~ x} when there are fewer than 1,000 observations and \code{formula = y ~ s(x, bs = "cs")} otherwise.} -\item{se}{Display confidence interval around smooth? (\code{TRUE} by default, see +\item{se}{Display confidence band around smooth? (\code{TRUE} by default, see \code{level} to control.)} \item{na.rm}{If \code{FALSE}, the default, missing values are removed with @@ -140,7 +140,9 @@ to either \code{"x"} or \code{"y"}. See the \emph{Orientation} section for more \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions @@ -168,7 +170,7 @@ created by \code{expansion}.} When \code{NULL} (default), \code{xseq} is internally evaluated as a sequence of \code{n} equally spaced points for continuous data.} -\item{level}{Level of confidence interval to use (0.95 by default).} +\item{level}{Level of confidence band to use (0.95 by default).} \item{method.args}{List of additional arguments passed on to the modelling function defined by \code{method}.} @@ -184,7 +186,7 @@ Calculation is performed by the (currently undocumented) \code{predictdf()} generic and its methods. For most methods the standard error bounds are computed using the \code{\link[=predict]{predict()}} method -- the exceptions are \code{loess()}, which uses a t-based approximation, and -\code{glm()}, where the normal confidence interval is constructed on the link +\code{glm()}, where the normal confidence band is constructed on the link scale and then back-transformed to the response scale. } \section{Orientation}{ @@ -216,8 +218,8 @@ Learn more about setting these aesthetics in \code{vignette("ggplot2-specs")}. These are calculated by the 'stat' part of layers and can be accessed with \link[=aes_eval]{delayed evaluation}. \code{stat_smooth()} provides the following variables, some of which depend on the orientation: \itemize{ \item \code{after_stat(y)} \emph{or} \code{after_stat(x)}\cr Predicted value. -\item \code{after_stat(ymin)} \emph{or} \code{after_stat(xmin)}\cr Lower pointwise confidence interval around the mean. -\item \code{after_stat(ymax)} \emph{or} \code{after_stat(xmax)}\cr Upper pointwise confidence interval around the mean. +\item \code{after_stat(ymin)} \emph{or} \code{after_stat(xmin)}\cr Lower pointwise confidence band around the mean. +\item \code{after_stat(ymax)} \emph{or} \code{after_stat(xmax)}\cr Upper pointwise confidence band around the mean. \item \code{after_stat(se)}\cr Standard error. } } diff --git a/man/geom_spoke.Rd b/man/geom_spoke.Rd index 216686f8ec..ea28f601c1 100644 --- a/man/geom_spoke.Rd +++ b/man/geom_spoke.Rd @@ -39,7 +39,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. @@ -98,7 +98,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_text.Rd b/man/geom_text.Rd index 9c64a258d5..91c241ab4b 100644 --- a/man/geom_text.Rd +++ b/man/geom_text.Rd @@ -62,7 +62,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. @@ -79,7 +79,7 @@ can be used in various ways, including to prevent overplotting and improving the display. The \code{position} argument accepts the following: \itemize{ \item The result of calling a position function, such as \code{position_jitter()}. -\item A string nameing the position adjustment. To give the position as a +\item A string naming the position adjustment. To give the position as a string, strip the function name of the \code{position_} prefix. For example, to use \code{position_jitter()}, give the position as \code{"jitter"}. \item For more information and other ways to specify the position, see the @@ -138,7 +138,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions @@ -247,10 +249,11 @@ p + geom_text(aes(colour = factor(cyl))) + scale_colour_discrete(l = 40) p + geom_label(aes(fill = factor(cyl)), colour = "white", fontface = "bold") -p + geom_text(aes(size = wt)) +# Scale size of text, and change legend key glyph from a to point +p + geom_text(aes(size = wt), key_glyph = "point") # Scale height of text, rather than sqrt(height) p + - geom_text(aes(size = wt)) + + geom_text(aes(size = wt), key_glyph = "point") + scale_radius(range = c(3,6)) # You can display expressions by setting parse = TRUE. The diff --git a/man/geom_tile.Rd b/man/geom_tile.Rd index ac32298ee7..34b9bb30bc 100644 --- a/man/geom_tile.Rd +++ b/man/geom_tile.Rd @@ -67,7 +67,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. @@ -133,7 +133,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_violin.Rd b/man/geom_violin.Rd index 4041d770c7..974d1c5bdc 100644 --- a/man/geom_violin.Rd +++ b/man/geom_violin.Rd @@ -130,7 +130,9 @@ to either \code{"x"} or \code{"y"}. See the \emph{Orientation} section for more \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/get_geom_defaults.Rd b/man/get_geom_defaults.Rd new file mode 100644 index 0000000000..a39f80d720 --- /dev/null +++ b/man/get_geom_defaults.Rd @@ -0,0 +1,43 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/geom-defaults.R +\name{get_geom_defaults} +\alias{get_geom_defaults} +\title{Resolve and get geom defaults} +\usage{ +get_geom_defaults(geom, theme = theme_get()) +} +\arguments{ +\item{geom}{Some definition of a geom: +\itemize{ +\item A \code{function} that creates a layer, e.g. \code{geom_path()}. +\item A layer created by such function +\item A string naming a geom class in snake case without the \code{geom_}-prefix, +e.g. \code{"contour_filled"}. +\item A geom class object. +}} + +\item{theme}{A \code{\link{theme}} object. Defaults to the current global theme.} +} +\value{ +A list of aesthetics +} +\description{ +Resolve and get geom defaults +} +\examples{ +# Using a function +get_geom_defaults(geom_raster) + +# Using a layer includes static aesthetics as default +get_geom_defaults(geom_tile(fill = "white")) + +# Using a class name +get_geom_defaults("density_2d") + +# Using a class +get_geom_defaults(GeomPoint) + +# Changed theme +get_geom_defaults("point", theme(geom = element_geom(ink = "purple"))) +} +\keyword{internal} diff --git a/man/ggplot_add.Rd b/man/ggplot_add.Rd index 0bd2e2a698..c71d6f863e 100644 --- a/man/ggplot_add.Rd +++ b/man/ggplot_add.Rd @@ -20,4 +20,29 @@ A modified ggplot object This generic allows you to add your own methods for adding custom objects to a ggplot with \link{+.gg}. } +\details{ +Custom methods for \code{ggplot_add()} are intended to update the \code{plot} variable +using information from a custom \code{object}. This can become convenient when +writing extensions that don't build on the pre-existing grammar like +layers, facets, coords and themes. The \code{ggplot_add()} function is never +intended to be used directly, but it is triggered when an object is added +to a plot via the \code{+} operator. Please note that the full \code{plot} object is +exposed at this point, which comes with the responsibility of returning +the plot intact. +} +\examples{ +# making a new method for the generic +# in this example, we apply a text element to the text theme setting +ggplot_add.element_text <- function(object, plot, object_name) { + plot + theme(text = object) +} + +# we can now use `+` to add our object to a plot +ggplot(mpg, aes(displ, cty)) + + geom_point() + + element_text(colour = "red") + +# clean-up +rm(ggplot_add.element_text) +} \keyword{internal} diff --git a/man/ggsf.Rd b/man/ggsf.Rd index 3b8ff90bd7..c4ec76bed1 100644 --- a/man/ggsf.Rd +++ b/man/ggsf.Rd @@ -197,7 +197,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. diff --git a/man/labeller.Rd b/man/labeller.Rd index 52481179f9..2c863d2aee 100644 --- a/man/labeller.Rd +++ b/man/labeller.Rd @@ -42,7 +42,7 @@ for the argument \code{labeller}. \description{ This function makes it easy to assign different labellers to different factors. The labeller can be a function or it can be a -named character vectors that will serve as a lookup table. +named character vector that will serve as a lookup table. } \details{ In case of functions, if the labeller has class \code{labeller}, it diff --git a/man/labellers.Rd b/man/labellers.Rd index 63a4980eb7..09f160bf40 100644 --- a/man/labellers.Rd +++ b/man/labellers.Rd @@ -108,6 +108,9 @@ p + facet_grid(am ~ vs+cyl, labeller = label_context) # Interpreting the labels as plotmath expressions p + facet_grid(. ~ cyl2) p + facet_grid(. ~ cyl2, labeller = label_parsed) + +# Include optional argument in label function +p + facet_grid(. ~ cyl, labeller = function(x) label_both(x, sep = "=")) } } \seealso{ diff --git a/man/layer.Rd b/man/layer.Rd index 8ce4e49715..e34ee05245 100644 --- a/man/layer.Rd +++ b/man/layer.Rd @@ -35,7 +35,7 @@ give the geom as \code{"point"}. \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. @@ -94,7 +94,9 @@ supplied parameters and aesthetics are understood by the \code{geom} or \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{key_glyph}{A legend key drawing function or a string providing the function name minus the \code{draw_key_} prefix. See \link{draw_key} for details.} diff --git a/man/layer_sf.Rd b/man/layer_sf.Rd index 8da9547aed..a10dfa8805 100644 --- a/man/layer_sf.Rd +++ b/man/layer_sf.Rd @@ -33,7 +33,7 @@ give the geom as \code{"point"}. \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. @@ -92,7 +92,9 @@ supplied parameters and aesthetics are understood by the \code{geom} or \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} } \description{ The \code{layer_sf()} function is a variant of \code{\link[=layer]{layer()}} meant to be used by diff --git a/man/position_jitter.Rd b/man/position_jitter.Rd index d0531116d6..b43f4ade40 100644 --- a/man/position_jitter.Rd +++ b/man/position_jitter.Rd @@ -49,7 +49,7 @@ ggplot(mtcars, aes(am, vs)) + geom_jitter(position = position_jitter(width = 0.1, height = 0.1)) # Create a jitter object for reproducible jitter: -jitter <- position_jitter(width = 0.1, height = 0.1) +jitter <- position_jitter(width = 0.1, height = 0.1, seed = 0) ggplot(mtcars, aes(am, vs)) + geom_point(position = jitter) + geom_point(position = jitter, color = "red", aes(am + 0.2, vs + 0.2)) diff --git a/man/position_stack.Rd b/man/position_stack.Rd index 024bfd80a4..646ab3c515 100644 --- a/man/position_stack.Rd +++ b/man/position_stack.Rd @@ -126,14 +126,12 @@ ggplot(series, aes(time, value, group = type)) + # Negative values ----------------------------------------------------------- -df <- tibble::tribble( - ~x, ~y, ~grp, - "a", 1, "x", - "a", 2, "y", - "b", 1, "x", - "b", 3, "y", - "b", -1, "y" +df <- data.frame( + x = rep(c("a", "b"), 2:3), + y = c(1, 2, 1, 3, -1), + grp = c("x", "y", "x", "y", "y") ) + ggplot(data = df, aes(x, y, group = grp)) + geom_col(aes(fill = grp), position = position_stack(reverse = TRUE)) + geom_hline(yintercept = 0) diff --git a/man/scale_gradient.Rd b/man/scale_gradient.Rd index f861378c0c..619e71f3ef 100644 --- a/man/scale_gradient.Rd +++ b/man/scale_gradient.Rd @@ -103,9 +103,6 @@ omitted.} \describe{ \item{\code{scale_name}}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} The name of the scale that should be used for error messages associated with this scale.} - \item{\code{palette}}{A palette function that when called with a numeric vector with -values between 0 and 1 returns the corresponding output values -(e.g., \code{\link[scales:pal_area]{scales::pal_area()}}).} \item{\code{breaks}}{One of: \itemize{ \item \code{NULL} for no breaks diff --git a/man/scale_grey.Rd b/man/scale_grey.Rd index 6b04f40688..0ee97a15de 100644 --- a/man/scale_grey.Rd +++ b/man/scale_grey.Rd @@ -33,9 +33,6 @@ omitted.} \item{...}{ Arguments passed on to \code{\link[=discrete_scale]{discrete_scale}} \describe{ - \item{\code{palette}}{A palette function that when called with a single integer -argument (the number of levels in the scale) returns the values that -they should take (e.g., \code{\link[scales:pal_hue]{scales::pal_hue()}}).} \item{\code{breaks}}{One of: \itemize{ \item \code{NULL} for no breaks diff --git a/man/scale_hue.Rd b/man/scale_hue.Rd index 99776d95d3..1280e741bb 100644 --- a/man/scale_hue.Rd +++ b/man/scale_hue.Rd @@ -39,9 +39,6 @@ omitted.} \item{...}{ Arguments passed on to \code{\link[=discrete_scale]{discrete_scale}} \describe{ - \item{\code{palette}}{A palette function that when called with a single integer -argument (the number of levels in the scale) returns the values that -they should take (e.g., \code{\link[scales:pal_hue]{scales::pal_hue()}}).} \item{\code{breaks}}{One of: \itemize{ \item \code{NULL} for no breaks diff --git a/man/scale_linetype.Rd b/man/scale_linetype.Rd index da4cf2b7c3..9b57b40978 100644 --- a/man/scale_linetype.Rd +++ b/man/scale_linetype.Rd @@ -24,9 +24,6 @@ omitted.} \item{...}{ Arguments passed on to \code{\link[=discrete_scale]{discrete_scale}} \describe{ - \item{\code{palette}}{A palette function that when called with a single integer -argument (the number of levels in the scale) returns the values that -they should take (e.g., \code{\link[scales:pal_hue]{scales::pal_hue()}}).} \item{\code{breaks}}{One of: \itemize{ \item \code{NULL} for no breaks diff --git a/man/scale_shape.Rd b/man/scale_shape.Rd index ffbb381481..8c8b8320fc 100644 --- a/man/scale_shape.Rd +++ b/man/scale_shape.Rd @@ -21,9 +21,6 @@ omitted.} \item{...}{ Arguments passed on to \code{\link[=discrete_scale]{discrete_scale}} \describe{ - \item{\code{palette}}{A palette function that when called with a single integer -argument (the number of levels in the scale) returns the values that -they should take (e.g., \code{\link[scales:pal_hue]{scales::pal_hue()}}).} \item{\code{breaks}}{One of: \itemize{ \item \code{NULL} for no breaks diff --git a/man/stat_ecdf.Rd b/man/stat_ecdf.Rd index d0941b2b56..8d92c51743 100644 --- a/man/stat_ecdf.Rd +++ b/man/stat_ecdf.Rd @@ -105,7 +105,9 @@ a warning. If \code{TRUE} silently removes missing values.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/stat_ellipse.Rd b/man/stat_ellipse.Rd index bed871d361..138bda2e65 100644 --- a/man/stat_ellipse.Rd +++ b/man/stat_ellipse.Rd @@ -112,7 +112,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/stat_identity.Rd b/man/stat_identity.Rd index 945eaafd87..f5dd6e1a5d 100644 --- a/man/stat_identity.Rd +++ b/man/stat_identity.Rd @@ -93,7 +93,9 @@ lists which parameters it can accept. \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/stat_sf_coordinates.Rd b/man/stat_sf_coordinates.Rd index 35ce136a6c..1a8aef4440 100644 --- a/man/stat_sf_coordinates.Rd +++ b/man/stat_sf_coordinates.Rd @@ -72,7 +72,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/stat_summary.Rd b/man/stat_summary.Rd index 034e11afdb..3ebf979e54 100644 --- a/man/stat_summary.Rd +++ b/man/stat_summary.Rd @@ -135,10 +135,9 @@ single number.} \item{bins}{Number of bins. Overridden by \code{binwidth}. Defaults to 30.} \item{binwidth}{The width of the bins. Can be specified as a numeric value -or as a function that calculates width from unscaled x. Here, "unscaled x" -refers to the original x values in the data, before application of any -scale transformation. When specifying a function along with a grouping -structure, the function will be called once per group. +or as a function that takes x after scale transformation as input and +returns a single numeric value. When specifying a function along with a +grouping structure, the function will be called once per group. The default is to use the number of bins in \code{bins}, covering the range of the data. You should always override this value, exploring multiple widths to find the best to illustrate the @@ -162,7 +161,9 @@ to either \code{"x"} or \code{"y"}. See the \emph{Orientation} section for more \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/stat_summary_2d.Rd b/man/stat_summary_2d.Rd index 464cdeacc3..9ee4604b65 100644 --- a/man/stat_summary_2d.Rd +++ b/man/stat_summary_2d.Rd @@ -132,7 +132,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/stat_unique.Rd b/man/stat_unique.Rd index 89a7e728b5..137c99f180 100644 --- a/man/stat_unique.Rd +++ b/man/stat_unique.Rd @@ -97,7 +97,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/theme.Rd b/man/theme.Rd index 1f12df3ba9..829254ecdf 100644 --- a/man/theme.Rd +++ b/man/theme.Rd @@ -10,6 +10,7 @@ theme( rect, text, title, + geom, spacing, margins, aspect.ratio, @@ -161,6 +162,8 @@ these should also be defined in the \verb{element tree} argument. \link[rlang:sp \item{title}{all title elements: plot, axes, legends (\code{\link[=element_text]{element_text()}}; inherits from \code{text})} +\item{geom}{defaults for geoms (\code{\link[=element_geom]{element_geom()}})} + \item{spacing}{all spacings (\code{\link[grid:unit]{unit()}})} \item{margins}{all margins (\code{\link[=margin]{margin()}})} diff --git a/man/update_defaults.Rd b/man/update_defaults.Rd index 8006bf8246..777182e24f 100644 --- a/man/update_defaults.Rd +++ b/man/update_defaults.Rd @@ -3,11 +3,17 @@ \name{update_geom_defaults} \alias{update_geom_defaults} \alias{update_stat_defaults} +\alias{reset_geom_defaults} +\alias{reset_stat_defaults} \title{Modify geom/stat aesthetic defaults for future plots} \usage{ update_geom_defaults(geom, new) update_stat_defaults(stat, new) + +reset_geom_defaults() + +reset_stat_defaults() } \arguments{ \item{new}{One of the following: @@ -21,7 +27,11 @@ update_stat_defaults(stat, new) \code{StatBin}).} } \description{ -Modify geom/stat aesthetic defaults for future plots +Functions to update or reset the default aesthetics of geoms and stats. +} +\note{ +Please note that geom defaults can be set \emph{en masse} via the \code{theme(geom)} +argument. } \examples{ @@ -32,9 +42,11 @@ update_geom_defaults("point", aes(color = "red")) GeomPoint$default_aes ggplot(mtcars, aes(mpg, wt)) + geom_point() -# reset default +# reset single default update_geom_defaults("point", NULL) +# reset all defaults +reset_geom_defaults() # updating a stat's default aesthetic settings # example: change stat_bin()'s default y-axis to the density scale @@ -45,8 +57,11 @@ ggplot(data.frame(x = rnorm(1e3)), aes(x)) + geom_histogram() + geom_function(fun = dnorm, color = "red") -# reset default +# reset single default update_stat_defaults("bin", NULL) +# reset all defaults +reset_stat_defaults() + } \keyword{internal} diff --git a/revdep/README.md b/revdep/README.md index d6c6b43f5e..8976e81c90 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,68 +1,57 @@ # Revdeps -## Failed to check (146) +## Failed to check (132) |package |version |error |warning |note | |:----------------------|:----------|:------|:-------|:----| |abctools |1.1.7 |1 | | | -|AnanseSeurat |? | | | | |animalEKF |1.2 |1 | | | |ANOM |0.5 |1 | | | -|APackOfTheClones |? | | | | |atRisk |0.1.0 |1 | | | |AutoScore |1.0.0 |1 | | | |bayesdfa |1.3.3 |1 | | | |bayesDP |1.3.6 |1 | | | |BayesianFactorZoo |0.0.0.2 |1 | | | -|BCClong |1.0.2 |1 | |1 | +|BayesSurvive |0.0.2 |1 | | | +|BCClong |1.0.3 |1 | | | +|BGGM |2.1.3 |1 | | | |binsreg |1.0 |1 | | | |bmstdr |0.7.9 |1 | | | |bspcov |1.0.0 |1 | | | -|CalibrationCurves |2.0.1 |1 | | | -|Canek |? | | | | +|BuyseTest |3.0.4 |1 | | | +|CalibrationCurves |2.0.3 |1 | | | |CARBayesST |4.0 |1 | | | |CaseBasedReasoning |0.3 |1 | | | -|cellpypes |? | | | | |CGPfunctions |0.6.3 |1 | | | -|CIARA |? | | | | -|ClustAssess |? | | | | -|clustree |? | | | | |cmprskcoxmsm |0.2.1 |1 | | | -|combiroc |? | | | | -|conos |? | | | | |contrast |0.24.2 |1 | | | -|countland |? | | | | |coxed |0.3.3 |1 | | | -|CRMetrics |? | | | | +|CRMetrics |0.3.0 |1 | | | |csmpv |1.0.3 |1 | | | |ctsem |3.10.0 |1 | | | -|CytoSimplex |? | | | | |DepthProc |2.1.5 |1 | | | -|DIscBIO |? | | | | -|DR.SC |? | | | | -|dyngen |? | | | | -|EcoEnsemble |1.0.5 |1 | | | +|DR.SC |3.4 |1 | | | +|DynNom |5.1 |1 | | | +|easybgm |0.1.2 |1 | | | |ecolottery |1.0.0 |1 | | | |EpiEstim |2.2-4 |1 | | | |evolqg |0.3-4 |1 | | | |ForecastComb |1.3.1 |1 | | | |gapfill |0.9.6-1 |1 | |1 | |GeomComb |1.0 |1 | | | -|[geostan](failures.md#geostan)|0.6.1 |__+1__ | |-3 | -|ggrcs |0.3.8 |1 | | | +|ggrcs |0.4.0 |1 | | | |ggrisk |1.3 |1 | | | -|ggsector |? | | | | |gJLS2 |0.2.0 |1 | | | -|grandR |? | | | | |Greg |2.0.2 |1 | | | |greport |0.7-4 |1 | | | -|harmony |? | | | | |hettx |0.1.3 |1 | | | |hIRT |0.3.0 |1 | | | |Hmsc |3.0-13 |1 | | | +|[inventorize](failures.md#inventorize)|1.1.1 |__+1__ | | | |iNZightPlots |2.15.3 |1 | | | |iNZightRegression |1.3.4 |1 | | | |IRexamples |0.0.4 |1 | | | +|jmBIG |0.1.2 |1 | | | |joineRML |0.4.6 |1 | | | |JWileymisc |1.4.1 |1 | | | |kmc |0.4-2 |1 | | | @@ -74,11 +63,10 @@ |MendelianRandomization |0.10.0 |1 | | | |MetabolicSurv |1.1.2 |1 | | | |miWQS |0.4.4 |1 | | | -|mlmts |1.1.1 |1 | | | |MRZero |0.2.0 |1 | | | |Multiaovbay |0.1.0 |1 | | | |multilevelTools |0.1.1 |1 | | | -|multinma |0.7.0 |1 | | | +|multinma |0.7.1 |1 | | | |NCA |4.0.1 |1 | | | |netcmc |1.0.2 |1 | | | |NetworkChange |0.8 |1 | | | @@ -92,11 +80,12 @@ |pould |1.0.1 |1 | | | |powerly |1.8.6 |1 | | | |pre |1.0.7 |1 | | | -|PRECAST |? | | | | |ProFAST |? | | | | +|psbcSpeedUp |2.0.7 |1 | | | |pscore |0.4.0 |1 | | | |psfmi |1.4.0 |1 | | | -|qreport |1.0-0 |1 | | | +|qPCRtools |1.0.1 |1 | | | +|qreport |1.0-1 |1 | | | |qris |1.1.1 |1 | | | |qte |1.3.1 |1 | | | |quid |0.0.1 |1 | | | @@ -104,35 +93,33 @@ |RcmdrPlugin.RiskDemo |3.2 |1 | | | |rddtools |1.6.0 |1 | | | |riskRegression |2023.12.21 |1 | | | -|rliger |? | | | | -|rms |6.8-0 |1 | |1 | -|rmsb |1.1-0 |1 | | | +|rms |6.8-1 |1 | |1 | +|rmsb |1.1-1 |1 | | | |robmed |1.0.2 |1 | | | |robmedExtra |0.1.0 |1 | | | |RPPanalyzer |1.4.9 |1 | | | -|rstanarm |2.32.1 |1 | | | -|scCustomize |? | | | | -|SCdeconR |? | | | | -|scDiffCom |? | | | | -|scGate |? | | | | -|scMappR |? | | | | -|SCORPIUS |? | | | | -|scpoisson |? | | | | -|SCpubr |? | | | | -|scRNAstat |? | | | | +|RQdeltaCT |1.3.0 |1 | | | +|scCustomize |2.1.2 |1 | |1 | +|SCdeconR |1.0.0 |1 | | | +|scGate |1.6.2 |1 | | | +|SCIntRuler |0.99.6 |1 | | | +|scMappR |1.0.11 |1 | | | +|scpi |2.2.5 |1 | | | +|scRNAstat |0.1.1 |1 | | | |sectorgap |0.1.0 |1 | | | |SEERaBomb |2019.2 |1 | | | |semicmprskcoxmsm |0.2.0 |1 | | | |SensMap |0.7 |1 | | | -|Signac |? | | | | +|Seurat |5.1.0 |1 | | | +|shinyTempSignal |0.0.8 |1 | | | +|sievePH |1.1 |1 | | | +|Signac |1.13.0 |1 | | | |SimplyAgree |0.2.0 |1 | | | |sMSROC |0.1.2 |1 | | | |SNPassoc |2.1-0 |1 | | | |snplinkage |? | | | | -|SoupX |? | | | | -|SpaDES.core |2.0.5 |1 | | | +|SoupX |1.6.2 |1 | | | |sparsereg |1.2 |1 | | | -|SPECK |? | | | | |spikeSlabGAM |1.1-19 |1 | | | |statsr |0.3.0 |1 | | | |streamDAG |? | | | | @@ -141,82 +128,259 @@ |tempted |0.1.1 |1 | | | |[tidydr](failures.md#tidydr)|0.0.5 |__+1__ | | | |tidyEdSurvey |0.1.3 |1 | | | -|tidyseurat |? | | | | +|tidyseurat |0.8.0 |1 | | | |tidyvpc |1.5.1 |1 | | | -|treefit |? | | | | |TriDimRegression |1.0.2 |1 | | | |TSrepr |1.1.0 |1 | | | |twang |2.6 |1 | | | -|valse |0.1-0 |1 | | | |vdg |1.2.3 |1 | | | +|visa |0.1.0 |1 | | | |WRTDStidal |1.1.4 |1 | | | -## New problems (64) +## New problems (242) -|package |version |error |warning |note | -|:---------------|:--------|:--------|:--------|:--------| -|[asmbPLS](problems.md#asmbpls)|1.0.0 | |__+1__ |1 | -|[bdl](problems.md#bdl)|1.0.5 | |__+1__ | | -|[bdscale](problems.md#bdscale)|2.0.0 |__+1__ | |__+1__ | -|[biclustermd](problems.md#biclustermd)|0.2.3 |__+1__ | |1 | -|[brolgar](problems.md#brolgar)|1.0.1 |__+2__ | |__+1__ | -|[bSi](problems.md#bsi)|1.0.0 | |__+1__ | | -|[CausalImpact](problems.md#causalimpact)|1.3.0 |__+2__ | |__+1__ | -|[ClusROC](problems.md#clusroc)|1.0.2 | |__+1__ | | -|[clustEff](problems.md#clusteff)|0.3.1 | |__+1__ | | -|[CLVTools](problems.md#clvtools)|0.10.0 |__+1__ | |1 __+1__ | -|[coda4microbiome](problems.md#coda4microbiome)|0.2.3 | |__+1__ | | -|[CompAREdesign](problems.md#comparedesign)|2.3.1 | |__+1__ | | -|[covidcast](problems.md#covidcast)|0.5.2 |__+2__ | |1 __+1__ | -|[Coxmos](problems.md#coxmos)|1.0.2 |1 |__+1__ |1 | -|[csa](problems.md#csa)|0.7.1 | |__+1__ | | -|[deeptime](problems.md#deeptime)|1.1.1 |__+2__ | | | -|[DEGRE](problems.md#degre)|0.2.0 | |__+1__ | | -|[did](problems.md#did)|2.1.2 | |1 __+1__ | | -|[EpiCurve](problems.md#epicurve)|2.4-2 |__+1__ | |1 __+1__ | -|[epiR](problems.md#epir)|2.0.74 |__+1__ | |__+1__ | -|[FuncNN](problems.md#funcnn)|1.0 | |__+1__ |1 | -|[ggedit](problems.md#ggedit)|0.4.1 |__+1__ | | | -|[ggfixest](problems.md#ggfixest)|0.1.0 |1 __+1__ | | | -|[ggfortify](problems.md#ggfortify)|0.4.17 | | |__+1__ | -|[ggh4x](problems.md#ggh4x)|0.2.8 |1 __+2__ | |__+1__ | -|[ggheatmap](problems.md#ggheatmap)|2.2 | |__+1__ | | -|[ggScatRidges](problems.md#ggscatridges)|0.1.1 | |__+1__ | | -|[GimmeMyPlot](problems.md#gimmemyplot)|0.1.0 | |__+1__ | | -|[hilldiv](problems.md#hilldiv)|1.5.1 | |__+1__ | | -|[hJAM](problems.md#hjam)|1.0.0 | |__+1__ | | -|[iglu](problems.md#iglu)|4.0.0 |__+2__ | |__+1__ | -|[ImFoR](problems.md#imfor)|0.1.0 | |__+1__ | | -|[iNEXT.4steps](problems.md#inext4steps)|1.0.0 | |__+1__ | | -|[insane](problems.md#insane)|1.0.3 | |__+1__ | | -|[MarketMatching](problems.md#marketmatching)|1.2.1 |__+1__ | | | -|[mc2d](problems.md#mc2d)|0.2.0 | |__+1__ |1 | -|[MetaIntegrator](problems.md#metaintegrator)|2.1.3 | |__+1__ |2 | -|[MF.beta4](problems.md#mfbeta4)|1.0.3 | |1 __+1__ | | -|[MIMSunit](problems.md#mimsunit)|0.11.2 |__+1__ | | | -|[missingHE](problems.md#missinghe)|1.5.0 | |__+1__ |1 | -|[MSPRT](problems.md#msprt)|3.0 | |__+1__ |1 | -|[nzelect](problems.md#nzelect)|0.4.0 |__+1__ | |2 | -|[OenoKPM](problems.md#oenokpm)|2.4.1 | |__+1__ | | -|[posologyr](problems.md#posologyr)|1.2.4 |__+1__ | | | -|[qicharts](problems.md#qicharts)|0.5.8 |__+1__ | | | -|[qicharts2](problems.md#qicharts2)|0.7.5 |__+1__ | |__+1__ | -|[QuadratiK](problems.md#quadratik)|1.1.0 | |__+1__ |1 | -|[RCTrep](problems.md#rctrep)|1.2.0 | |__+1__ | | -|[scdtb](problems.md#scdtb)|0.1.0 |__+1__ | | | -|[SCOUTer](problems.md#scouter)|1.0.0 | |__+1__ | | -|[sievePH](problems.md#sieveph)|1.0.4 | |__+1__ | | -|[SouthParkRshiny](problems.md#southparkrshiny)|1.0.0 | |__+1__ |2 | -|[SqueakR](problems.md#squeakr)|1.3.0 |1 |__+1__ |1 | -|[survminer](problems.md#survminer)|0.4.9 | |__+1__ |1 | -|[symptomcheckR](problems.md#symptomcheckr)|0.1.3 | |__+1__ | | -|[tcgaViz](problems.md#tcgaviz)|1.0.2 | |__+1__ | | -|[TestGardener](problems.md#testgardener)|3.3.3 | |__+1__ | | -|[tis](problems.md#tis)|1.39 |__+1__ | |1 | -|[UniprotR](problems.md#uniprotr)|2.4.0 | |__+1__ | | -|[VALERIE](problems.md#valerie)|1.1.0 | |__+1__ |1 | -|[vannstats](problems.md#vannstats)|1.3.4.14 | |__+1__ | | -|[vici](problems.md#vici)|0.7.3 | |__+1__ | | -|[Wats](problems.md#wats)|1.0.1 |__+2__ | |__+1__ | -|[xaringanthemer](problems.md#xaringanthemer)|0.4.2 |1 __+1__ | | | +|package |version |error |warning |note | +|:------------------|:-------|:--------|:-------|:--------| +|[activAnalyzer](problems.md#activanalyzer)|2.1.1 |__+1__ | |1 __+1__ | +|[actxps](problems.md#actxps)|1.5.0 |__+1__ | |__+1__ | +|[AeRobiology](problems.md#aerobiology)|2.0.1 |1 | |__+1__ | +|[agricolaeplotr](problems.md#agricolaeplotr)|0.5.0 |__+1__ | | | +|[AnalysisLin](problems.md#analysislin)|0.1.2 |__+1__ | | | +|[animbook](problems.md#animbook)|1.0.0 |__+1__ | | | +|[ANN2](problems.md#ann2)|2.3.4 |__+1__ | |3 | +|[aplot](problems.md#aplot)|0.2.3 |__+1__ | | | +|[applicable](problems.md#applicable)|0.1.1 |__+1__ | | | +|[ASRgenomics](problems.md#asrgenomics)|1.1.4 |__+1__ | |1 | +|[autoplotly](problems.md#autoplotly)|0.1.4 |__+2__ | | | +|[autoReg](problems.md#autoreg)|0.3.3 |__+2__ | |__+1__ | +|[bartMan](problems.md#bartman)|0.1.0 |__+1__ | | | +|[bayesAB](problems.md#bayesab)|1.1.3 |__+1__ | | | +|[BayesGrowth](problems.md#bayesgrowth)|1.0.0 |__+1__ | |2 __+1__ | +|[BayesianReasoning](problems.md#bayesianreasoning)|0.4.2 |__+2__ | |__+1__ | +|[BayesMallows](problems.md#bayesmallows)|2.2.1 |__+1__ | |1 | +|[bayesplot](problems.md#bayesplot)|1.11.1 |1 __+1__ | |1 | +|[bayestestR](problems.md#bayestestr)|0.13.2 |1 __+1__ | | | +|[beastt](problems.md#beastt)|0.0.1 |__+2__ | |__+1__ | +|[besthr](problems.md#besthr)|0.3.2 |__+2__ | |__+1__ | +|[biclustermd](problems.md#biclustermd)|0.2.3 |__+1__ | |1 | +|[biodosetools](problems.md#biodosetools)|3.6.1 |__+1__ | | | +|[boxly](problems.md#boxly)|0.1.1 |__+1__ | | | +|[braidReports](problems.md#braidreports)|0.5.4 |__+1__ | | | +|[breathtestcore](problems.md#breathtestcore)|0.8.7 |__+1__ | | | +|[brolgar](problems.md#brolgar)|1.0.1 |1 __+1__ | |1 | +|[cartograflow](problems.md#cartograflow)|1.0.5 |__+1__ | | | +|[cartographr](problems.md#cartographr)|0.2.2 |__+1__ | |1 | +|[cats](problems.md#cats)|1.0.2 |__+1__ | |1 | +|[cheem](problems.md#cheem)|0.4.0.0 |1 __+1__ | | | +|[chillR](problems.md#chillr)|0.75 |__+1__ | | | +|[chronicle](problems.md#chronicle)|0.3 |__+2__ | |1 __+1__ | +|[circhelp](problems.md#circhelp)|1.1 |__+2__ | |__+1__ | +|[clifro](problems.md#clifro)|3.2-5 |__+1__ | | | +|[clinDataReview](problems.md#clindatareview)|1.6.1 |__+2__ | |1 __+1__ | +|[clinUtils](problems.md#clinutils)|0.2.0 |__+1__ |-1 |1 __+1__ | +|[CohortPlat](problems.md#cohortplat)|1.0.5 |__+2__ | |__+1__ | +|[CoreMicrobiomeR](problems.md#coremicrobiomer)|0.1.0 |__+1__ | | | +|[correlationfunnel](problems.md#correlationfunnel)|0.2.0 |__+1__ | |1 | +|[corrViz](problems.md#corrviz)|0.1.0 |__+2__ | |1 __+1__ | +|[countfitteR](problems.md#countfitter)|1.4 |__+1__ | | | +|[covidcast](problems.md#covidcast)|0.5.2 |__+2__ | |1 __+1__ | +|[crosshap](problems.md#crosshap)|1.4.0 |__+1__ | | | +|[ctrialsgov](problems.md#ctrialsgov)|0.2.5 |__+1__ | |1 | +|[cubble](problems.md#cubble)|0.3.1 |__+1__ | |1 __+1__ | +|[deeptime](problems.md#deeptime)|1.1.1 |__+1__ | | | +|[distributional](problems.md#distributional)|0.4.0 |__+1__ | | | +|[dittoViz](problems.md#dittoviz)|1.0.1 |__+2__ | | | +|[EGM](problems.md#egm)|0.1.0 |__+1__ | | | +|[entropart](problems.md#entropart)|1.6-13 |__+2__ | |__+1__ | 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| +|[foqat](problems.md#foqat)|2.0.8.2 |__+1__ | |__+1__ | +|[forestly](problems.md#forestly)|0.1.1 |__+1__ | |__+1__ | +|[frailtyEM](problems.md#frailtyem)|1.0.1 |__+1__ | |2 | +|[funcharts](problems.md#funcharts)|1.4.1 |__+1__ | | | +|[geomtextpath](problems.md#geomtextpath)|0.1.4 |__+2__ | | | +|[GGally](problems.md#ggally)|2.2.1 |__+1__ | | | +|[gganimate](problems.md#gganimate)|1.0.9 |__+2__ | |__+1__ | +|[ggbrain](problems.md#ggbrain)|0.8.1 |__+1__ | |1 __+1__ | +|[ggbreak](problems.md#ggbreak)|0.1.2 |__+2__ | |__+1__ | +|[ggdark](problems.md#ggdark)|0.2.1 |__+2__ | |1 | +|[ggdist](problems.md#ggdist)|3.3.2 |1 __+2__ | |1 __+1__ | +|[ggDoubleHeat](problems.md#ggdoubleheat)|0.1.2 |__+1__ | | | +|[ggeasy](problems.md#ggeasy)|0.1.4 |__+3__ | |__+1__ | +|[ggedit](problems.md#ggedit)|0.4.1 |__+1__ | | | +|[ggESDA](problems.md#ggesda)|0.2.0 |__+1__ | | | +|[ggfixest](problems.md#ggfixest)|0.1.0 |1 __+1__ | | | +|[ggforce](problems.md#ggforce)|0.4.2 |__+1__ | |1 | 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|__+1__ | | | +|[ggraph](problems.md#ggraph)|2.2.1 |1 __+1__ | |1 __+1__ | +|[ggredist](problems.md#ggredist)|0.0.2 |__+1__ | | | +|[ggRtsy](problems.md#ggrtsy)|0.1.0 |__+2__ | |1 __+1__ | +|[ggseqplot](problems.md#ggseqplot)|0.8.4 |__+3__ | |__+1__ | +|[ggside](problems.md#ggside)|0.3.1 |__+1__ |__+1__ | | +|[ggspatial](problems.md#ggspatial)|1.1.9 |__+2__ | | | +|[ggtern](problems.md#ggtern)|3.5.0 |__+1__ | |2 | +|[ggupset](problems.md#ggupset)|0.4.0 |__+1__ | | | +|[ggVennDiagram](problems.md#ggvenndiagram)|1.5.2 |__+1__ | |1 __+1__ | +|[greatR](problems.md#greatr)|2.0.0 |__+1__ | |__+1__ | +|[Greymodels](problems.md#greymodels)|2.0.1 |__+1__ | | | +|[gtExtras](problems.md#gtextras)|0.5.0 |__+1__ | | | +|[HaploCatcher](problems.md#haplocatcher)|1.0.4 |__+1__ | |__+1__ | +|[healthyR](problems.md#healthyr)|0.2.2 |__+1__ | |1 __+1__ | +|[healthyR.ts](problems.md#healthyrts)|0.3.0 |__+2__ | |1 __+1__ | +|[heatmaply](problems.md#heatmaply)|1.5.0 |__+2__ | |1 __+1__ | 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__+1__ | +|[manydata](problems.md#manydata)|0.9.3 |__+1__ | |1 | +|[MARVEL](problems.md#marvel)|1.4.0 |__+2__ | |__+1__ | +|[MBNMAdose](problems.md#mbnmadose)|0.4.3 |__+1__ | |1 __+1__ | +|[MBNMAtime](problems.md#mbnmatime)|0.2.4 |1 | |__+1__ | +|[MetaNet](problems.md#metanet)|0.1.2 |__+1__ | | | +|[metR](problems.md#metr)|0.15.0 |__+2__ | |1 __+1__ | +|[migraph](problems.md#migraph)|1.3.4 |__+1__ | | | +|[MiMIR](problems.md#mimir)|1.5 |__+1__ | | | +|[miRetrieve](problems.md#miretrieve)|1.3.4 |__+1__ | | | +|[misspi](problems.md#misspi)|0.1.0 |__+1__ | | | +|[mizer](problems.md#mizer)|2.5.1 |__+1__ | |1 | +|[mlr3spatiotempcv](problems.md#mlr3spatiotempcv)|2.3.1 |1 __+1__ | |1 | +|[mlr3viz](problems.md#mlr3viz)|0.9.0 |__+1__ | | | +|[modeltime.resample](problems.md#modeltimeresample)|0.2.3 |__+1__ | |1 | +|[move](problems.md#move)|4.2.4 |1 | |__+1__ | +|[mtb](problems.md#mtb)|0.1.8 |__+1__ | | | +|[neatmaps](problems.md#neatmaps)|2.1.0 |__+1__ | |1 | +|[NetFACS](problems.md#netfacs)|0.5.0 |__+2__ | | | +|[NeuralSens](problems.md#neuralsens)|1.1.3 |__+1__ | | | +|[NHSRplotthedots](problems.md#nhsrplotthedots)|0.1.0 |__+1__ | |1 | +|[NIMAA](problems.md#nimaa)|0.2.1 |__+3__ | |2 __+1__ | +|[OBIC](problems.md#obic)|3.0.2 |__+1__ | |1 __+1__ | +|[OmicNavigator](problems.md#omicnavigator)|1.13.13 |__+1__ | |1 | +|[oncomsm](problems.md#oncomsm)|0.1.4 |__+2__ | |2 __+1__ | +|[pafr](problems.md#pafr)|0.0.2 |__+1__ | |1 | +|[patchwork](problems.md#patchwork)|1.2.0 |__+1__ | | | +|[pathviewr](problems.md#pathviewr)|1.1.7 |__+1__ | | | +|[pcutils](problems.md#pcutils)|0.2.6 |__+1__ | | | +|[pdxTrees](problems.md#pdxtrees)|0.4.0 |__+1__ | |1 __+1__ | +|[personalized](problems.md#personalized)|0.2.7 |__+1__ | | | +|[phylepic](problems.md#phylepic)|0.2.0 |__+1__ | |__+1__ | +|[Plasmidprofiler](problems.md#plasmidprofiler)|0.1.6 |__+1__ | | | +|[platetools](problems.md#platetools)|0.1.7 |__+1__ | | | +|[plotDK](problems.md#plotdk)|0.1.0 |__+1__ | |2 | +|[plotly](problems.md#plotly)|4.10.4 |__+2__ | |1 | +|[pmartR](problems.md#pmartr)|2.4.5 |__+1__ | |1 | +|[pmxTools](problems.md#pmxtools)|1.3 |__+1__ | |1 | +|[posterior](problems.md#posterior)|1.6.0 |1 | |__+1__ | +|[PPQplan](problems.md#ppqplan)|1.1.0 |1 | |2 __+1__ | +|[ppseq](problems.md#ppseq)|0.2.4 |__+1__ | |1 __+1__ | +|[precrec](problems.md#precrec)|0.14.4 |__+1__ | |1 __+1__ | +|[priorsense](problems.md#priorsense)|1.0.1 |__+2__ | |__+1__ | +|[ProAE](problems.md#proae)|1.0.1 |__+1__ | |__+1__ | +|[probably](problems.md#probably)|1.0.3 |__+1__ | | | +|[processmapR](problems.md#processmapr)|0.5.4 |__+1__ | | | +|[psborrow](problems.md#psborrow)|0.2.1 |__+1__ | | | +|[r2dii.plot](problems.md#r2diiplot)|0.4.0 |__+1__ | | | +|[Radviz](problems.md#radviz)|0.9.3 |__+2__ | |__+1__ | +|[rassta](problems.md#rassta)|1.0.5 |__+3__ | | | +|[REddyProc](problems.md#reddyproc)|1.3.3 | | |__+1__ | +|[redist](problems.md#redist)|4.2.0 |__+1__ | |1 __+1__ | +|[reReg](problems.md#rereg)|1.4.6 |__+1__ | | | +|[reservr](problems.md#reservr)|0.0.3 |1 __+1__ | |2 __+1__ | +|[rKOMICS](problems.md#rkomics)|1.3 |__+1__ | |2 | +|[RKorAPClient](problems.md#rkorapclient)|0.8.1 |__+1__ | | | +|[RNAseqQC](problems.md#rnaseqqc)|0.2.1 |__+1__ | |1 __+1__ | +|[roahd](problems.md#roahd)|1.4.3 |__+1__ | |1 | +|[romic](problems.md#romic)|1.1.3 |__+1__ | | | +|[roptions](problems.md#roptions)|1.0.3 |__+1__ | |1 | +|[santaR](problems.md#santar)|1.2.4 |1 __+1__ | | | +|[scdtb](problems.md#scdtb)|0.1.0 |__+1__ | | | +|[scoringutils](problems.md#scoringutils)|1.2.2 |1 __+1__ | |__+1__ | +|[scUtils](problems.md#scutils)|0.1.0 |__+1__ | |1 | +|[SCVA](problems.md#scva)|1.3.1 |__+1__ | | | +|[SDMtune](problems.md#sdmtune)|1.3.1 |1 __+1__ | |1 | +|[SeaVal](problems.md#seaval)|1.2.0 |__+1__ | |1 | +|[sglg](problems.md#sglg)|0.2.2 |__+1__ | | | +|[sgsR](problems.md#sgsr)|1.4.5 |__+1__ | | | +|[SHAPforxgboost](problems.md#shapforxgboost)|0.1.3 |__+1__ | | | +|[SHELF](problems.md#shelf)|1.10.0 | | |__+1__ | +|[shinipsum](problems.md#shinipsum)|0.1.1 |__+1__ | | | +|[SimNPH](problems.md#simnph)|0.5.5 |__+1__ | | | +|[smallsets](problems.md#smallsets)|2.0.0 |__+2__ | |1 __+1__ | +|[spbal](problems.md#spbal)|1.0.0 |__+1__ | |__+1__ | +|[spinifex](problems.md#spinifex)|0.3.7.0 |__+1__ | | | +|[sport](problems.md#sport)|0.2.1 |__+1__ | |1 | +|[SqueakR](problems.md#squeakr)|1.3.0 |1 | |1 __+1__ | +|[statgenGWAS](problems.md#statgengwas)|1.0.9 |__+1__ | |2 | +|[surveyexplorer](problems.md#surveyexplorer)|0.2.0 |__+1__ | | | +|[Sysrecon](problems.md#sysrecon)|0.1.3 |__+1__ | |1 | +|[tabledown](problems.md#tabledown)|1.0.0 |__+1__ | |1 | +|[TCIU](problems.md#tciu)|1.2.6 |__+2__ | |1 __+1__ | +|[tensorEVD](problems.md#tensorevd)|0.1.3 |__+1__ | |__+1__ | +|[thematic](problems.md#thematic)|0.1.5 |__+2__ | | | +|[tidybayes](problems.md#tidybayes)|3.0.6 |2 __+1__ | | | +|[tidycat](problems.md#tidycat)|0.1.2 |__+2__ | |1 __+1__ | +|[tidyCDISC](problems.md#tidycdisc)|0.2.1 |__+1__ | |1 | +|[tidysdm](problems.md#tidysdm)|0.9.5 |__+1__ | |1 __+1__ | +|[tidytreatment](problems.md#tidytreatment)|0.2.2 |__+1__ | |1 __+1__ | +|[timetk](problems.md#timetk)|2.9.0 |__+1__ | |1 | +|[tinyarray](problems.md#tinyarray)|2.4.2 |__+1__ | | | +|[tornado](problems.md#tornado)|0.1.3 |__+3__ | |__+1__ | +|[TOSTER](problems.md#toster)|0.8.3 |__+3__ | |__+1__ | +|[TreatmentPatterns](problems.md#treatmentpatterns)|2.6.7 |__+1__ | | | +|[trelliscopejs](problems.md#trelliscopejs)|0.2.6 |__+1__ | | | +|[tricolore](problems.md#tricolore)|1.2.4 |__+2__ | |1 __+1__ | +|[triptych](problems.md#triptych)|0.1.3 |__+1__ | | | +|[tsnet](problems.md#tsnet)|0.1.0 |__+1__ | |2 | +|[umiAnalyzer](problems.md#umianalyzer)|1.0.0 |__+1__ | | | +|[valr](problems.md#valr)|0.8.1 |__+1__ | |1 | +|[vivaldi](problems.md#vivaldi)|1.0.1 |__+3__ | |1 __+1__ | +|[vivid](problems.md#vivid)|0.2.8 |__+1__ | | | +|[vvshiny](problems.md#vvshiny)|0.1.1 |__+1__ | | | +|[wilson](problems.md#wilson)|2.4.2 |__+1__ | | | +|[xaringanthemer](problems.md#xaringanthemer)|0.4.2 |1 __+1__ | | | +|[yamlet](problems.md#yamlet)|1.0.3 |__+2__ | | | diff --git a/revdep/cran.md b/revdep/cran.md index f1da4a685a..4a9f813633 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,96 +1,332 @@ ## revdepcheck results -We checked 5034 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. +We checked 5166 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. - * We saw 64 new problems - * We failed to check 146 packages + * We saw 242 new problems + * We failed to check 132 packages Issues with CRAN packages are summarised below. ### New problems (This reports the first line of each new failure) -* asmbPLS - checking whether package ‘asmbPLS’ can be installed ... WARNING +* activAnalyzer + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* actxps + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* AeRobiology + checking re-building of vignette outputs ... NOTE + +* agricolaeplotr + checking tests ... ERROR + +* AnalysisLin + checking examples ... ERROR + +* animbook + checking examples ... ERROR + +* ANN2 + checking tests ... ERROR + +* aplot + checking examples ... ERROR + +* applicable + checking tests ... ERROR + +* ASRgenomics + checking examples ... ERROR + +* autoplotly + checking examples ... ERROR + checking tests ... ERROR + +* autoReg + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* bartMan + checking examples ... ERROR + +* bayesAB + checking tests ... ERROR -* bdl - checking whether package ‘bdl’ can be installed ... WARNING +* BayesGrowth + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* BayesianReasoning + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* BayesMallows + checking tests ... ERROR + +* bayesplot + checking tests ... ERROR + +* bayestestR + checking examples ... ERROR + +* beastt + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* bdscale +* besthr + checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE * biclustermd checking tests ... ERROR +* biodosetools + checking tests ... ERROR + +* boxly + checking tests ... ERROR + +* braidReports + checking examples ... ERROR + +* breathtestcore + checking tests ... ERROR + * brolgar checking examples ... ERROR + +* cartograflow + checking examples ... ERROR + +* cartographr + checking tests ... ERROR + +* cats + checking examples ... ERROR + +* cheem + checking tests ... ERROR + +* chillR + checking examples ... ERROR + +* chronicle + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* circhelp + checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* bSi - checking whether package ‘bSi’ can be installed ... WARNING +* clifro + checking tests ... ERROR -* CausalImpact +* clinDataReview + checking examples ... ERROR checking tests ... ERROR + checking re-building of vignette outputs ... NOTE + +* clinUtils + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* CohortPlat + checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* ClusROC - checking whether package ‘ClusROC’ can be installed ... WARNING +* CoreMicrobiomeR + checking examples ... ERROR -* clustEff - checking whether package ‘clustEff’ can be installed ... WARNING +* correlationfunnel + checking tests ... ERROR -* CLVTools +* corrViz + checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* coda4microbiome - checking whether package ‘coda4microbiome’ can be installed ... WARNING - -* CompAREdesign - checking whether package ‘CompAREdesign’ can be installed ... WARNING +* countfitteR + checking tests ... ERROR * covidcast checking tests ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* Coxmos - checking Rd files ... WARNING +* crosshap + checking examples ... ERROR + +* ctrialsgov + checking tests ... ERROR -* csa - checking whether package ‘csa’ can be installed ... WARNING +* cubble + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE * deeptime checking examples ... ERROR + +* distributional + checking examples ... ERROR + +* dittoViz + checking examples ... ERROR + checking tests ... ERROR + +* EGM + checking tests ... ERROR + +* entropart + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* epiCleanr + checking examples ... ERROR + +* esci + checking examples ... ERROR + checking tests ... ERROR + +* evalITR + checking re-building of vignette outputs ... NOTE + +* eventstudyr + checking tests ... ERROR + +* EvoPhylo + checking examples ... ERROR + checking re-building of vignette outputs ... NOTE + +* expirest + checking tests ... ERROR + +* explainer + checking examples ... ERROR + +* ezEDA + checking tests ... ERROR + +* ezplot + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* fable.prophet + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* fabletools + checking examples ... ERROR + checking tests ... ERROR + +* factoextra + checking examples ... ERROR + +* fairmodels + checking tests ... ERROR + +* fddm + checking running R code from vignettes ... ERROR + +* feasts + checking tests ... ERROR + +* ffp + checking examples ... ERROR + +* fido + checking examples ... ERROR + checking tests ... ERROR + +* flipr + checking re-building of vignette outputs ... NOTE + +* foqat + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* forestly + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* frailtyEM + checking examples ... ERROR + +* funcharts + checking examples ... ERROR + +* geomtextpath + checking examples ... ERROR checking tests ... ERROR -* DEGRE - checking whether package ‘DEGRE’ can be installed ... WARNING +* GGally + checking tests ... ERROR -* did - checking whether package ‘did’ can be installed ... WARNING +* gganimate + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* EpiCurve +* ggbrain checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* epiR +* ggbreak + checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* FuncNN - checking whether package ‘FuncNN’ can be installed ... WARNING +* ggdark + checking examples ... ERROR + checking tests ... ERROR + +* ggdist + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... NOTE + +* ggDoubleHeat + checking examples ... ERROR + +* ggeasy + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE * ggedit checking examples ... ERROR +* ggESDA + checking examples ... ERROR + * ggfixest checking tests ... ERROR +* ggforce + checking examples ... ERROR + +* ggformula + checking for code/documentation mismatches ... WARNING + * ggfortify + checking tests ... ERROR + +* gggenomes + checking examples ... ERROR + checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE * ggh4x @@ -98,189 +334,607 @@ Issues with CRAN packages are summarised below. checking tests ... ERROR checking re-building of vignette outputs ... NOTE -* ggheatmap - checking whether package ‘ggheatmap’ can be installed ... WARNING +* gghighlight + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* ggScatRidges - checking whether package ‘ggScatRidges’ can be installed ... WARNING +* ggHoriPlot + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* GimmeMyPlot - checking whether package ‘GimmeMyPlot’ can be installed ... WARNING +* ggiraph + checking examples ... ERROR + checking tests ... ERROR -* hilldiv - checking whether package ‘hilldiv’ can be installed ... WARNING +* ggiraphExtra + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* hJAM - checking whether package ‘hJAM’ can be installed ... WARNING +* ggmice + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* iglu +* ggmulti checking examples ... ERROR + checking tests ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* ImFoR - checking whether package ‘ImFoR’ can be installed ... WARNING +* ggnewscale + checking examples ... ERROR + checking tests ... ERROR -* iNEXT.4steps - checking whether package ‘iNEXT.4steps’ can be installed ... WARNING +* ggparallel + checking tests ... ERROR -* insane - checking whether package ‘insane’ can be installed ... WARNING +* ggpicrust2 + checking examples ... ERROR -* MarketMatching - checking re-building of vignette outputs ... ERROR +* ggpie + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* mc2d - checking whether package ‘mc2d’ can be installed ... WARNING +* ggplotlyExtra + checking examples ... ERROR -* MetaIntegrator - checking whether package ‘MetaIntegrator’ can be installed ... WARNING +* ggpol + checking examples ... ERROR -* MF.beta4 - checking whether package ‘MF.beta4’ can be installed ... WARNING +* ggpubr + checking tests ... ERROR -* MIMSunit +* ggraph checking examples ... ERROR + checking re-building of vignette outputs ... NOTE -* missingHE - checking whether package ‘missingHE’ can be installed ... WARNING +* ggredist + checking examples ... ERROR -* MSPRT - checking whether package ‘MSPRT’ can be installed ... WARNING +* ggRtsy + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* nzelect +* ggseqplot checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* OenoKPM - checking whether package ‘OenoKPM’ can be installed ... WARNING +* ggside + checking tests ... ERROR + checking for code/documentation mismatches ... WARNING -* posologyr - checking running R code from vignettes ... ERROR +* ggspatial + checking examples ... ERROR + checking tests ... ERROR -* qicharts +* ggtern checking examples ... ERROR -* qicharts2 +* ggupset + checking examples ... ERROR + +* ggVennDiagram checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* QuadratiK - checking whether package ‘QuadratiK’ can be installed ... WARNING +* greatR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* RCTrep - checking whether package ‘RCTrep’ can be installed ... WARNING +* Greymodels + checking examples ... ERROR -* scdtb +* gtExtras checking tests ... ERROR -* SCOUTer - checking whether package ‘SCOUTer’ can be installed ... WARNING - -* sievePH - checking whether package ‘sievePH’ can be installed ... WARNING +* HaploCatcher + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* SouthParkRshiny - checking whether package ‘SouthParkRshiny’ can be installed ... WARNING +* healthyR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* SqueakR - checking whether package ‘SqueakR’ can be installed ... WARNING +* healthyR.ts + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* survminer - checking whether package ‘survminer’ can be installed ... WARNING +* heatmaply + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* symptomcheckR - checking whether package ‘symptomcheckR’ can be installed ... WARNING +* hermiter + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* tcgaViz - checking whether package ‘tcgaViz’ can be installed ... WARNING +* hesim + checking tests ... ERROR -* TestGardener - checking whether package ‘TestGardener’ can be installed ... WARNING +* hidecan + checking tests ... ERROR + checking re-building of vignette outputs ... NOTE -* tis +* HVT checking examples ... ERROR -* UniprotR - checking whether package ‘UniprotR’ can be installed ... WARNING +* hypsoLoop + checking whether package ‘hypsoLoop’ can be installed ... WARNING -* VALERIE - checking whether package ‘VALERIE’ can be installed ... WARNING +* ICvectorfields + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* vannstats - checking whether package ‘vannstats’ can be installed ... WARNING +* idopNetwork + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* vici - checking whether package ‘vici’ can be installed ... WARNING +* inferCSN + checking examples ... ERROR -* Wats +* insurancerating checking examples ... ERROR + +* inTextSummaryTable + checking tests ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* xaringanthemer +* karel + checking examples ... ERROR + checking tests ... ERROR + +* kDGLM + checking examples ... ERROR + +* latentcor + checking examples ... ERROR + +* lcars + checking examples ... ERROR + checking running R code from vignettes ... ERROR + +* lemon + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* lfproQC + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* LMoFit + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* manydata + checking tests ... ERROR + +* MARVEL + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* MBNMAdose + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* MBNMAtime + checking re-building of vignette outputs ... NOTE + +* MetaNet + checking examples ... ERROR + +* metR + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* migraph + checking tests ... ERROR + +* MiMIR + checking examples ... ERROR + +* miRetrieve + checking tests ... ERROR + +* misspi + checking examples ... ERROR + +* mizer + checking tests ... ERROR + +* mlr3spatiotempcv + checking examples ... ERROR + +* mlr3viz + checking examples ... ERROR + +* modeltime.resample + checking tests ... ERROR + +* move + checking installed package size ... NOTE + +* mtb + checking tests ... ERROR + +* neatmaps + checking examples ... ERROR + +* NetFACS + checking examples ... ERROR + checking running R code from vignettes ... ERROR + +* NeuralSens + checking examples ... ERROR + +* NHSRplotthedots + checking tests ... ERROR + +* NIMAA + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* OBIC + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* OmicNavigator + checking tests ... ERROR + +* oncomsm + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* pafr + checking tests ... ERROR + +* patchwork + checking examples ... ERROR + +* pathviewr + checking tests ... ERROR + +* pcutils + checking examples ... ERROR + +* pdxTrees + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* personalized + checking tests ... ERROR + +* phylepic + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* Plasmidprofiler + checking examples ... ERROR + +* platetools + checking tests ... ERROR + +* plotDK + checking tests ... ERROR + +* plotly + checking examples ... ERROR + checking tests ... ERROR + +* pmartR + checking tests ... ERROR + +* pmxTools + checking tests ... ERROR + +* posterior + checking re-building of vignette outputs ... NOTE + +* PPQplan + checking re-building of vignette outputs ... NOTE + +* ppseq + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* precrec + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* priorsense + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* ProAE + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* probably + checking tests ... ERROR + +* processmapR + checking tests ... ERROR + +* psborrow + checking tests ... ERROR + +* r2dii.plot + checking tests ... ERROR + +* Radviz + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* rassta + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + +* REddyProc + checking installed package size ... NOTE + +* redist + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* reReg + checking examples ... ERROR + +* reservr + checking examples ... ERROR + checking re-building of vignette outputs ... NOTE + +* rKOMICS + checking examples ... ERROR + +* RKorAPClient + checking tests ... ERROR + +* RNAseqQC + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* roahd + checking examples ... ERROR + +* romic + checking tests ... ERROR + +* roptions + checking examples ... ERROR + +* santaR + checking tests ... ERROR + +* scdtb + checking tests ... ERROR + +* scoringutils + checking examples ... ERROR + checking re-building of vignette outputs ... NOTE + +* scUtils + checking tests ... ERROR + +* SCVA + checking examples ... ERROR + +* SDMtune + checking tests ... ERROR + +* SeaVal + checking examples ... ERROR + +* sglg + checking examples ... ERROR + +* sgsR + checking tests ... ERROR + +* SHAPforxgboost + checking examples ... ERROR + +* SHELF + checking re-building of vignette outputs ... NOTE + +* shinipsum + checking tests ... ERROR + +* SimNPH + checking tests ... ERROR + +* smallsets + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* spbal + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* spinifex + checking tests ... ERROR + +* sport + checking tests ... ERROR + +* SqueakR + checking re-building of vignette outputs ... NOTE + +* statgenGWAS + checking tests ... ERROR + +* surveyexplorer + checking examples ... ERROR + +* Sysrecon + checking examples ... ERROR + +* tabledown + checking examples ... ERROR + +* TCIU + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* tensorEVD + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* thematic + checking examples ... ERROR + checking tests ... ERROR + +* tidybayes + checking examples ... ERROR + +* tidycat + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* tidyCDISC + checking tests ... ERROR + +* tidysdm + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* tidytreatment + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* timetk + checking tests ... ERROR + +* tinyarray + checking examples ... ERROR + +* tornado + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* TOSTER + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* TreatmentPatterns + checking tests ... ERROR + +* trelliscopejs + checking tests ... ERROR + +* tricolore + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* triptych + checking examples ... ERROR + +* tsnet + checking tests ... ERROR + +* umiAnalyzer + checking examples ... ERROR + +* valr + checking tests ... ERROR + +* vivaldi + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* vivid + checking examples ... ERROR + +* vvshiny + checking tests ... ERROR + +* wilson + checking tests ... ERROR + +* xaringanthemer + checking tests ... ERROR + +* yamlet + checking examples ... ERROR checking tests ... ERROR ### Failed to check * abctools (NA) -* AnanseSeurat (NA) * animalEKF (NA) * ANOM (NA) -* APackOfTheClones (NA) * atRisk (NA) * AutoScore (NA) * bayesdfa (NA) * bayesDP (NA) * BayesianFactorZoo (NA) +* BayesSurvive (NA) * BCClong (NA) +* BGGM (NA) * binsreg (NA) * bmstdr (NA) * bspcov (NA) +* BuyseTest (NA) * CalibrationCurves (NA) -* Canek (NA) * CARBayesST (NA) * CaseBasedReasoning (NA) -* cellpypes (NA) * CGPfunctions (NA) -* CIARA (NA) -* ClustAssess (NA) -* clustree (NA) * cmprskcoxmsm (NA) -* combiroc (NA) -* conos (NA) * contrast (NA) -* countland (NA) * coxed (NA) * CRMetrics (NA) * csmpv (NA) * ctsem (NA) -* CytoSimplex (NA) * DepthProc (NA) -* DIscBIO (NA) * DR.SC (NA) -* dyngen (NA) -* EcoEnsemble (NA) +* DynNom (NA) +* easybgm (NA) * ecolottery (NA) * EpiEstim (NA) * evolqg (NA) * ForecastComb (NA) * gapfill (NA) * GeomComb (NA) -* geostan (NA) * ggrcs (NA) * ggrisk (NA) -* ggsector (NA) * gJLS2 (NA) -* grandR (NA) * Greg (NA) * greport (NA) -* harmony (NA) * hettx (NA) * hIRT (NA) * Hmsc (NA) +* inventorize (NA) * iNZightPlots (NA) * iNZightRegression (NA) * IRexamples (NA) +* jmBIG (NA) * joineRML (NA) * JWileymisc (NA) * kmc (NA) @@ -292,7 +946,6 @@ Issues with CRAN packages are summarised below. * MendelianRandomization (NA) * MetabolicSurv (NA) * miWQS (NA) -* mlmts (NA) * MRZero (NA) * Multiaovbay (NA) * multilevelTools (NA) @@ -310,10 +963,11 @@ Issues with CRAN packages are summarised below. * pould (NA) * powerly (NA) * pre (NA) -* PRECAST (NA) * ProFAST (NA) +* psbcSpeedUp (NA) * pscore (NA) * psfmi (NA) +* qPCRtools (NA) * qreport (NA) * qris (NA) * qte (NA) @@ -322,35 +976,33 @@ Issues with CRAN packages are summarised below. * RcmdrPlugin.RiskDemo (NA) * rddtools (NA) * riskRegression (NA) -* rliger (NA) * rms (NA) * rmsb (NA) * robmed (NA) * robmedExtra (NA) * RPPanalyzer (NA) -* rstanarm (NA) +* RQdeltaCT (NA) * scCustomize (NA) * SCdeconR (NA) -* scDiffCom (NA) * scGate (NA) +* SCIntRuler (NA) * scMappR (NA) -* SCORPIUS (NA) -* scpoisson (NA) -* SCpubr (NA) +* scpi (NA) * scRNAstat (NA) * sectorgap (NA) * SEERaBomb (NA) * semicmprskcoxmsm (NA) * SensMap (NA) +* Seurat (NA) +* shinyTempSignal (NA) +* sievePH (NA) * Signac (NA) * SimplyAgree (NA) * sMSROC (NA) * SNPassoc (NA) * snplinkage (NA) * SoupX (NA) -* SpaDES.core (NA) * sparsereg (NA) -* SPECK (NA) * spikeSlabGAM (NA) * statsr (NA) * streamDAG (NA) @@ -361,10 +1013,9 @@ Issues with CRAN packages are summarised below. * tidyEdSurvey (NA) * tidyseurat (NA) * tidyvpc (NA) -* treefit (NA) * TriDimRegression (NA) * TSrepr (NA) * twang (NA) -* valse (NA) * vdg (NA) +* visa (NA) * WRTDStidal (NA) diff --git a/revdep/failures.md b/revdep/failures.md index 5eb2ead6c6..84ae909aa5 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -69,82 +69,6 @@ ERROR: lazy loading failed for package ‘abctools’ * removing ‘/tmp/workdir/abctools/old/abctools.Rcheck/abctools’ -``` -# AnanseSeurat - -
- -* Version: 1.2.0 -* GitHub: https://github.com/JGASmits/AnanseSeurat -* Source code: https://github.com/cran/AnanseSeurat -* Date/Publication: 2023-11-11 21:43:17 UTC -* Number of recursive dependencies: 201 - -Run `revdepcheck::cloud_details(, "AnanseSeurat")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/AnanseSeurat/new/AnanseSeurat.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘AnanseSeurat/DESCRIPTION’ ... OK -... -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -Package suggested but not available for checking: ‘Signac’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/AnanseSeurat/old/AnanseSeurat.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘AnanseSeurat/DESCRIPTION’ ... OK -... -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -Package suggested but not available for checking: ‘Signac’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - ``` # animalEKF @@ -216,7 +140,7 @@ ERROR: lazy loading failed for package ‘animalEKF’ * GitHub: https://github.com/PhilipPallmann/ANOM * Source code: https://github.com/cran/ANOM * Date/Publication: 2017-04-12 13:32:33 UTC -* Number of recursive dependencies: 77 +* Number of recursive dependencies: 60 Run `revdepcheck::cloud_details(, "ANOM")` for more info @@ -271,82 +195,6 @@ ERROR: lazy loading failed for package ‘ANOM’ * removing ‘/tmp/workdir/ANOM/old/ANOM.Rcheck/ANOM’ -``` -# APackOfTheClones - -
- -* Version: 1.2.0 -* GitHub: https://github.com/Qile0317/APackOfTheClones -* Source code: https://github.com/cran/APackOfTheClones -* Date/Publication: 2024-04-16 09:50:02 UTC -* Number of recursive dependencies: 176 - -Run `revdepcheck::cloud_details(, "APackOfTheClones")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/APackOfTheClones/new/APackOfTheClones.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘APackOfTheClones/DESCRIPTION’ ... OK -... -* this is package ‘APackOfTheClones’ version ‘1.2.0’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'Seurat', 'SeuratObject' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/APackOfTheClones/old/APackOfTheClones.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘APackOfTheClones/DESCRIPTION’ ... OK -... -* this is package ‘APackOfTheClones’ version ‘1.2.0’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'Seurat', 'SeuratObject' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - ``` # atRisk @@ -418,7 +266,7 @@ ERROR: lazy loading failed for package ‘atRisk’ * GitHub: https://github.com/nliulab/AutoScore * Source code: https://github.com/cran/AutoScore * Date/Publication: 2022-10-15 22:15:26 UTC -* Number of recursive dependencies: 180 +* Number of recursive dependencies: 170 Run `revdepcheck::cloud_details(, "AutoScore")` for more info @@ -689,16 +537,94 @@ ERROR: lazy loading failed for package ‘BayesianFactorZoo’ * removing ‘/tmp/workdir/BayesianFactorZoo/old/BayesianFactorZoo.Rcheck/BayesianFactorZoo’ +``` +# BayesSurvive + +
+ +* Version: 0.0.2 +* GitHub: https://github.com/ocbe-uio/BayesSurvive +* Source code: https://github.com/cran/BayesSurvive +* Date/Publication: 2024-06-04 13:20:12 UTC +* Number of recursive dependencies: 128 + +Run `revdepcheck::cloud_details(, "BayesSurvive")` for more info + +
+ +## In both + +* checking whether package ‘BayesSurvive’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/BayesSurvive/new/BayesSurvive.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘BayesSurvive’ ... +** package ‘BayesSurvive’ successfully unpacked and MD5 sums checked +** using staged installation +checking whether the C++ compiler works... yes +checking for C++ compiler default output file name... a.out +checking for suffix of executables... +checking whether we are cross compiling... no +checking for suffix of object files... o +checking whether the compiler supports GNU C++... yes +checking whether g++ -std=gnu++17 accepts -g... yes +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘BayesSurvive’ +* removing ‘/tmp/workdir/BayesSurvive/new/BayesSurvive.Rcheck/BayesSurvive’ + + +``` +### CRAN + +``` +* installing *source* package ‘BayesSurvive’ ... +** package ‘BayesSurvive’ successfully unpacked and MD5 sums checked +** using staged installation +checking whether the C++ compiler works... yes +checking for C++ compiler default output file name... a.out +checking for suffix of executables... +checking whether we are cross compiling... no +checking for suffix of object files... o +checking whether the compiler supports GNU C++... yes +checking whether g++ -std=gnu++17 accepts -g... yes +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘BayesSurvive’ +* removing ‘/tmp/workdir/BayesSurvive/old/BayesSurvive.Rcheck/BayesSurvive’ + + ``` # BCClong
-* Version: 1.0.2 +* Version: 1.0.3 * GitHub: NA * Source code: https://github.com/cran/BCClong -* Date/Publication: 2024-02-05 11:50:06 UTC -* Number of recursive dependencies: 142 +* Date/Publication: 2024-06-24 00:00:02 UTC +* Number of recursive dependencies: 145 Run `revdepcheck::cloud_details(, "BCClong")` for more info @@ -712,11 +638,6 @@ Run `revdepcheck::cloud_details(, "BCClong")` for more info See ‘/tmp/workdir/BCClong/new/BCClong.Rcheck/00install.out’ for details. ``` -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘joineRML’ - ``` - ## Installation ### Devel @@ -733,8 +654,8 @@ g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/ g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c c_which.cpp -o c_which.o g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o BCClong.so BCC.o Likelihood.o RcppExports.o c_which.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR ... -installing to /tmp/workdir/BCClong/new/BCClong.Rcheck/00LOCK-BCClong/00new/BCClong/libs ** R +** data ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : @@ -760,8 +681,8 @@ g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/ g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c c_which.cpp -o c_which.o g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o BCClong.so BCC.o Likelihood.o RcppExports.o c_which.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR ... -installing to /tmp/workdir/BCClong/old/BCClong.Rcheck/00LOCK-BCClong/00new/BCClong/libs ** R +** data ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : @@ -772,6 +693,84 @@ ERROR: lazy loading failed for package ‘BCClong’ * removing ‘/tmp/workdir/BCClong/old/BCClong.Rcheck/BCClong’ +``` +# BGGM + +
+ +* Version: 2.1.3 +* GitHub: https://github.com/donaldRwilliams/BGGM +* Source code: https://github.com/cran/BGGM +* Date/Publication: 2024-07-05 20:30:02 UTC +* Number of recursive dependencies: 208 + +Run `revdepcheck::cloud_details(, "BGGM")` for more info + +
+ +## In both + +* checking whether package ‘BGGM’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/BGGM/new/BGGM.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘BGGM’ ... +** package ‘BGGM’ successfully unpacked and MD5 sums checked +** using staged installation +checking whether the C++ compiler works... yes +checking for C++ compiler default output file name... a.out +checking for suffix of executables... +checking whether we are cross compiling... no +checking for suffix of object files... o +checking whether we are using the GNU C++ compiler... yes +checking whether g++ -std=gnu++17 accepts -g... yes +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘BGGM’ +* removing ‘/tmp/workdir/BGGM/new/BGGM.Rcheck/BGGM’ + + +``` +### CRAN + +``` +* installing *source* package ‘BGGM’ ... +** package ‘BGGM’ successfully unpacked and MD5 sums checked +** using staged installation +checking whether the C++ compiler works... yes +checking for C++ compiler default output file name... a.out +checking for suffix of executables... +checking whether we are cross compiling... no +checking for suffix of object files... o +checking whether we are using the GNU C++ compiler... yes +checking whether g++ -std=gnu++17 accepts -g... yes +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘BGGM’ +* removing ‘/tmp/workdir/BGGM/old/BGGM.Rcheck/BGGM’ + + ``` # binsreg @@ -839,7 +838,7 @@ ERROR: lazy loading failed for package ‘binsreg’ * GitHub: https://github.com/sujit-sahu/bmstdr * Source code: https://github.com/cran/bmstdr * Date/Publication: 2023-12-18 15:00:02 UTC -* Number of recursive dependencies: 212 +* Number of recursive dependencies: 215 Run `revdepcheck::cloud_details(, "bmstdr")` for more info @@ -917,7 +916,7 @@ ERROR: lazy loading failed for package ‘bmstdr’ * GitHub: https://github.com/statjs/bspcov * Source code: https://github.com/cran/bspcov * Date/Publication: 2024-02-06 16:50:08 UTC -* Number of recursive dependencies: 122 +* Number of recursive dependencies: 121 Run `revdepcheck::cloud_details(, "bspcov")` for more info @@ -971,26 +970,26 @@ ERROR: lazy loading failed for package ‘bspcov’ ``` -# CalibrationCurves +# BuyseTest
-* Version: 2.0.1 -* GitHub: NA -* Source code: https://github.com/cran/CalibrationCurves -* Date/Publication: 2024-03-01 10:12:35 UTC -* Number of recursive dependencies: 78 +* Version: 3.0.4 +* GitHub: https://github.com/bozenne/BuyseTest +* Source code: https://github.com/cran/BuyseTest +* Date/Publication: 2024-07-01 09:20:02 UTC +* Number of recursive dependencies: 133 -Run `revdepcheck::cloud_details(, "CalibrationCurves")` for more info +Run `revdepcheck::cloud_details(, "BuyseTest")` for more info
## In both -* checking whether package ‘CalibrationCurves’ can be installed ... ERROR +* checking whether package ‘BuyseTest’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/CalibrationCurves/new/CalibrationCurves.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/BuyseTest/new/BuyseTest.Rcheck/00install.out’ for details. ``` ## Installation @@ -998,114 +997,116 @@ Run `revdepcheck::cloud_details(, "CalibrationCurves")` for more info ### Devel ``` -* installing *source* package ‘CalibrationCurves’ ... -** package ‘CalibrationCurves’ successfully unpacked and MD5 sums checked +* installing *source* package ‘BuyseTest’ ... +** package ‘BuyseTest’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c FCT_buyseTest.cpp -o FCT_buyseTest.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c FCT_precompute.cpp -o FCT_precompute.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c utils-from-riskRegression.cpp -o utils-from-riskRegression.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o BuyseTest.so FCT_buyseTest.o FCT_precompute.o RcppExports.o utils-from-riskRegression.o -L/opt/R/4.3.1/lib/R/lib -lR +... +installing to /tmp/workdir/BuyseTest/new/BuyseTest.Rcheck/00LOCK-BuyseTest/00new/BuyseTest/libs ** R -** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error: unable to load R code in package ‘BuyseTest’ Execution halted -ERROR: lazy loading failed for package ‘CalibrationCurves’ -* removing ‘/tmp/workdir/CalibrationCurves/new/CalibrationCurves.Rcheck/CalibrationCurves’ +ERROR: lazy loading failed for package ‘BuyseTest’ +* removing ‘/tmp/workdir/BuyseTest/new/BuyseTest.Rcheck/BuyseTest’ ``` ### CRAN ``` -* installing *source* package ‘CalibrationCurves’ ... -** package ‘CalibrationCurves’ successfully unpacked and MD5 sums checked +* installing *source* package ‘BuyseTest’ ... +** package ‘BuyseTest’ successfully unpacked and MD5 sums checked ** using staged installation -** R -** data -*** moving datasets to lazyload DB +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c FCT_buyseTest.cpp -o FCT_buyseTest.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c FCT_precompute.cpp -o FCT_precompute.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c utils-from-riskRegression.cpp -o utils-from-riskRegression.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o BuyseTest.so FCT_buyseTest.o FCT_precompute.o RcppExports.o utils-from-riskRegression.o -L/opt/R/4.3.1/lib/R/lib -lR +... +installing to /tmp/workdir/BuyseTest/old/BuyseTest.Rcheck/00LOCK-BuyseTest/00new/BuyseTest/libs +** R ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error: unable to load R code in package ‘BuyseTest’ Execution halted -ERROR: lazy loading failed for package ‘CalibrationCurves’ -* removing ‘/tmp/workdir/CalibrationCurves/old/CalibrationCurves.Rcheck/CalibrationCurves’ +ERROR: lazy loading failed for package ‘BuyseTest’ +* removing ‘/tmp/workdir/BuyseTest/old/BuyseTest.Rcheck/BuyseTest’ ``` -# Canek +# CalibrationCurves
-* Version: 0.2.5 -* GitHub: https://github.com/MartinLoza/Canek -* Source code: https://github.com/cran/Canek -* Date/Publication: 2023-12-08 05:30:02 UTC -* Number of recursive dependencies: 220 +* Version: 2.0.3 +* GitHub: NA +* Source code: https://github.com/cran/CalibrationCurves +* Date/Publication: 2024-07-02 08:50:02 UTC +* Number of recursive dependencies: 78 -Run `revdepcheck::cloud_details(, "Canek")` for more info +Run `revdepcheck::cloud_details(, "CalibrationCurves")` for more info
-## Error before installation - -### Devel +## In both -``` -* using log directory ‘/tmp/workdir/Canek/new/Canek.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘Canek/DESCRIPTION’ ... OK -... - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 74 ] - Error: Test failures - Execution halted -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘toy_example.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 ERROR, 1 NOTE +* checking whether package ‘CalibrationCurves’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/CalibrationCurves/new/CalibrationCurves.Rcheck/00install.out’ for details. + ``` +## Installation +### Devel +``` +* installing *source* package ‘CalibrationCurves’ ... +** package ‘CalibrationCurves’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘CalibrationCurves’ +* removing ‘/tmp/workdir/CalibrationCurves/new/CalibrationCurves.Rcheck/CalibrationCurves’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/Canek/old/Canek.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘Canek/DESCRIPTION’ ... OK -... - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 74 ] - Error: Test failures - Execution halted -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘toy_example.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 ERROR, 1 NOTE - - - +* installing *source* package ‘CalibrationCurves’ ... +** package ‘CalibrationCurves’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘CalibrationCurves’ +* removing ‘/tmp/workdir/CalibrationCurves/old/CalibrationCurves.Rcheck/CalibrationCurves’ ``` @@ -1117,7 +1118,7 @@ Status: 1 ERROR, 1 NOTE * GitHub: https://github.com/duncanplee/CARBayesST * Source code: https://github.com/cran/CARBayesST * Date/Publication: 2023-10-30 16:40:02 UTC -* Number of recursive dependencies: 118 +* Number of recursive dependencies: 117 Run `revdepcheck::cloud_details(, "CARBayesST")` for more info @@ -1258,82 +1259,6 @@ ERROR: lazy loading failed for package ‘CaseBasedReasoning’ * removing ‘/tmp/workdir/CaseBasedReasoning/old/CaseBasedReasoning.Rcheck/CaseBasedReasoning’ -``` -# cellpypes - -
- -* Version: 0.3.0 -* GitHub: https://github.com/FelixTheStudent/cellpypes -* Source code: https://github.com/cran/cellpypes -* Date/Publication: 2024-01-27 07:30:07 UTC -* Number of recursive dependencies: 183 - -Run `revdepcheck::cloud_details(, "cellpypes")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/cellpypes/new/cellpypes.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘cellpypes/DESCRIPTION’ ... OK -... -* checking contents of ‘data’ directory ... OK -* checking data for non-ASCII characters ... OK -* checking LazyData ... OK -* checking data for ASCII and uncompressed saves ... OK -* checking examples ... OK -* checking for unstated dependencies in ‘tests’ ... OK -* checking tests ... OK - Running ‘testthat.R’ -* DONE -Status: 1 NOTE - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/cellpypes/old/cellpypes.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘cellpypes/DESCRIPTION’ ... OK -... -* checking contents of ‘data’ directory ... OK -* checking data for non-ASCII characters ... OK -* checking LazyData ... OK -* checking data for ASCII and uncompressed saves ... OK -* checking examples ... OK -* checking for unstated dependencies in ‘tests’ ... OK -* checking tests ... OK - Running ‘testthat.R’ -* DONE -Status: 1 NOTE - - - - - ``` # CGPfunctions @@ -1399,254 +1324,214 @@ ERROR: lazy loading failed for package ‘CGPfunctions’ ``` -# CIARA +# cmprskcoxmsm
-* Version: 0.1.0 +* Version: 0.2.1 * GitHub: NA -* Source code: https://github.com/cran/CIARA -* Date/Publication: 2022-02-22 20:00:02 UTC -* Number of recursive dependencies: 181 +* Source code: https://github.com/cran/cmprskcoxmsm +* Date/Publication: 2021-09-04 05:50:02 UTC +* Number of recursive dependencies: 71 -Run `revdepcheck::cloud_details(, "CIARA")` for more info +Run `revdepcheck::cloud_details(, "cmprskcoxmsm")` for more info
-## Error before installation - -### Devel +## In both -``` -* using log directory ‘/tmp/workdir/CIARA/new/CIARA.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘CIARA/DESCRIPTION’ ... OK -... -* checking tests ... OK - Running ‘testthat.R’ -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘CIARA.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... NOTE -Note: skipping ‘CIARA.Rmd’ due to unavailable dependencies: 'Seurat' -* DONE -Status: 3 NOTEs +* checking whether package ‘cmprskcoxmsm’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/cmprskcoxmsm/new/cmprskcoxmsm.Rcheck/00install.out’ for details. + ``` +## Installation +### Devel +``` +* installing *source* package ‘cmprskcoxmsm’ ... +** package ‘cmprskcoxmsm’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘cmprskcoxmsm’ +* removing ‘/tmp/workdir/cmprskcoxmsm/new/cmprskcoxmsm.Rcheck/cmprskcoxmsm’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/CIARA/old/CIARA.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘CIARA/DESCRIPTION’ ... OK -... -* checking tests ... OK - Running ‘testthat.R’ -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘CIARA.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... NOTE -Note: skipping ‘CIARA.Rmd’ due to unavailable dependencies: 'Seurat' -* DONE -Status: 3 NOTEs - - - +* installing *source* package ‘cmprskcoxmsm’ ... +** package ‘cmprskcoxmsm’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘cmprskcoxmsm’ +* removing ‘/tmp/workdir/cmprskcoxmsm/old/cmprskcoxmsm.Rcheck/cmprskcoxmsm’ ``` -# ClustAssess +# contrast
-* Version: 0.3.0 -* GitHub: https://github.com/Core-Bioinformatics/ClustAssess -* Source code: https://github.com/cran/ClustAssess -* Date/Publication: 2022-01-26 16:52:46 UTC -* Number of recursive dependencies: 164 +* Version: 0.24.2 +* GitHub: https://github.com/Alanocallaghan/contrast +* Source code: https://github.com/cran/contrast +* Date/Publication: 2022-10-05 17:20:09 UTC +* Number of recursive dependencies: 111 -Run `revdepcheck::cloud_details(, "ClustAssess")` for more info +Run `revdepcheck::cloud_details(, "contrast")` for more info
-## Error before installation +## In both -### Devel +* checking whether package ‘contrast’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/contrast/new/contrast.Rcheck/00install.out’ for details. + ``` -``` -* using log directory ‘/tmp/workdir/ClustAssess/new/ClustAssess.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘ClustAssess/DESCRIPTION’ ... OK -... ---- finished re-building ‘comparing-soft-and-hierarchical.Rmd’ +## Installation -SUMMARY: processing the following file failed: - ‘ClustAssess.Rmd’ +### Devel -Error: Vignette re-building failed. +``` +* installing *source* package ‘contrast’ ... +** package ‘contrast’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted - -* DONE -Status: 1 ERROR, 1 WARNING, 2 NOTEs - - - +ERROR: lazy loading failed for package ‘contrast’ +* removing ‘/tmp/workdir/contrast/new/contrast.Rcheck/contrast’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/ClustAssess/old/ClustAssess.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘ClustAssess/DESCRIPTION’ ... OK -... ---- finished re-building ‘comparing-soft-and-hierarchical.Rmd’ - -SUMMARY: processing the following file failed: - ‘ClustAssess.Rmd’ - -Error: Vignette re-building failed. +* installing *source* package ‘contrast’ ... +** package ‘contrast’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted - -* DONE -Status: 1 ERROR, 1 WARNING, 2 NOTEs - - - +ERROR: lazy loading failed for package ‘contrast’ +* removing ‘/tmp/workdir/contrast/old/contrast.Rcheck/contrast’ ``` -# clustree +# coxed
-* Version: 0.5.1 -* GitHub: https://github.com/lazappi/clustree -* Source code: https://github.com/cran/clustree -* Date/Publication: 2023-11-05 19:10:02 UTC -* Number of recursive dependencies: 192 +* Version: 0.3.3 +* GitHub: https://github.com/jkropko/coxed +* Source code: https://github.com/cran/coxed +* Date/Publication: 2020-08-02 01:20:07 UTC +* Number of recursive dependencies: 95 -Run `revdepcheck::cloud_details(, "clustree")` for more info +Run `revdepcheck::cloud_details(, "coxed")` for more info
-## Error before installation - -### Devel +## In both -``` -* using log directory ‘/tmp/workdir/clustree/new/clustree.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘clustree/DESCRIPTION’ ... OK -... -* checking tests ... OK - Running ‘spelling.R’ - Running ‘testthat.R’ -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘clustree.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 NOTE +* checking whether package ‘coxed’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/coxed/new/coxed.Rcheck/00install.out’ for details. + ``` +## Installation +### Devel +``` +* installing *source* package ‘coxed’ ... +** package ‘coxed’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘coxed’ +* removing ‘/tmp/workdir/coxed/new/coxed.Rcheck/coxed’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/clustree/old/clustree.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘clustree/DESCRIPTION’ ... OK -... -* checking tests ... OK - Running ‘spelling.R’ - Running ‘testthat.R’ -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘clustree.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 NOTE - - - +* installing *source* package ‘coxed’ ... +** package ‘coxed’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘coxed’ +* removing ‘/tmp/workdir/coxed/old/coxed.Rcheck/coxed’ ``` -# cmprskcoxmsm +# CRMetrics
-* Version: 0.2.1 -* GitHub: NA -* Source code: https://github.com/cran/cmprskcoxmsm -* Date/Publication: 2021-09-04 05:50:02 UTC -* Number of recursive dependencies: 71 +* Version: 0.3.0 +* GitHub: https://github.com/khodosevichlab/CRMetrics +* Source code: https://github.com/cran/CRMetrics +* Date/Publication: 2023-09-01 09:00:06 UTC +* Number of recursive dependencies: 239 -Run `revdepcheck::cloud_details(, "cmprskcoxmsm")` for more info +Run `revdepcheck::cloud_details(, "CRMetrics")` for more info
## In both -* checking whether package ‘cmprskcoxmsm’ can be installed ... ERROR +* checking whether package ‘CRMetrics’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/cmprskcoxmsm/new/cmprskcoxmsm.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/CRMetrics/new/CRMetrics.Rcheck/00install.out’ for details. ``` ## Installation @@ -1654,213 +1539,59 @@ Run `revdepcheck::cloud_details(, "cmprskcoxmsm")` for more info ### Devel ``` -* installing *source* package ‘cmprskcoxmsm’ ... -** package ‘cmprskcoxmsm’ successfully unpacked and MD5 sums checked +* installing *source* package ‘CRMetrics’ ... +** package ‘CRMetrics’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘cmprskcoxmsm’ -* removing ‘/tmp/workdir/cmprskcoxmsm/new/cmprskcoxmsm.Rcheck/cmprskcoxmsm’ +ERROR: lazy loading failed for package ‘CRMetrics’ +* removing ‘/tmp/workdir/CRMetrics/new/CRMetrics.Rcheck/CRMetrics’ ``` ### CRAN ``` -* installing *source* package ‘cmprskcoxmsm’ ... -** package ‘cmprskcoxmsm’ successfully unpacked and MD5 sums checked +* installing *source* package ‘CRMetrics’ ... +** package ‘CRMetrics’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘cmprskcoxmsm’ -* removing ‘/tmp/workdir/cmprskcoxmsm/old/cmprskcoxmsm.Rcheck/cmprskcoxmsm’ - - -``` -# combiroc - -
- -* Version: 0.3.4 -* GitHub: https://github.com/ingmbioinfo/combiroc -* Source code: https://github.com/cran/combiroc -* Date/Publication: 2023-07-06 12:53:12 UTC -* Number of recursive dependencies: 160 - -Run `revdepcheck::cloud_details(, "combiroc")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/combiroc/new/combiroc.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘combiroc/DESCRIPTION’ ... OK -... - - When sourcing ‘combiroc_vignette_2.R’: -Error: Cannot find the file(s): "/tmp/RtmpA38BUi/file1c6675fecb04/vignettes/vignettes/atlas_dimplot.png" -Execution halted - - ‘combiroc_vignette_1.Rmd’ using ‘UTF-8’... OK - ‘combiroc_vignette_2.Rmd’ using ‘UTF-8’... failed -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 ERROR, 1 NOTE - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/combiroc/old/combiroc.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘combiroc/DESCRIPTION’ ... OK -... - - When sourcing ‘combiroc_vignette_2.R’: -Error: Cannot find the file(s): "/tmp/RtmpD5SHHa/file14446c22f1bc/vignettes/vignettes/atlas_dimplot.png" -Execution halted - - ‘combiroc_vignette_1.Rmd’ using ‘UTF-8’... OK - ‘combiroc_vignette_2.Rmd’ using ‘UTF-8’... failed -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 ERROR, 1 NOTE - - - - - -``` -# conos - -
- -* Version: 1.5.2 -* GitHub: https://github.com/kharchenkolab/conos -* Source code: https://github.com/cran/conos -* Date/Publication: 2024-02-26 19:30:05 UTC -* Number of recursive dependencies: 239 - -Run `revdepcheck::cloud_details(, "conos")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/conos/new/conos.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘conos/DESCRIPTION’ ... OK -... -* checking for GNU extensions in Makefiles ... OK -* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK -* checking use of PKG_*FLAGS in Makefiles ... OK -* checking compiled code ... OK -* checking examples ... OK -* checking for unstated dependencies in ‘tests’ ... OK -* checking tests ... OK - Running ‘testthat.R’ -* DONE -Status: 2 NOTEs - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/conos/old/conos.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘conos/DESCRIPTION’ ... OK -... -* checking for GNU extensions in Makefiles ... OK -* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK -* checking use of PKG_*FLAGS in Makefiles ... OK -* checking compiled code ... OK -* checking examples ... OK -* checking for unstated dependencies in ‘tests’ ... OK -* checking tests ... OK - Running ‘testthat.R’ -* DONE -Status: 2 NOTEs - - - +ERROR: lazy loading failed for package ‘CRMetrics’ +* removing ‘/tmp/workdir/CRMetrics/old/CRMetrics.Rcheck/CRMetrics’ ``` -# contrast +# csmpv
-* Version: 0.24.2 -* GitHub: https://github.com/Alanocallaghan/contrast -* Source code: https://github.com/cran/contrast -* Date/Publication: 2022-10-05 17:20:09 UTC -* Number of recursive dependencies: 112 +* Version: 1.0.3 +* GitHub: NA +* Source code: https://github.com/cran/csmpv +* Date/Publication: 2024-03-01 18:12:44 UTC +* Number of recursive dependencies: 178 -Run `revdepcheck::cloud_details(, "contrast")` for more info +Run `revdepcheck::cloud_details(, "csmpv")` for more info
## In both -* checking whether package ‘contrast’ can be installed ... ERROR +* checking whether package ‘csmpv’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/contrast/new/contrast.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/csmpv/new/csmpv.Rcheck/00install.out’ for details. ``` ## Installation @@ -1868,8 +1599,8 @@ Run `revdepcheck::cloud_details(, "contrast")` for more info ### Devel ``` -* installing *source* package ‘contrast’ ... -** package ‘contrast’ successfully unpacked and MD5 sums checked +* installing *source* package ‘csmpv’ ... +** package ‘csmpv’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data @@ -1880,16 +1611,16 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘contrast’ -* removing ‘/tmp/workdir/contrast/new/contrast.Rcheck/contrast’ +ERROR: lazy loading failed for package ‘csmpv’ +* removing ‘/tmp/workdir/csmpv/new/csmpv.Rcheck/csmpv’ ``` ### CRAN ``` -* installing *source* package ‘contrast’ ... -** package ‘contrast’ successfully unpacked and MD5 sums checked +* installing *source* package ‘csmpv’ ... +** package ‘csmpv’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data @@ -1900,107 +1631,109 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘contrast’ -* removing ‘/tmp/workdir/contrast/old/contrast.Rcheck/contrast’ +ERROR: lazy loading failed for package ‘csmpv’ +* removing ‘/tmp/workdir/csmpv/old/csmpv.Rcheck/csmpv’ ``` -# countland +# ctsem
-* Version: 0.1.2 -* GitHub: https://github.com/shchurch/countland -* Source code: https://github.com/cran/countland -* Date/Publication: 2024-02-01 18:00:02 UTC -* Number of recursive dependencies: 199 +* Version: 3.10.0 +* GitHub: https://github.com/cdriveraus/ctsem +* Source code: https://github.com/cran/ctsem +* Date/Publication: 2024-05-09 14:40:03 UTC +* Number of recursive dependencies: 158 -Run `revdepcheck::cloud_details(, "countland")` for more info +Run `revdepcheck::cloud_details(, "ctsem")` for more info
-## Error before installation +## In both + +* checking whether package ‘ctsem’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/ctsem/new/ctsem.Rcheck/00install.out’ for details. + ``` + +## Installation ### Devel ``` -* using log directory ‘/tmp/workdir/countland/new/countland.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘countland/DESCRIPTION’ ... OK -... - 1. └─base::loadNamespace(x) at test-countland_subset.R:2:1 - 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) - 3. └─base (local) withOneRestart(expr, restarts[[1L]]) - 4. └─base (local) doWithOneRestart(return(expr), restart) - - [ FAIL 7 | WARN 0 | SKIP 0 | PASS 13 ] - Error: Test failures - Execution halted -* DONE -Status: 2 ERRORs, 1 NOTE - +* installing *source* package ‘ctsem’ ... +** package ‘ctsem’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ctsm_namespace::model_ctsm; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ctsm.o] Error 1 +ERROR: compilation failed for package ‘ctsem’ +* removing ‘/tmp/workdir/ctsem/new/ctsem.Rcheck/ctsem’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/countland/old/countland.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘countland/DESCRIPTION’ ... OK -... - 1. └─base::loadNamespace(x) at test-countland_subset.R:2:1 - 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) - 3. └─base (local) withOneRestart(expr, restarts[[1L]]) - 4. └─base (local) doWithOneRestart(return(expr), restart) - - [ FAIL 7 | WARN 0 | SKIP 0 | PASS 13 ] - Error: Test failures - Execution halted -* DONE -Status: 2 ERRORs, 1 NOTE - +* installing *source* package ‘ctsem’ ... +** package ‘ctsem’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ctsm_namespace::model_ctsm; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ctsm.o] Error 1 +ERROR: compilation failed for package ‘ctsem’ +* removing ‘/tmp/workdir/ctsem/old/ctsem.Rcheck/ctsem’ ``` -# coxed +# DepthProc
-* Version: 0.3.3 -* GitHub: https://github.com/jkropko/coxed -* Source code: https://github.com/cran/coxed -* Date/Publication: 2020-08-02 01:20:07 UTC -* Number of recursive dependencies: 109 +* Version: 2.1.5 +* GitHub: https://github.com/zzawadz/DepthProc +* Source code: https://github.com/cran/DepthProc +* Date/Publication: 2022-02-03 20:30:02 UTC +* Number of recursive dependencies: 134 -Run `revdepcheck::cloud_details(, "coxed")` for more info +Run `revdepcheck::cloud_details(, "DepthProc")` for more info
## In both -* checking whether package ‘coxed’ can be installed ... ERROR +* checking whether package ‘DepthProc’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/coxed/new/coxed.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/DepthProc/new/DepthProc.Rcheck/00install.out’ for details. ``` ## Installation @@ -2008,137 +1741,155 @@ Run `revdepcheck::cloud_details(, "coxed")` for more info ### Devel ``` -* installing *source* package ‘coxed’ ... -** package ‘coxed’ successfully unpacked and MD5 sums checked +* installing *source* package ‘DepthProc’ ... +** package ‘DepthProc’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Depth.cpp -o Depth.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationEstimators.cpp -o LocationEstimators.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepth.cpp -o LocationScaleDepth.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepthCPP.cpp -o LocationScaleDepthCPP.o +... +installing to /tmp/workdir/DepthProc/new/DepthProc.Rcheck/00LOCK-DepthProc/00new/DepthProc/libs ** R ** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): +Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘coxed’ -* removing ‘/tmp/workdir/coxed/new/coxed.Rcheck/coxed’ +ERROR: lazy loading failed for package ‘DepthProc’ +* removing ‘/tmp/workdir/DepthProc/new/DepthProc.Rcheck/DepthProc’ ``` ### CRAN ``` -* installing *source* package ‘coxed’ ... -** package ‘coxed’ successfully unpacked and MD5 sums checked +* installing *source* package ‘DepthProc’ ... +** package ‘DepthProc’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Depth.cpp -o Depth.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationEstimators.cpp -o LocationEstimators.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepth.cpp -o LocationScaleDepth.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepthCPP.cpp -o LocationScaleDepthCPP.o +... +installing to /tmp/workdir/DepthProc/old/DepthProc.Rcheck/00LOCK-DepthProc/00new/DepthProc/libs ** R ** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): +Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘coxed’ -* removing ‘/tmp/workdir/coxed/old/coxed.Rcheck/coxed’ +ERROR: lazy loading failed for package ‘DepthProc’ +* removing ‘/tmp/workdir/DepthProc/old/DepthProc.Rcheck/DepthProc’ ``` -# CRMetrics +# DR.SC
-* Version: 0.3.0 -* GitHub: https://github.com/khodosevichlab/CRMetrics -* Source code: https://github.com/cran/CRMetrics -* Date/Publication: 2023-09-01 09:00:06 UTC -* Number of recursive dependencies: 235 +* Version: 3.4 +* GitHub: https://github.com/feiyoung/DR.SC +* Source code: https://github.com/cran/DR.SC +* Date/Publication: 2024-03-19 08:40:02 UTC +* Number of recursive dependencies: 151 -Run `revdepcheck::cloud_details(, "CRMetrics")` for more info +Run `revdepcheck::cloud_details(, "DR.SC")` for more info
-## Error before installation +## In both + +* checking whether package ‘DR.SC’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/DR.SC/new/DR.SC.Rcheck/00install.out’ for details. + ``` + +## Installation ### Devel ``` -* using log directory ‘/tmp/workdir/CRMetrics/new/CRMetrics.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘CRMetrics/DESCRIPTION’ ... OK +* installing *source* package ‘DR.SC’ ... +** package ‘DR.SC’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c getNB_fast.cpp -o getNB_fast.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c mt_paral_job.cpp -o mt_paral_job.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c mt_paral_job2.cpp -o mt_paral_job2.o ... -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘ggpmisc’ - -Package suggested but not available for checking: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘DR.SC’ +* removing ‘/tmp/workdir/DR.SC/new/DR.SC.Rcheck/DR.SC’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/CRMetrics/old/CRMetrics.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘CRMetrics/DESCRIPTION’ ... OK +* installing *source* package ‘DR.SC’ ... +** package ‘DR.SC’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c getNB_fast.cpp -o getNB_fast.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c mt_paral_job.cpp -o mt_paral_job.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c mt_paral_job2.cpp -o mt_paral_job2.o ... -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘ggpmisc’ - -Package suggested but not available for checking: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘DR.SC’ +* removing ‘/tmp/workdir/DR.SC/old/DR.SC.Rcheck/DR.SC’ ``` -# csmpv +# DynNom
-* Version: 1.0.3 +* Version: 5.1 * GitHub: NA -* Source code: https://github.com/cran/csmpv -* Date/Publication: 2024-03-01 18:12:44 UTC -* Number of recursive dependencies: 175 +* Source code: https://github.com/cran/DynNom +* Date/Publication: 2024-06-07 12:20:21 UTC +* Number of recursive dependencies: 104 -Run `revdepcheck::cloud_details(, "csmpv")` for more info +Run `revdepcheck::cloud_details(, "DynNom")` for more info
## In both -* checking whether package ‘csmpv’ can be installed ... ERROR +* checking whether package ‘DynNom’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/csmpv/new/csmpv.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/DynNom/new/DynNom.Rcheck/00install.out’ for details. ``` ## Installation @@ -2146,64 +1897,57 @@ Run `revdepcheck::cloud_details(, "csmpv")` for more info ### Devel ``` -* installing *source* package ‘csmpv’ ... -** package ‘csmpv’ successfully unpacked and MD5 sums checked +* installing *source* package ‘DynNom’ ... +** package ‘DynNom’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data -*** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading -Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘csmpv’ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘csmpv’ -* removing ‘/tmp/workdir/csmpv/new/csmpv.Rcheck/csmpv’ +ERROR: lazy loading failed for package ‘DynNom’ +* removing ‘/tmp/workdir/DynNom/new/DynNom.Rcheck/DynNom’ ``` ### CRAN ``` -* installing *source* package ‘csmpv’ ... -** package ‘csmpv’ successfully unpacked and MD5 sums checked +* installing *source* package ‘DynNom’ ... +** package ‘DynNom’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data -*** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘csmpv’ -* removing ‘/tmp/workdir/csmpv/old/csmpv.Rcheck/csmpv’ +ERROR: lazy loading failed for package ‘DynNom’ +* removing ‘/tmp/workdir/DynNom/old/DynNom.Rcheck/DynNom’ ``` -# ctsem +# easybgm
-* Version: 3.10.0 -* GitHub: https://github.com/cdriveraus/ctsem -* Source code: https://github.com/cran/ctsem -* Date/Publication: 2024-05-09 14:40:03 UTC -* Number of recursive dependencies: 159 +* Version: 0.1.2 +* GitHub: https://github.com/KarolineHuth/easybgm +* Source code: https://github.com/cran/easybgm +* Date/Publication: 2024-03-13 13:40:02 UTC +* Number of recursive dependencies: 174 -Run `revdepcheck::cloud_details(, "ctsem")` for more info +Run `revdepcheck::cloud_details(, "easybgm")` for more info
## In both -* checking whether package ‘ctsem’ can be installed ... ERROR +* checking whether package ‘easybgm’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/ctsem/new/ctsem.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/easybgm/new/easybgm.Rcheck/00install.out’ for details. ``` ## Installation @@ -2211,153 +1955,117 @@ Run `revdepcheck::cloud_details(, "ctsem")` for more info ### Devel ``` -* installing *source* package ‘ctsem’ ... -** package ‘ctsem’ successfully unpacked and MD5 sums checked +* installing *source* package ‘easybgm’ ... +** package ‘easybgm’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ctsm_namespace::model_ctsm; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ctsm.o] Error 1 -ERROR: compilation failed for package ‘ctsem’ -* removing ‘/tmp/workdir/ctsem/new/ctsem.Rcheck/ctsem’ +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘easybgm’ +* removing ‘/tmp/workdir/easybgm/new/easybgm.Rcheck/easybgm’ ``` ### CRAN ``` -* installing *source* package ‘ctsem’ ... -** package ‘ctsem’ successfully unpacked and MD5 sums checked +* installing *source* package ‘easybgm’ ... +** package ‘easybgm’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ctsm_namespace::model_ctsm; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ctsm.o] Error 1 -ERROR: compilation failed for package ‘ctsem’ -* removing ‘/tmp/workdir/ctsem/old/ctsem.Rcheck/ctsem’ +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘easybgm’ +* removing ‘/tmp/workdir/easybgm/old/easybgm.Rcheck/easybgm’ ``` -# CytoSimplex +# ecolottery
-* Version: 0.1.1 -* GitHub: https://github.com/welch-lab/CytoSimplex -* Source code: https://github.com/cran/CytoSimplex -* Date/Publication: 2023-12-15 09:30:06 UTC -* Number of recursive dependencies: 177 +* Version: 1.0.0 +* GitHub: https://github.com/frmunoz/ecolottery +* Source code: https://github.com/cran/ecolottery +* Date/Publication: 2017-07-03 11:01:29 UTC +* Number of recursive dependencies: 88 -Run `revdepcheck::cloud_details(, "CytoSimplex")` for more info +Run `revdepcheck::cloud_details(, "ecolottery")` for more info
-## Error before installation - -### Devel +## In both -``` -* using log directory ‘/tmp/workdir/CytoSimplex/new/CytoSimplex.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘CytoSimplex/DESCRIPTION’ ... OK -... -* checking for unstated dependencies in ‘tests’ ... OK -* checking tests ... OK - Running ‘testthat.R’ -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘CytoSimplex.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 2 NOTEs +* checking whether package ‘ecolottery’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/ecolottery/new/ecolottery.Rcheck/00install.out’ for details. + ``` +## Installation +### Devel +``` +* installing *source* package ‘ecolottery’ ... +** package ‘ecolottery’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘ecolottery’ +* removing ‘/tmp/workdir/ecolottery/new/ecolottery.Rcheck/ecolottery’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/CytoSimplex/old/CytoSimplex.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘CytoSimplex/DESCRIPTION’ ... OK -... -* checking for unstated dependencies in ‘tests’ ... OK -* checking tests ... OK - Running ‘testthat.R’ -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘CytoSimplex.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 2 NOTEs - - - +* installing *source* package ‘ecolottery’ ... +** package ‘ecolottery’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘ecolottery’ +* removing ‘/tmp/workdir/ecolottery/old/ecolottery.Rcheck/ecolottery’ ``` -# DepthProc +# EpiEstim
-* Version: 2.1.5 -* GitHub: https://github.com/zzawadz/DepthProc -* Source code: https://github.com/cran/DepthProc -* Date/Publication: 2022-02-03 20:30:02 UTC -* Number of recursive dependencies: 134 +* Version: 2.2-4 +* GitHub: https://github.com/mrc-ide/EpiEstim +* Source code: https://github.com/cran/EpiEstim +* Date/Publication: 2021-01-07 16:20:10 UTC +* Number of recursive dependencies: 91 -Run `revdepcheck::cloud_details(, "DepthProc")` for more info +Run `revdepcheck::cloud_details(, "EpiEstim")` for more info
## In both -* checking whether package ‘DepthProc’ can be installed ... ERROR +* checking whether package ‘EpiEstim’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/DepthProc/new/DepthProc.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/EpiEstim/new/EpiEstim.Rcheck/00install.out’ for details. ``` ## Installation @@ -2365,305 +2073,203 @@ Run `revdepcheck::cloud_details(, "DepthProc")` for more info ### Devel ``` -* installing *source* package ‘DepthProc’ ... -** package ‘DepthProc’ successfully unpacked and MD5 sums checked +* installing *source* package ‘EpiEstim’ ... +** package ‘EpiEstim’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Depth.cpp -o Depth.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationEstimators.cpp -o LocationEstimators.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepth.cpp -o LocationScaleDepth.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepthCPP.cpp -o LocationScaleDepthCPP.o -... -installing to /tmp/workdir/DepthProc/new/DepthProc.Rcheck/00LOCK-DepthProc/00new/DepthProc/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘DepthProc’ -* removing ‘/tmp/workdir/DepthProc/new/DepthProc.Rcheck/DepthProc’ +ERROR: lazy loading failed for package ‘EpiEstim’ +* removing ‘/tmp/workdir/EpiEstim/new/EpiEstim.Rcheck/EpiEstim’ ``` ### CRAN ``` -* installing *source* package ‘DepthProc’ ... -** package ‘DepthProc’ successfully unpacked and MD5 sums checked +* installing *source* package ‘EpiEstim’ ... +** package ‘EpiEstim’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Depth.cpp -o Depth.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationEstimators.cpp -o LocationEstimators.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepth.cpp -o LocationScaleDepth.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepthCPP.cpp -o LocationScaleDepthCPP.o -... -installing to /tmp/workdir/DepthProc/old/DepthProc.Rcheck/00LOCK-DepthProc/00new/DepthProc/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘DepthProc’ -* removing ‘/tmp/workdir/DepthProc/old/DepthProc.Rcheck/DepthProc’ +ERROR: lazy loading failed for package ‘EpiEstim’ +* removing ‘/tmp/workdir/EpiEstim/old/EpiEstim.Rcheck/EpiEstim’ ``` -# DIscBIO +# evolqg
-* Version: 1.2.2 -* GitHub: https://github.com/ocbe-uio/DIscBIO -* Source code: https://github.com/cran/DIscBIO -* Date/Publication: 2023-11-06 10:50:02 UTC -* Number of recursive dependencies: 209 +* Version: 0.3-4 +* GitHub: https://github.com/lem-usp/evolqg +* Source code: https://github.com/cran/evolqg +* Date/Publication: 2023-12-05 15:20:12 UTC +* Number of recursive dependencies: 111 -Run `revdepcheck::cloud_details(, "DIscBIO")` for more info +Run `revdepcheck::cloud_details(, "evolqg")` for more info
-## Error before installation - -### Devel +## In both -``` -* using log directory ‘/tmp/workdir/DIscBIO/new/DIscBIO.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘DIscBIO/DESCRIPTION’ ... OK -... -* checking Rd \usage sections ... OK -* checking Rd contents ... OK -* checking for unstated dependencies in examples ... OK -* checking contents of ‘data’ directory ... OK -* checking data for non-ASCII characters ... OK -* checking LazyData ... OK -* checking data for ASCII and uncompressed saves ... OK -* checking examples ... OK -* DONE -Status: 1 NOTE +* checking whether package ‘evolqg’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/evolqg/new/evolqg.Rcheck/00install.out’ for details. + ``` +## Installation +### Devel +``` +* installing *source* package ‘evolqg’ ... +** package ‘evolqg’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c fast_RS.cpp -o fast_RS.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o evolqg.so RcppExports.o fast_RS.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/evolqg/new/evolqg.Rcheck/00LOCK-evolqg/00new/evolqg/libs +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘evolqg’ +* removing ‘/tmp/workdir/evolqg/new/evolqg.Rcheck/evolqg’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/DIscBIO/old/DIscBIO.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘DIscBIO/DESCRIPTION’ ... OK -... -* checking Rd \usage sections ... OK -* checking Rd contents ... OK -* checking for unstated dependencies in examples ... OK -* checking contents of ‘data’ directory ... OK -* checking data for non-ASCII characters ... OK -* checking LazyData ... OK -* checking data for ASCII and uncompressed saves ... OK -* checking examples ... OK -* DONE -Status: 1 NOTE - - - +* installing *source* package ‘evolqg’ ... +** package ‘evolqg’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c fast_RS.cpp -o fast_RS.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o evolqg.so RcppExports.o fast_RS.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/evolqg/old/evolqg.Rcheck/00LOCK-evolqg/00new/evolqg/libs +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘evolqg’ +* removing ‘/tmp/workdir/evolqg/old/evolqg.Rcheck/evolqg’ ``` -# DR.SC +# ForecastComb
-* Version: 3.4 -* GitHub: https://github.com/feiyoung/DR.SC -* Source code: https://github.com/cran/DR.SC -* Date/Publication: 2024-03-19 08:40:02 UTC -* Number of recursive dependencies: 150 - -Run `revdepcheck::cloud_details(, "DR.SC")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/DR.SC/new/DR.SC.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘DR.SC/DESCRIPTION’ ... OK -... -* this is package ‘DR.SC’ version ‘3.4’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/DR.SC/old/DR.SC.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘DR.SC/DESCRIPTION’ ... OK -... -* this is package ‘DR.SC’ version ‘3.4’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -# dyngen +* Version: 1.3.1 +* GitHub: https://github.com/ceweiss/ForecastComb +* Source code: https://github.com/cran/ForecastComb +* Date/Publication: 2018-08-07 13:50:08 UTC +* Number of recursive dependencies: 74 -
+Run `revdepcheck::cloud_details(, "ForecastComb")` for more info -* Version: 1.0.5 -* GitHub: https://github.com/dynverse/dyngen -* Source code: https://github.com/cran/dyngen -* Date/Publication: 2022-10-12 15:22:39 UTC -* Number of recursive dependencies: 209 +
-Run `revdepcheck::cloud_details(, "dyngen")` for more info +## In both -
+* checking whether package ‘ForecastComb’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/ForecastComb/new/ForecastComb.Rcheck/00install.out’ for details. + ``` -## Error before installation +## Installation ### Devel ``` -* using log directory ‘/tmp/workdir/dyngen/new/dyngen.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘dyngen/DESCRIPTION’ ... OK -... -* checking tests ... OK - Running ‘testthat.R’ -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... NONE - ‘getting_started.html.asis’ using ‘UTF-8’... OK - ‘installation.html.asis’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 NOTE - - - +* installing *source* package ‘ForecastComb’ ... +** package ‘ForecastComb’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘ForecastComb’ +* removing ‘/tmp/workdir/ForecastComb/new/ForecastComb.Rcheck/ForecastComb’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/dyngen/old/dyngen.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘dyngen/DESCRIPTION’ ... OK -... -* checking tests ... OK - Running ‘testthat.R’ -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... NONE - ‘getting_started.html.asis’ using ‘UTF-8’... OK - ‘installation.html.asis’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 NOTE - - - +* installing *source* package ‘ForecastComb’ ... +** package ‘ForecastComb’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘ForecastComb’ +* removing ‘/tmp/workdir/ForecastComb/old/ForecastComb.Rcheck/ForecastComb’ ``` -# EcoEnsemble +# gapfill
-* Version: 1.0.5 -* GitHub: NA -* Source code: https://github.com/cran/EcoEnsemble -* Date/Publication: 2023-09-18 11:50:02 UTC -* Number of recursive dependencies: 91 +* Version: 0.9.6-1 +* GitHub: https://github.com/florafauna/gapfill +* Source code: https://github.com/cran/gapfill +* Date/Publication: 2021-02-12 10:10:05 UTC +* Number of recursive dependencies: 71 -Run `revdepcheck::cloud_details(, "EcoEnsemble")` for more info +Run `revdepcheck::cloud_details(, "gapfill")` for more info
## In both -* checking whether package ‘EcoEnsemble’ can be installed ... ERROR +* checking whether package ‘gapfill’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/EcoEnsemble/new/EcoEnsemble.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/gapfill/new/gapfill.Rcheck/00install.out’ for details. + ``` + +* checking package dependencies ... NOTE + ``` + Packages which this enhances but not available for checking: + 'raster', 'doParallel', 'doMPI' ``` ## Installation @@ -2671,77 +2277,77 @@ Run `revdepcheck::cloud_details(, "EcoEnsemble")` for more info ### Devel ``` -* installing *source* package ‘EcoEnsemble’ ... -** package ‘EcoEnsemble’ successfully unpacked and MD5 sums checked +* installing *source* package ‘gapfill’ ... +** package ‘gapfill’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c KF_back.cpp -o KF_back.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c gapfill.cpp -o gapfill.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o gapfill.so RcppExports.o gapfill.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/gapfill/new/gapfill.Rcheck/00LOCK-gapfill/00new/gapfill/libs +** R ... -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -stanExports_ensemble_model_hierarchical.cc:32:1: fatal error: error writing to /tmp/ccqp74mc.s: Cannot allocate memory - 32 | } - | ^ -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ensemble_model_hierarchical.o] Error 1 -ERROR: compilation failed for package ‘EcoEnsemble’ -* removing ‘/tmp/workdir/EcoEnsemble/new/EcoEnsemble.Rcheck/EcoEnsemble’ +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘gapfill’ +* removing ‘/tmp/workdir/gapfill/new/gapfill.Rcheck/gapfill’ ``` ### CRAN ``` -* installing *source* package ‘EcoEnsemble’ ... -** package ‘EcoEnsemble’ successfully unpacked and MD5 sums checked +* installing *source* package ‘gapfill’ ... +** package ‘gapfill’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c KF_back.cpp -o KF_back.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c gapfill.cpp -o gapfill.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o gapfill.so RcppExports.o gapfill.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/gapfill/old/gapfill.Rcheck/00LOCK-gapfill/00new/gapfill/libs +** R ... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ensemble_model_hierarchical_namespace::model_ensemble_model_hierarchical; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ensemble_model_hierarchical.o] Error 1 -ERROR: compilation failed for package ‘EcoEnsemble’ -* removing ‘/tmp/workdir/EcoEnsemble/old/EcoEnsemble.Rcheck/EcoEnsemble’ +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘gapfill’ +* removing ‘/tmp/workdir/gapfill/old/gapfill.Rcheck/gapfill’ ``` -# ecolottery +# GeomComb
-* Version: 1.0.0 -* GitHub: https://github.com/frmunoz/ecolottery -* Source code: https://github.com/cran/ecolottery -* Date/Publication: 2017-07-03 11:01:29 UTC -* Number of recursive dependencies: 88 +* Version: 1.0 +* GitHub: https://github.com/ceweiss/GeomComb +* Source code: https://github.com/cran/GeomComb +* Date/Publication: 2016-11-27 16:02:26 +* Number of recursive dependencies: 75 -Run `revdepcheck::cloud_details(, "ecolottery")` for more info +Run `revdepcheck::cloud_details(, "GeomComb")` for more info
## In both -* checking whether package ‘ecolottery’ can be installed ... ERROR +* checking whether package ‘GeomComb’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/ecolottery/new/ecolottery.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/GeomComb/new/GeomComb.Rcheck/00install.out’ for details. ``` ## Installation @@ -2749,59 +2355,57 @@ Run `revdepcheck::cloud_details(, "ecolottery")` for more info ### Devel ``` -* installing *source* package ‘ecolottery’ ... -** package ‘ecolottery’ successfully unpacked and MD5 sums checked +* installing *source* package ‘GeomComb’ ... +** package ‘GeomComb’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘ecolottery’ -* removing ‘/tmp/workdir/ecolottery/new/ecolottery.Rcheck/ecolottery’ +ERROR: lazy loading failed for package ‘GeomComb’ +* removing ‘/tmp/workdir/GeomComb/new/GeomComb.Rcheck/GeomComb’ ``` ### CRAN ``` -* installing *source* package ‘ecolottery’ ... -** package ‘ecolottery’ successfully unpacked and MD5 sums checked +* installing *source* package ‘GeomComb’ ... +** package ‘GeomComb’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘ecolottery’ -* removing ‘/tmp/workdir/ecolottery/old/ecolottery.Rcheck/ecolottery’ +ERROR: lazy loading failed for package ‘GeomComb’ +* removing ‘/tmp/workdir/GeomComb/old/GeomComb.Rcheck/GeomComb’ ``` -# EpiEstim +# ggrcs
-* Version: 2.2-4 -* GitHub: https://github.com/mrc-ide/EpiEstim -* Source code: https://github.com/cran/EpiEstim -* Date/Publication: 2021-01-07 16:20:10 UTC -* Number of recursive dependencies: 91 +* Version: 0.4.0 +* GitHub: NA +* Source code: https://github.com/cran/ggrcs +* Date/Publication: 2024-06-29 02:40:02 UTC +* Number of recursive dependencies: 78 -Run `revdepcheck::cloud_details(, "EpiEstim")` for more info +Run `revdepcheck::cloud_details(, "ggrcs")` for more info
## In both -* checking whether package ‘EpiEstim’ can be installed ... ERROR +* checking whether package ‘ggrcs’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/EpiEstim/new/EpiEstim.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/ggrcs/new/ggrcs.Rcheck/00install.out’ for details. ``` ## Installation @@ -2809,61 +2413,63 @@ Run `revdepcheck::cloud_details(, "EpiEstim")` for more info ### Devel ``` -* installing *source* package ‘EpiEstim’ ... -** package ‘EpiEstim’ successfully unpacked and MD5 sums checked +* installing *source* package ‘ggrcs’ ... +** package ‘ggrcs’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘EpiEstim’ -* removing ‘/tmp/workdir/EpiEstim/new/EpiEstim.Rcheck/EpiEstim’ +ERROR: lazy loading failed for package ‘ggrcs’ +* removing ‘/tmp/workdir/ggrcs/new/ggrcs.Rcheck/ggrcs’ ``` ### CRAN ``` -* installing *source* package ‘EpiEstim’ ... -** package ‘EpiEstim’ successfully unpacked and MD5 sums checked +* installing *source* package ‘ggrcs’ ... +** package ‘ggrcs’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘EpiEstim’ -* removing ‘/tmp/workdir/EpiEstim/old/EpiEstim.Rcheck/EpiEstim’ +ERROR: lazy loading failed for package ‘ggrcs’ +* removing ‘/tmp/workdir/ggrcs/old/ggrcs.Rcheck/ggrcs’ ``` -# evolqg +# ggrisk
-* Version: 0.3-4 -* GitHub: https://github.com/lem-usp/evolqg -* Source code: https://github.com/cran/evolqg -* Date/Publication: 2023-12-05 15:20:12 UTC -* Number of recursive dependencies: 111 +* Version: 1.3 +* GitHub: https://github.com/yikeshu0611/ggrisk +* Source code: https://github.com/cran/ggrisk +* Date/Publication: 2021-08-09 07:40:06 UTC +* Number of recursive dependencies: 115 -Run `revdepcheck::cloud_details(, "evolqg")` for more info +Run `revdepcheck::cloud_details(, "ggrisk")` for more info
## In both -* checking whether package ‘evolqg’ can be installed ... ERROR +* checking whether package ‘ggrisk’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/evolqg/new/evolqg.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/ggrisk/new/ggrisk.Rcheck/00install.out’ for details. ``` ## Installation @@ -2871,73 +2477,61 @@ Run `revdepcheck::cloud_details(, "evolqg")` for more info ### Devel ``` -* installing *source* package ‘evolqg’ ... -** package ‘evolqg’ successfully unpacked and MD5 sums checked +* installing *source* package ‘ggrisk’ ... +** package ‘ggrisk’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c fast_RS.cpp -o fast_RS.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o evolqg.so RcppExports.o fast_RS.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/evolqg/new/evolqg.Rcheck/00LOCK-evolqg/00new/evolqg/libs ** R ** data -** inst +*** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘evolqg’ -* removing ‘/tmp/workdir/evolqg/new/evolqg.Rcheck/evolqg’ +ERROR: lazy loading failed for package ‘ggrisk’ +* removing ‘/tmp/workdir/ggrisk/new/ggrisk.Rcheck/ggrisk’ ``` ### CRAN ``` -* installing *source* package ‘evolqg’ ... -** package ‘evolqg’ successfully unpacked and MD5 sums checked +* installing *source* package ‘ggrisk’ ... +** package ‘ggrisk’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c fast_RS.cpp -o fast_RS.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o evolqg.so RcppExports.o fast_RS.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/evolqg/old/evolqg.Rcheck/00LOCK-evolqg/00new/evolqg/libs ** R ** data -** inst +*** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘evolqg’ -* removing ‘/tmp/workdir/evolqg/old/evolqg.Rcheck/evolqg’ +ERROR: lazy loading failed for package ‘ggrisk’ +* removing ‘/tmp/workdir/ggrisk/old/ggrisk.Rcheck/ggrisk’ ``` -# ForecastComb +# gJLS2
-* Version: 1.3.1 -* GitHub: https://github.com/ceweiss/ForecastComb -* Source code: https://github.com/cran/ForecastComb -* Date/Publication: 2018-08-07 13:50:08 UTC -* Number of recursive dependencies: 73 +* Version: 0.2.0 +* GitHub: NA +* Source code: https://github.com/cran/gJLS2 +* Date/Publication: 2021-09-30 09:00:05 UTC +* Number of recursive dependencies: 45 -Run `revdepcheck::cloud_details(, "ForecastComb")` for more info +Run `revdepcheck::cloud_details(, "gJLS2")` for more info
## In both -* checking whether package ‘ForecastComb’ can be installed ... ERROR +* checking whether package ‘gJLS2’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/ForecastComb/new/ForecastComb.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/gJLS2/new/gJLS2.Rcheck/00install.out’ for details. ``` ## Installation @@ -2945,67 +2539,63 @@ Run `revdepcheck::cloud_details(, "ForecastComb")` for more info ### Devel ``` -* installing *source* package ‘ForecastComb’ ... -** package ‘ForecastComb’ successfully unpacked and MD5 sums checked +* installing *source* package ‘gJLS2’ ... +** package ‘gJLS2’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘ForecastComb’ -* removing ‘/tmp/workdir/ForecastComb/new/ForecastComb.Rcheck/ForecastComb’ +ERROR: lazy loading failed for package ‘gJLS2’ +* removing ‘/tmp/workdir/gJLS2/new/gJLS2.Rcheck/gJLS2’ ``` ### CRAN ``` -* installing *source* package ‘ForecastComb’ ... -** package ‘ForecastComb’ successfully unpacked and MD5 sums checked +* installing *source* package ‘gJLS2’ ... +** package ‘gJLS2’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘ForecastComb’ -* removing ‘/tmp/workdir/ForecastComb/old/ForecastComb.Rcheck/ForecastComb’ +ERROR: lazy loading failed for package ‘gJLS2’ +* removing ‘/tmp/workdir/gJLS2/old/gJLS2.Rcheck/gJLS2’ ``` -# gapfill +# Greg
-* Version: 0.9.6-1 -* GitHub: https://github.com/florafauna/gapfill -* Source code: https://github.com/cran/gapfill -* Date/Publication: 2021-02-12 10:10:05 UTC -* Number of recursive dependencies: 71 +* Version: 2.0.2 +* GitHub: https://github.com/gforge/Greg +* Source code: https://github.com/cran/Greg +* Date/Publication: 2024-01-29 13:30:21 UTC +* Number of recursive dependencies: 151 -Run `revdepcheck::cloud_details(, "gapfill")` for more info +Run `revdepcheck::cloud_details(, "Greg")` for more info
## In both -* checking whether package ‘gapfill’ can be installed ... ERROR +* checking whether package ‘Greg’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/gapfill/new/gapfill.Rcheck/00install.out’ for details. - ``` - -* checking package dependencies ... NOTE - ``` - Packages which this enhances but not available for checking: - 'raster', 'doParallel', 'doMPI' + See ‘/tmp/workdir/Greg/new/Greg.Rcheck/00install.out’ for details. ``` ## Installation @@ -3013,77 +2603,59 @@ Run `revdepcheck::cloud_details(, "gapfill")` for more info ### Devel ``` -* installing *source* package ‘gapfill’ ... -** package ‘gapfill’ successfully unpacked and MD5 sums checked +* installing *source* package ‘Greg’ ... +** package ‘Greg’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c gapfill.cpp -o gapfill.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o gapfill.so RcppExports.o gapfill.o -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/gapfill/new/gapfill.Rcheck/00LOCK-gapfill/00new/gapfill/libs ** R -... -** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘gapfill’ -* removing ‘/tmp/workdir/gapfill/new/gapfill.Rcheck/gapfill’ +ERROR: lazy loading failed for package ‘Greg’ +* removing ‘/tmp/workdir/Greg/new/Greg.Rcheck/Greg’ ``` ### CRAN ``` -* installing *source* package ‘gapfill’ ... -** package ‘gapfill’ successfully unpacked and MD5 sums checked +* installing *source* package ‘Greg’ ... +** package ‘Greg’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c gapfill.cpp -o gapfill.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o gapfill.so RcppExports.o gapfill.o -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/gapfill/old/gapfill.Rcheck/00LOCK-gapfill/00new/gapfill/libs ** R -... -** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘gapfill’ -* removing ‘/tmp/workdir/gapfill/old/gapfill.Rcheck/gapfill’ +ERROR: lazy loading failed for package ‘Greg’ +* removing ‘/tmp/workdir/Greg/old/Greg.Rcheck/Greg’ ``` -# GeomComb +# greport
-* Version: 1.0 -* GitHub: https://github.com/ceweiss/GeomComb -* Source code: https://github.com/cran/GeomComb -* Date/Publication: 2016-11-27 16:02:26 -* Number of recursive dependencies: 74 +* Version: 0.7-4 +* GitHub: https://github.com/harrelfe/greport +* Source code: https://github.com/cran/greport +* Date/Publication: 2023-09-02 22:20:02 UTC +* Number of recursive dependencies: 84 -Run `revdepcheck::cloud_details(, "GeomComb")` for more info +Run `revdepcheck::cloud_details(, "greport")` for more info
## In both -* checking whether package ‘GeomComb’ can be installed ... ERROR +* checking whether package ‘greport’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/GeomComb/new/GeomComb.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/greport/new/greport.Rcheck/00install.out’ for details. ``` ## Installation @@ -3091,78 +2663,59 @@ Run `revdepcheck::cloud_details(, "GeomComb")` for more info ### Devel ``` -* installing *source* package ‘GeomComb’ ... -** package ‘GeomComb’ successfully unpacked and MD5 sums checked +* installing *source* package ‘greport’ ... +** package ‘greport’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘GeomComb’ -* removing ‘/tmp/workdir/GeomComb/new/GeomComb.Rcheck/GeomComb’ +ERROR: lazy loading failed for package ‘greport’ +* removing ‘/tmp/workdir/greport/new/greport.Rcheck/greport’ ``` ### CRAN ``` -* installing *source* package ‘GeomComb’ ... -** package ‘GeomComb’ successfully unpacked and MD5 sums checked +* installing *source* package ‘greport’ ... +** package ‘greport’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘GeomComb’ -* removing ‘/tmp/workdir/GeomComb/old/GeomComb.Rcheck/GeomComb’ +ERROR: lazy loading failed for package ‘greport’ +* removing ‘/tmp/workdir/greport/old/greport.Rcheck/greport’ ``` -# geostan +# hettx
-* Version: 0.6.1 -* GitHub: https://github.com/ConnorDonegan/geostan -* Source code: https://github.com/cran/geostan -* Date/Publication: 2024-05-10 22:23:01 UTC -* Number of recursive dependencies: 108 +* Version: 0.1.3 +* GitHub: https://github.com/bfifield/hettx +* Source code: https://github.com/cran/hettx +* Date/Publication: 2023-08-19 22:22:34 UTC +* Number of recursive dependencies: 85 -Run `revdepcheck::cloud_details(, "geostan")` for more info +Run `revdepcheck::cloud_details(, "hettx")` for more info
-## Newly broken +## In both -* checking whether package ‘geostan’ can be installed ... ERROR +* checking whether package ‘hettx’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/geostan/new/geostan.Rcheck/00install.out’ for details. - ``` - -## Newly fixed - -* checking installed package size ... NOTE - ``` - installed size is 129.8Mb - sub-directories of 1Mb or more: - libs 127.6Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘RcppParallel’ ‘rstantools’ - All declared Imports should be used. - ``` - -* checking for GNU extensions in Makefiles ... NOTE - ``` - GNU make is a SystemRequirements. + See ‘/tmp/workdir/hettx/new/hettx.Rcheck/00install.out’ for details. ``` ## Installation @@ -3170,77 +2723,63 @@ Run `revdepcheck::cloud_details(, "geostan")` for more info ### Devel ``` -* installing *source* package ‘geostan’ ... -** package ‘geostan’ successfully unpacked and MD5 sums checked +* installing *source* package ‘hettx’ ... +** package ‘hettx’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -stanExports_foundation.cc:32:1: fatal error: error writing to /tmp/cccy6wQ6.s: Cannot allocate memory - 32 | } - | ^ -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_foundation.o] Error 1 -ERROR: compilation failed for package ‘geostan’ -* removing ‘/tmp/workdir/geostan/new/geostan.Rcheck/geostan’ +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘hettx’ +* removing ‘/tmp/workdir/hettx/new/hettx.Rcheck/hettx’ ``` ### CRAN ``` -* installing *source* package ‘geostan’ ... -** package ‘geostan’ successfully unpacked and MD5 sums checked +* installing *source* package ‘hettx’ ... +** package ‘hettx’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -** help -*** installing help indices -*** copying figures -** building package indices -** installing vignettes -** testing if installed package can be loaded from temporary location -** checking absolute paths in shared objects and dynamic libraries -** testing if installed package can be loaded from final location -** testing if installed package keeps a record of temporary installation path -* DONE (geostan) +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘hettx’ +* removing ‘/tmp/workdir/hettx/old/hettx.Rcheck/hettx’ ``` -# ggrcs +# hIRT
-* Version: 0.3.8 -* GitHub: NA -* Source code: https://github.com/cran/ggrcs -* Date/Publication: 2024-01-30 03:20:08 UTC -* Number of recursive dependencies: 78 +* Version: 0.3.0 +* GitHub: https://github.com/xiangzhou09/hIRT +* Source code: https://github.com/cran/hIRT +* Date/Publication: 2020-03-26 17:10:02 UTC +* Number of recursive dependencies: 88 -Run `revdepcheck::cloud_details(, "ggrcs")` for more info +Run `revdepcheck::cloud_details(, "hIRT")` for more info
## In both -* checking whether package ‘ggrcs’ can be installed ... ERROR +* checking whether package ‘hIRT’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/ggrcs/new/ggrcs.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/hIRT/new/hIRT.Rcheck/00install.out’ for details. ``` ## Installation @@ -3248,63 +2787,61 @@ Run `revdepcheck::cloud_details(, "ggrcs")` for more info ### Devel ``` -* installing *source* package ‘ggrcs’ ... -** package ‘ggrcs’ successfully unpacked and MD5 sums checked +* installing *source* package ‘hIRT’ ... +** package ‘hIRT’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘ggrcs’ -* removing ‘/tmp/workdir/ggrcs/new/ggrcs.Rcheck/ggrcs’ +ERROR: lazy loading failed for package ‘hIRT’ +* removing ‘/tmp/workdir/hIRT/new/hIRT.Rcheck/hIRT’ ``` ### CRAN ``` -* installing *source* package ‘ggrcs’ ... -** package ‘ggrcs’ successfully unpacked and MD5 sums checked +* installing *source* package ‘hIRT’ ... +** package ‘hIRT’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘ggrcs’ -* removing ‘/tmp/workdir/ggrcs/old/ggrcs.Rcheck/ggrcs’ +ERROR: lazy loading failed for package ‘hIRT’ +* removing ‘/tmp/workdir/hIRT/old/hIRT.Rcheck/hIRT’ ``` -# ggrisk +# Hmsc
-* Version: 1.3 -* GitHub: https://github.com/yikeshu0611/ggrisk -* Source code: https://github.com/cran/ggrisk -* Date/Publication: 2021-08-09 07:40:06 UTC -* Number of recursive dependencies: 115 +* Version: 3.0-13 +* GitHub: https://github.com/hmsc-r/HMSC +* Source code: https://github.com/cran/Hmsc +* Date/Publication: 2022-08-11 14:10:14 UTC +* Number of recursive dependencies: 76 -Run `revdepcheck::cloud_details(, "ggrisk")` for more info +Run `revdepcheck::cloud_details(, "Hmsc")` for more info
## In both -* checking whether package ‘ggrisk’ can be installed ... ERROR +* checking whether package ‘Hmsc’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/ggrisk/new/ggrisk.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/Hmsc/new/Hmsc.Rcheck/00install.out’ for details. ``` ## Installation @@ -3312,137 +2849,123 @@ Run `revdepcheck::cloud_details(, "ggrisk")` for more info ### Devel ``` -* installing *source* package ‘ggrisk’ ... -** package ‘ggrisk’ successfully unpacked and MD5 sums checked +* installing *source* package ‘Hmsc’ ... +** package ‘Hmsc’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘ggrisk’ -* removing ‘/tmp/workdir/ggrisk/new/ggrisk.Rcheck/ggrisk’ +ERROR: lazy loading failed for package ‘Hmsc’ +* removing ‘/tmp/workdir/Hmsc/new/Hmsc.Rcheck/Hmsc’ ``` ### CRAN ``` -* installing *source* package ‘ggrisk’ ... -** package ‘ggrisk’ successfully unpacked and MD5 sums checked +* installing *source* package ‘Hmsc’ ... +** package ‘Hmsc’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘ggrisk’ -* removing ‘/tmp/workdir/ggrisk/old/ggrisk.Rcheck/ggrisk’ +ERROR: lazy loading failed for package ‘Hmsc’ +* removing ‘/tmp/workdir/Hmsc/old/Hmsc.Rcheck/Hmsc’ ``` -# ggsector +# inventorize
-* Version: 1.6.6 -* GitHub: https://github.com/yanpd01/ggsector -* Source code: https://github.com/cran/ggsector -* Date/Publication: 2022-12-05 15:20:02 UTC -* Number of recursive dependencies: 159 +* Version: 1.1.1 +* GitHub: NA +* Source code: https://github.com/cran/inventorize +* Date/Publication: 2022-05-31 22:20:09 UTC +* Number of recursive dependencies: 71 -Run `revdepcheck::cloud_details(, "ggsector")` for more info +Run `revdepcheck::cloud_details(, "inventorize")` for more info
-## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/ggsector/new/ggsector.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘ggsector/DESCRIPTION’ ... OK -... -* this is package ‘ggsector’ version ‘1.6.6’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ +## Newly broken -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR +* checking whether package ‘inventorize’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/inventorize/new/inventorize.Rcheck/00install.out’ for details. + ``` +## Installation +### Devel +``` +* installing *source* package ‘inventorize’ ... +** package ‘inventorize’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in pm[[2]] : subscript out of bounds +Error: unable to load R code in package ‘inventorize’ +Execution halted +ERROR: lazy loading failed for package ‘inventorize’ +* removing ‘/tmp/workdir/inventorize/new/inventorize.Rcheck/inventorize’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/ggsector/old/ggsector.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘ggsector/DESCRIPTION’ ... OK -... -* this is package ‘ggsector’ version ‘1.6.6’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - +* installing *source* package ‘inventorize’ ... +** package ‘inventorize’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Warning in qgamma(service_level, alpha, beta) : NaNs produced +Warning in qgamma(service_level, alpha, beta) : NaNs produced +** help +*** installing help indices +** building package indices +** testing if installed package can be loaded from temporary location +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (inventorize) ``` -# gJLS2 +# iNZightPlots
-* Version: 0.2.0 -* GitHub: NA -* Source code: https://github.com/cran/gJLS2 -* Date/Publication: 2021-09-30 09:00:05 UTC -* Number of recursive dependencies: 45 +* Version: 2.15.3 +* GitHub: https://github.com/iNZightVIT/iNZightPlots +* Source code: https://github.com/cran/iNZightPlots +* Date/Publication: 2023-10-14 05:00:02 UTC +* Number of recursive dependencies: 162 -Run `revdepcheck::cloud_details(, "gJLS2")` for more info +Run `revdepcheck::cloud_details(, "iNZightPlots")` for more info
## In both -* checking whether package ‘gJLS2’ can be installed ... ERROR +* checking whether package ‘iNZightPlots’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/gJLS2/new/gJLS2.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/iNZightPlots/new/iNZightPlots.Rcheck/00install.out’ for details. ``` ## Installation @@ -3450,139 +2973,59 @@ Run `revdepcheck::cloud_details(, "gJLS2")` for more info ### Devel ``` -* installing *source* package ‘gJLS2’ ... -** package ‘gJLS2’ successfully unpacked and MD5 sums checked +* installing *source* package ‘iNZightPlots’ ... +** package ‘iNZightPlots’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘gJLS2’ -* removing ‘/tmp/workdir/gJLS2/new/gJLS2.Rcheck/gJLS2’ +ERROR: lazy loading failed for package ‘iNZightPlots’ +* removing ‘/tmp/workdir/iNZightPlots/new/iNZightPlots.Rcheck/iNZightPlots’ ``` ### CRAN ``` -* installing *source* package ‘gJLS2’ ... -** package ‘gJLS2’ successfully unpacked and MD5 sums checked +* installing *source* package ‘iNZightPlots’ ... +** package ‘iNZightPlots’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘gJLS2’ -* removing ‘/tmp/workdir/gJLS2/old/gJLS2.Rcheck/gJLS2’ - - -``` -# grandR - -
- -* Version: 0.2.5 -* GitHub: https://github.com/erhard-lab/grandR -* Source code: https://github.com/cran/grandR -* Date/Publication: 2024-02-15 15:30:02 UTC -* Number of recursive dependencies: 265 - -Run `revdepcheck::cloud_details(, "grandR")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/grandR/new/grandR.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘grandR/DESCRIPTION’ ... OK -... -* checking installed files from ‘inst/doc’ ... OK -* checking files in ‘vignettes’ ... OK -* checking examples ... OK -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘getting-started.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 NOTE - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/grandR/old/grandR.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘grandR/DESCRIPTION’ ... OK -... -* checking installed files from ‘inst/doc’ ... OK -* checking files in ‘vignettes’ ... OK -* checking examples ... OK -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘getting-started.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 NOTE - - - +ERROR: lazy loading failed for package ‘iNZightPlots’ +* removing ‘/tmp/workdir/iNZightPlots/old/iNZightPlots.Rcheck/iNZightPlots’ ``` -# Greg +# iNZightRegression
-* Version: 2.0.2 -* GitHub: https://github.com/gforge/Greg -* Source code: https://github.com/cran/Greg -* Date/Publication: 2024-01-29 13:30:21 UTC -* Number of recursive dependencies: 152 +* Version: 1.3.4 +* GitHub: https://github.com/iNZightVIT/iNZightRegression +* Source code: https://github.com/cran/iNZightRegression +* Date/Publication: 2024-04-05 02:32:59 UTC +* Number of recursive dependencies: 158 -Run `revdepcheck::cloud_details(, "Greg")` for more info +Run `revdepcheck::cloud_details(, "iNZightRegression")` for more info
## In both -* checking whether package ‘Greg’ can be installed ... ERROR +* checking whether package ‘iNZightRegression’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/Greg/new/Greg.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/iNZightRegression/new/iNZightRegression.Rcheck/00install.out’ for details. ``` ## Installation @@ -3590,8 +3033,8 @@ Run `revdepcheck::cloud_details(, "Greg")` for more info ### Devel ``` -* installing *source* package ‘Greg’ ... -** package ‘Greg’ successfully unpacked and MD5 sums checked +* installing *source* package ‘iNZightRegression’ ... +** package ‘iNZightRegression’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst @@ -3600,16 +3043,16 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘Greg’ -* removing ‘/tmp/workdir/Greg/new/Greg.Rcheck/Greg’ +ERROR: lazy loading failed for package ‘iNZightRegression’ +* removing ‘/tmp/workdir/iNZightRegression/new/iNZightRegression.Rcheck/iNZightRegression’ ``` ### CRAN ``` -* installing *source* package ‘Greg’ ... -** package ‘Greg’ successfully unpacked and MD5 sums checked +* installing *source* package ‘iNZightRegression’ ... +** package ‘iNZightRegression’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst @@ -3618,31 +3061,31 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘Greg’ -* removing ‘/tmp/workdir/Greg/old/Greg.Rcheck/Greg’ +ERROR: lazy loading failed for package ‘iNZightRegression’ +* removing ‘/tmp/workdir/iNZightRegression/old/iNZightRegression.Rcheck/iNZightRegression’ ``` -# greport +# IRexamples
-* Version: 0.7-4 -* GitHub: https://github.com/harrelfe/greport -* Source code: https://github.com/cran/greport -* Date/Publication: 2023-09-02 22:20:02 UTC -* Number of recursive dependencies: 84 +* Version: 0.0.4 +* GitHub: https://github.com/vinhdizzo/IRexamples +* Source code: https://github.com/cran/IRexamples +* Date/Publication: 2023-10-06 06:40:02 UTC +* Number of recursive dependencies: 177 -Run `revdepcheck::cloud_details(, "greport")` for more info +Run `revdepcheck::cloud_details(, "IRexamples")` for more info
## In both -* checking whether package ‘greport’ can be installed ... ERROR +* checking whether package ‘IRexamples’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/greport/new/greport.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/IRexamples/new/IRexamples.Rcheck/00install.out’ for details. ``` ## Installation @@ -3650,135 +3093,73 @@ Run `revdepcheck::cloud_details(, "greport")` for more info ### Devel ``` -* installing *source* package ‘greport’ ... -** package ‘greport’ successfully unpacked and MD5 sums checked +* installing *source* package ‘IRexamples’ ... +** package ‘IRexamples’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘greport’ -* removing ‘/tmp/workdir/greport/new/greport.Rcheck/greport’ +ERROR: lazy loading failed for package ‘IRexamples’ +* removing ‘/tmp/workdir/IRexamples/new/IRexamples.Rcheck/IRexamples’ ``` ### CRAN ``` -* installing *source* package ‘greport’ ... -** package ‘greport’ successfully unpacked and MD5 sums checked +* installing *source* package ‘IRexamples’ ... +** package ‘IRexamples’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘greport’ -* removing ‘/tmp/workdir/greport/old/greport.Rcheck/greport’ +ERROR: lazy loading failed for package ‘IRexamples’ +* removing ‘/tmp/workdir/IRexamples/old/IRexamples.Rcheck/IRexamples’ ``` -# harmony +# jmBIG
-* Version: 1.2.0 +* Version: 0.1.2 * GitHub: NA -* Source code: https://github.com/cran/harmony -* Date/Publication: 2023-11-29 08:30:04 UTC -* Number of recursive dependencies: 214 - -Run `revdepcheck::cloud_details(, "harmony")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/harmony/new/harmony.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘harmony/DESCRIPTION’ ... OK -... ---- finished re-building ‘quickstart.Rmd’ - -SUMMARY: processing the following file failed: - ‘Seurat.Rmd’ - -Error: Vignette re-building failed. -Execution halted - -* DONE -Status: 1 WARNING, 3 NOTEs - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/harmony/old/harmony.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘harmony/DESCRIPTION’ ... OK -... ---- finished re-building ‘quickstart.Rmd’ - -SUMMARY: processing the following file failed: - ‘Seurat.Rmd’ - -Error: Vignette re-building failed. -Execution halted - -* DONE -Status: 1 WARNING, 3 NOTEs - - - - - -``` -# hettx - -
- -* Version: 0.1.3 -* GitHub: https://github.com/bfifield/hettx -* Source code: https://github.com/cran/hettx -* Date/Publication: 2023-08-19 22:22:34 UTC -* Number of recursive dependencies: 85 +* Source code: https://github.com/cran/jmBIG +* Date/Publication: 2024-03-20 23:40:02 UTC +* Number of recursive dependencies: 184 -Run `revdepcheck::cloud_details(, "hettx")` for more info +Run `revdepcheck::cloud_details(, "jmBIG")` for more info
## In both -* checking whether package ‘hettx’ can be installed ... ERROR +* checking whether package ‘jmBIG’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/hettx/new/hettx.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/jmBIG/new/jmBIG.Rcheck/00install.out’ for details. ``` ## Installation @@ -3786,63 +3167,61 @@ Run `revdepcheck::cloud_details(, "hettx")` for more info ### Devel ``` -* installing *source* package ‘hettx’ ... -** package ‘hettx’ successfully unpacked and MD5 sums checked +* installing *source* package ‘jmBIG’ ... +** package ‘jmBIG’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘hettx’ -* removing ‘/tmp/workdir/hettx/new/hettx.Rcheck/hettx’ +ERROR: lazy loading failed for package ‘jmBIG’ +* removing ‘/tmp/workdir/jmBIG/new/jmBIG.Rcheck/jmBIG’ ``` ### CRAN ``` -* installing *source* package ‘hettx’ ... -** package ‘hettx’ successfully unpacked and MD5 sums checked +* installing *source* package ‘jmBIG’ ... +** package ‘jmBIG’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘hettx’ -* removing ‘/tmp/workdir/hettx/old/hettx.Rcheck/hettx’ +ERROR: lazy loading failed for package ‘jmBIG’ +* removing ‘/tmp/workdir/jmBIG/old/jmBIG.Rcheck/jmBIG’ ``` -# hIRT +# joineRML
-* Version: 0.3.0 -* GitHub: https://github.com/xiangzhou09/hIRT -* Source code: https://github.com/cran/hIRT -* Date/Publication: 2020-03-26 17:10:02 UTC -* Number of recursive dependencies: 88 +* Version: 0.4.6 +* GitHub: https://github.com/graemeleehickey/joineRML +* Source code: https://github.com/cran/joineRML +* Date/Publication: 2023-01-20 04:50:02 UTC +* Number of recursive dependencies: 91 -Run `revdepcheck::cloud_details(, "hIRT")` for more info +Run `revdepcheck::cloud_details(, "joineRML")` for more info
## In both -* checking whether package ‘hIRT’ can be installed ... ERROR +* checking whether package ‘joineRML’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/hIRT/new/hIRT.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/joineRML/new/joineRML.Rcheck/00install.out’ for details. ``` ## Installation @@ -3850,61 +3229,77 @@ Run `revdepcheck::cloud_details(, "hIRT")` for more info ### Devel ``` -* installing *source* package ‘hIRT’ ... -** package ‘hIRT’ successfully unpacked and MD5 sums checked +* installing *source* package ‘joineRML’ ... +** package ‘joineRML’ successfully unpacked and MD5 sums checked ** using staged installation -** R +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c expW.cpp -o expW.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c gammaUpdate.cpp -o gammaUpdate.o +... ** data *** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘hIRT’ -* removing ‘/tmp/workdir/hIRT/new/hIRT.Rcheck/hIRT’ +ERROR: lazy loading failed for package ‘joineRML’ +* removing ‘/tmp/workdir/joineRML/new/joineRML.Rcheck/joineRML’ ``` ### CRAN ``` -* installing *source* package ‘hIRT’ ... -** package ‘hIRT’ successfully unpacked and MD5 sums checked +* installing *source* package ‘joineRML’ ... +** package ‘joineRML’ successfully unpacked and MD5 sums checked ** using staged installation -** R +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c expW.cpp -o expW.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c gammaUpdate.cpp -o gammaUpdate.o +... ** data *** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘hIRT’ -* removing ‘/tmp/workdir/hIRT/old/hIRT.Rcheck/hIRT’ +ERROR: lazy loading failed for package ‘joineRML’ +* removing ‘/tmp/workdir/joineRML/old/joineRML.Rcheck/joineRML’ ``` -# Hmsc +# JWileymisc
-* Version: 3.0-13 -* GitHub: https://github.com/hmsc-r/HMSC -* Source code: https://github.com/cran/Hmsc -* Date/Publication: 2022-08-11 14:10:14 UTC -* Number of recursive dependencies: 76 +* Version: 1.4.1 +* GitHub: https://github.com/JWiley/JWileymisc +* Source code: https://github.com/cran/JWileymisc +* Date/Publication: 2023-10-05 04:50:02 UTC +* Number of recursive dependencies: 167 -Run `revdepcheck::cloud_details(, "Hmsc")` for more info +Run `revdepcheck::cloud_details(, "JWileymisc")` for more info
## In both -* checking whether package ‘Hmsc’ can be installed ... ERROR +* checking whether package ‘JWileymisc’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/Hmsc/new/Hmsc.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/JWileymisc/new/JWileymisc.Rcheck/00install.out’ for details. ``` ## Installation @@ -3912,63 +3307,73 @@ Run `revdepcheck::cloud_details(, "Hmsc")` for more info ### Devel ``` -* installing *source* package ‘Hmsc’ ... -** package ‘Hmsc’ successfully unpacked and MD5 sums checked +* installing *source* package ‘JWileymisc’ ... +** package ‘JWileymisc’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘Hmsc’ -* removing ‘/tmp/workdir/Hmsc/new/Hmsc.Rcheck/Hmsc’ +ERROR: lazy loading failed for package ‘JWileymisc’ +* removing ‘/tmp/workdir/JWileymisc/new/JWileymisc.Rcheck/JWileymisc’ ``` ### CRAN ``` -* installing *source* package ‘Hmsc’ ... -** package ‘Hmsc’ successfully unpacked and MD5 sums checked +* installing *source* package ‘JWileymisc’ ... +** package ‘JWileymisc’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘Hmsc’ -* removing ‘/tmp/workdir/Hmsc/old/Hmsc.Rcheck/Hmsc’ +ERROR: lazy loading failed for package ‘JWileymisc’ +* removing ‘/tmp/workdir/JWileymisc/old/JWileymisc.Rcheck/JWileymisc’ ``` -# iNZightPlots +# kmc
-* Version: 2.15.3 -* GitHub: https://github.com/iNZightVIT/iNZightPlots -* Source code: https://github.com/cran/iNZightPlots -* Date/Publication: 2023-10-14 05:00:02 UTC -* Number of recursive dependencies: 162 +* Version: 0.4-2 +* GitHub: https://github.com/yfyang86/kmc +* Source code: https://github.com/cran/kmc +* Date/Publication: 2022-11-22 08:30:02 UTC +* Number of recursive dependencies: 61 -Run `revdepcheck::cloud_details(, "iNZightPlots")` for more info +Run `revdepcheck::cloud_details(, "kmc")` for more info
## In both -* checking whether package ‘iNZightPlots’ can be installed ... ERROR +* checking whether package ‘kmc’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/iNZightPlots/new/iNZightPlots.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/kmc/new/kmc.Rcheck/00install.out’ for details. ``` ## Installation @@ -3976,59 +3381,73 @@ Run `revdepcheck::cloud_details(, "iNZightPlots")` for more info ### Devel ``` -* installing *source* package ‘iNZightPlots’ ... -** package ‘iNZightPlots’ successfully unpacked and MD5 sums checked +* installing *source* package ‘kmc’ ... +** package ‘kmc’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExport.cpp -o RcppExport.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c kmc.cpp -o kmc.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c kmc_init.c -o kmc_init.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c surv2.c -o surv2.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o kmc.so RcppExport.o kmc.o kmc_init.o surv2.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/kmc/new/kmc.Rcheck/00LOCK-kmc/00new/kmc/libs ** R -** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘emplik’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘iNZightPlots’ -* removing ‘/tmp/workdir/iNZightPlots/new/iNZightPlots.Rcheck/iNZightPlots’ +ERROR: lazy loading failed for package ‘kmc’ +* removing ‘/tmp/workdir/kmc/new/kmc.Rcheck/kmc’ ``` ### CRAN ``` -* installing *source* package ‘iNZightPlots’ ... -** package ‘iNZightPlots’ successfully unpacked and MD5 sums checked +* installing *source* package ‘kmc’ ... +** package ‘kmc’ successfully unpacked and MD5 sums checked ** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExport.cpp -o RcppExport.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c kmc.cpp -o kmc.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c kmc_init.c -o kmc_init.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c surv2.c -o surv2.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o kmc.so RcppExport.o kmc.o kmc_init.o surv2.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/kmc/old/kmc.Rcheck/00LOCK-kmc/00new/kmc/libs +** R +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘emplik’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘iNZightPlots’ -* removing ‘/tmp/workdir/iNZightPlots/old/iNZightPlots.Rcheck/iNZightPlots’ +ERROR: lazy loading failed for package ‘kmc’ +* removing ‘/tmp/workdir/kmc/old/kmc.Rcheck/kmc’ ``` -# iNZightRegression +# L2E
-* Version: 1.3.4 -* GitHub: https://github.com/iNZightVIT/iNZightRegression -* Source code: https://github.com/cran/iNZightRegression -* Date/Publication: 2024-04-05 02:32:59 UTC -* Number of recursive dependencies: 154 +* Version: 2.0 +* GitHub: NA +* Source code: https://github.com/cran/L2E +* Date/Publication: 2022-09-08 21:13:00 UTC +* Number of recursive dependencies: 65 -Run `revdepcheck::cloud_details(, "iNZightRegression")` for more info +Run `revdepcheck::cloud_details(, "L2E")` for more info
## In both -* checking whether package ‘iNZightRegression’ can be installed ... ERROR +* checking whether package ‘L2E’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/iNZightRegression/new/iNZightRegression.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/L2E/new/L2E.Rcheck/00install.out’ for details. ``` ## Installation @@ -4036,59 +3455,61 @@ Run `revdepcheck::cloud_details(, "iNZightRegression")` for more info ### Devel ``` -* installing *source* package ‘iNZightRegression’ ... -** package ‘iNZightRegression’ successfully unpacked and MD5 sums checked +* installing *source* package ‘L2E’ ... +** package ‘L2E’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘osqp’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.1 is required Execution halted -ERROR: lazy loading failed for package ‘iNZightRegression’ -* removing ‘/tmp/workdir/iNZightRegression/new/iNZightRegression.Rcheck/iNZightRegression’ +ERROR: lazy loading failed for package ‘L2E’ +* removing ‘/tmp/workdir/L2E/new/L2E.Rcheck/L2E’ ``` ### CRAN ``` -* installing *source* package ‘iNZightRegression’ ... -** package ‘iNZightRegression’ successfully unpacked and MD5 sums checked +* installing *source* package ‘L2E’ ... +** package ‘L2E’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘osqp’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.1 is required Execution halted -ERROR: lazy loading failed for package ‘iNZightRegression’ -* removing ‘/tmp/workdir/iNZightRegression/old/iNZightRegression.Rcheck/iNZightRegression’ +ERROR: lazy loading failed for package ‘L2E’ +* removing ‘/tmp/workdir/L2E/old/L2E.Rcheck/L2E’ ``` -# IRexamples +# llbayesireg
-* Version: 0.0.4 -* GitHub: https://github.com/vinhdizzo/IRexamples -* Source code: https://github.com/cran/IRexamples -* Date/Publication: 2023-10-06 06:40:02 UTC -* Number of recursive dependencies: 185 +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/llbayesireg +* Date/Publication: 2019-04-04 16:20:03 UTC +* Number of recursive dependencies: 60 -Run `revdepcheck::cloud_details(, "IRexamples")` for more info +Run `revdepcheck::cloud_details(, "llbayesireg")` for more info
## In both -* checking whether package ‘IRexamples’ can be installed ... ERROR +* checking whether package ‘llbayesireg’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/IRexamples/new/IRexamples.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/llbayesireg/new/llbayesireg.Rcheck/00install.out’ for details. ``` ## Installation @@ -4096,63 +3517,61 @@ Run `revdepcheck::cloud_details(, "IRexamples")` for more info ### Devel ``` -* installing *source* package ‘IRexamples’ ... -** package ‘IRexamples’ successfully unpacked and MD5 sums checked +* installing *source* package ‘llbayesireg’ ... +** package ‘llbayesireg’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘IRexamples’ -* removing ‘/tmp/workdir/IRexamples/new/IRexamples.Rcheck/IRexamples’ +ERROR: lazy loading failed for package ‘llbayesireg’ +* removing ‘/tmp/workdir/llbayesireg/new/llbayesireg.Rcheck/llbayesireg’ ``` ### CRAN ``` -* installing *source* package ‘IRexamples’ ... -** package ‘IRexamples’ successfully unpacked and MD5 sums checked +* installing *source* package ‘llbayesireg’ ... +** package ‘llbayesireg’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘IRexamples’ -* removing ‘/tmp/workdir/IRexamples/old/IRexamples.Rcheck/IRexamples’ +ERROR: lazy loading failed for package ‘llbayesireg’ +* removing ‘/tmp/workdir/llbayesireg/old/llbayesireg.Rcheck/llbayesireg’ ``` -# joineRML +# LorenzRegression
-* Version: 0.4.6 -* GitHub: https://github.com/graemeleehickey/joineRML -* Source code: https://github.com/cran/joineRML -* Date/Publication: 2023-01-20 04:50:02 UTC -* Number of recursive dependencies: 91 +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/LorenzRegression +* Date/Publication: 2023-02-28 17:32:34 UTC +* Number of recursive dependencies: 63 -Run `revdepcheck::cloud_details(, "joineRML")` for more info +Run `revdepcheck::cloud_details(, "LorenzRegression")` for more info
## In both -* checking whether package ‘joineRML’ can be installed ... ERROR +* checking whether package ‘LorenzRegression’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/joineRML/new/joineRML.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/LorenzRegression/new/LorenzRegression.Rcheck/00install.out’ for details. ``` ## Installation @@ -4160,16 +3579,16 @@ Run `revdepcheck::cloud_details(, "joineRML")` for more info ### Devel ``` -* installing *source* package ‘joineRML’ ... -** package ‘joineRML’ successfully unpacked and MD5 sums checked +* installing *source* package ‘LorenzRegression’ ... +** package ‘LorenzRegression’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c expW.cpp -o expW.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c gammaUpdate.cpp -o gammaUpdate.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c GA_fitness.cpp -o GA_fitness.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c GA_meanrank.cpp -o GA_meanrank.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c PLR_derivative.cpp -o PLR_derivative.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c PLR_loss.cpp -o PLR_loss.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o ... ** data *** moving datasets to lazyload DB @@ -4179,24 +3598,24 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘joineRML’ -* removing ‘/tmp/workdir/joineRML/new/joineRML.Rcheck/joineRML’ +ERROR: lazy loading failed for package ‘LorenzRegression’ +* removing ‘/tmp/workdir/LorenzRegression/new/LorenzRegression.Rcheck/LorenzRegression’ ``` ### CRAN ``` -* installing *source* package ‘joineRML’ ... -** package ‘joineRML’ successfully unpacked and MD5 sums checked +* installing *source* package ‘LorenzRegression’ ... +** package ‘LorenzRegression’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c expW.cpp -o expW.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c gammaUpdate.cpp -o gammaUpdate.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c GA_fitness.cpp -o GA_fitness.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c GA_meanrank.cpp -o GA_meanrank.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c PLR_derivative.cpp -o PLR_derivative.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c PLR_loss.cpp -o PLR_loss.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o ... ** data *** moving datasets to lazyload DB @@ -4206,31 +3625,31 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘joineRML’ -* removing ‘/tmp/workdir/joineRML/old/joineRML.Rcheck/joineRML’ +ERROR: lazy loading failed for package ‘LorenzRegression’ +* removing ‘/tmp/workdir/LorenzRegression/old/LorenzRegression.Rcheck/LorenzRegression’ ``` -# JWileymisc +# lsirm12pl
-* Version: 1.4.1 -* GitHub: https://github.com/JWiley/JWileymisc -* Source code: https://github.com/cran/JWileymisc -* Date/Publication: 2023-10-05 04:50:02 UTC -* Number of recursive dependencies: 164 +* Version: 1.3.1 +* GitHub: NA +* Source code: https://github.com/cran/lsirm12pl +* Date/Publication: 2023-06-22 14:12:35 UTC +* Number of recursive dependencies: 124 -Run `revdepcheck::cloud_details(, "JWileymisc")` for more info +Run `revdepcheck::cloud_details(, "lsirm12pl")` for more info
## In both -* checking whether package ‘JWileymisc’ can be installed ... ERROR +* checking whether package ‘lsirm12pl’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/JWileymisc/new/JWileymisc.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/lsirm12pl/new/lsirm12pl.Rcheck/00install.out’ for details. ``` ## Installation @@ -4238,63 +3657,77 @@ Run `revdepcheck::cloud_details(, "JWileymisc")` for more info ### Devel ``` -* installing *source* package ‘JWileymisc’ ... -** package ‘JWileymisc’ successfully unpacked and MD5 sums checked +* installing *source* package ‘lsirm12pl’ ... +** package ‘lsirm12pl’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c log_likelihood.cpp -o log_likelihood.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl.cpp -o lsirm1pl.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl_fixed_gamma.cpp -o lsirm1pl_fixed_gamma.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl_fixed_gamma_mar.cpp -o lsirm1pl_fixed_gamma_mar.o +... ** R ** data *** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘JWileymisc’ -* removing ‘/tmp/workdir/JWileymisc/new/JWileymisc.Rcheck/JWileymisc’ +ERROR: lazy loading failed for package ‘lsirm12pl’ +* removing ‘/tmp/workdir/lsirm12pl/new/lsirm12pl.Rcheck/lsirm12pl’ ``` ### CRAN ``` -* installing *source* package ‘JWileymisc’ ... -** package ‘JWileymisc’ successfully unpacked and MD5 sums checked +* installing *source* package ‘lsirm12pl’ ... +** package ‘lsirm12pl’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c log_likelihood.cpp -o log_likelihood.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl.cpp -o lsirm1pl.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl_fixed_gamma.cpp -o lsirm1pl_fixed_gamma.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl_fixed_gamma_mar.cpp -o lsirm1pl_fixed_gamma_mar.o +... ** R ** data *** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘JWileymisc’ -* removing ‘/tmp/workdir/JWileymisc/old/JWileymisc.Rcheck/JWileymisc’ +ERROR: lazy loading failed for package ‘lsirm12pl’ +* removing ‘/tmp/workdir/lsirm12pl/old/lsirm12pl.Rcheck/lsirm12pl’ ``` -# kmc +# mbsts
-* Version: 0.4-2 -* GitHub: https://github.com/yfyang86/kmc -* Source code: https://github.com/cran/kmc -* Date/Publication: 2022-11-22 08:30:02 UTC -* Number of recursive dependencies: 61 +* Version: 3.0 +* GitHub: NA +* Source code: https://github.com/cran/mbsts +* Date/Publication: 2023-01-07 01:10:02 UTC +* Number of recursive dependencies: 82 -Run `revdepcheck::cloud_details(, "kmc")` for more info +Run `revdepcheck::cloud_details(, "mbsts")` for more info
## In both -* checking whether package ‘kmc’ can be installed ... ERROR +* checking whether package ‘mbsts’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/kmc/new/kmc.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/mbsts/new/mbsts.Rcheck/00install.out’ for details. ``` ## Installation @@ -4302,73 +3735,59 @@ Run `revdepcheck::cloud_details(, "kmc")` for more info ### Devel ``` -* installing *source* package ‘kmc’ ... -** package ‘kmc’ successfully unpacked and MD5 sums checked +* installing *source* package ‘mbsts’ ... +** package ‘mbsts’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExport.cpp -o RcppExport.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c kmc.cpp -o kmc.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c kmc_init.c -o kmc_init.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c surv2.c -o surv2.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o kmc.so RcppExport.o kmc.o kmc_init.o surv2.o -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/kmc/new/kmc.Rcheck/00LOCK-kmc/00new/kmc/libs ** R +** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘emplik’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘kmc’ -* removing ‘/tmp/workdir/kmc/new/kmc.Rcheck/kmc’ +ERROR: lazy loading failed for package ‘mbsts’ +* removing ‘/tmp/workdir/mbsts/new/mbsts.Rcheck/mbsts’ ``` ### CRAN ``` -* installing *source* package ‘kmc’ ... -** package ‘kmc’ successfully unpacked and MD5 sums checked +* installing *source* package ‘mbsts’ ... +** package ‘mbsts’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExport.cpp -o RcppExport.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c kmc.cpp -o kmc.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c kmc_init.c -o kmc_init.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c surv2.c -o surv2.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o kmc.so RcppExport.o kmc.o kmc_init.o surv2.o -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/kmc/old/kmc.Rcheck/00LOCK-kmc/00new/kmc/libs ** R +** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘emplik’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘kmc’ -* removing ‘/tmp/workdir/kmc/old/kmc.Rcheck/kmc’ +ERROR: lazy loading failed for package ‘mbsts’ +* removing ‘/tmp/workdir/mbsts/old/mbsts.Rcheck/mbsts’ ``` -# L2E +# MendelianRandomization
-* Version: 2.0 +* Version: 0.10.0 * GitHub: NA -* Source code: https://github.com/cran/L2E -* Date/Publication: 2022-09-08 21:13:00 UTC -* Number of recursive dependencies: 65 +* Source code: https://github.com/cran/MendelianRandomization +* Date/Publication: 2024-04-12 10:10:02 UTC +* Number of recursive dependencies: 88 -Run `revdepcheck::cloud_details(, "L2E")` for more info +Run `revdepcheck::cloud_details(, "MendelianRandomization")` for more info
## In both -* checking whether package ‘L2E’ can be installed ... ERROR +* checking whether package ‘MendelianRandomization’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/L2E/new/L2E.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/MendelianRandomization/new/MendelianRandomization.Rcheck/00install.out’ for details. ``` ## Installation @@ -4376,61 +3795,71 @@ Run `revdepcheck::cloud_details(, "L2E")` for more info ### Devel ``` -* installing *source* package ‘L2E’ ... -** package ‘L2E’ successfully unpacked and MD5 sums checked +* installing *source* package ‘MendelianRandomization’ ... +** package ‘MendelianRandomization’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c mvmrcML.cpp -o mvmrcML.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o MendelianRandomization.so RcppExports.o mvmrcML.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/MendelianRandomization/new/MendelianRandomization.Rcheck/00LOCK-MendelianRandomization/00new/MendelianRandomization/libs ** R -** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘osqp’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.1 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘L2E’ -* removing ‘/tmp/workdir/L2E/new/L2E.Rcheck/L2E’ +ERROR: lazy loading failed for package ‘MendelianRandomization’ +* removing ‘/tmp/workdir/MendelianRandomization/new/MendelianRandomization.Rcheck/MendelianRandomization’ ``` ### CRAN ``` -* installing *source* package ‘L2E’ ... -** package ‘L2E’ successfully unpacked and MD5 sums checked +* installing *source* package ‘MendelianRandomization’ ... +** package ‘MendelianRandomization’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c mvmrcML.cpp -o mvmrcML.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o MendelianRandomization.so RcppExports.o mvmrcML.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/MendelianRandomization/old/MendelianRandomization.Rcheck/00LOCK-MendelianRandomization/00new/MendelianRandomization/libs ** R -** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘osqp’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.1 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘L2E’ -* removing ‘/tmp/workdir/L2E/old/L2E.Rcheck/L2E’ +ERROR: lazy loading failed for package ‘MendelianRandomization’ +* removing ‘/tmp/workdir/MendelianRandomization/old/MendelianRandomization.Rcheck/MendelianRandomization’ ``` -# llbayesireg +# MetabolicSurv
-* Version: 1.0.0 -* GitHub: NA -* Source code: https://github.com/cran/llbayesireg -* Date/Publication: 2019-04-04 16:20:03 UTC -* Number of recursive dependencies: 61 +* Version: 1.1.2 +* GitHub: https://github.com/OlajumokeEvangelina/MetabolicSurv +* Source code: https://github.com/cran/MetabolicSurv +* Date/Publication: 2021-06-11 08:30:02 UTC +* Number of recursive dependencies: 131 -Run `revdepcheck::cloud_details(, "llbayesireg")` for more info +Run `revdepcheck::cloud_details(, "MetabolicSurv")` for more info
## In both -* checking whether package ‘llbayesireg’ can be installed ... ERROR +* checking whether package ‘MetabolicSurv’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/llbayesireg/new/llbayesireg.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/MetabolicSurv/new/MetabolicSurv.Rcheck/00install.out’ for details. ``` ## Installation @@ -4438,61 +3867,63 @@ Run `revdepcheck::cloud_details(, "llbayesireg")` for more info ### Devel ``` -* installing *source* package ‘llbayesireg’ ... -** package ‘llbayesireg’ successfully unpacked and MD5 sums checked +* installing *source* package ‘MetabolicSurv’ ... +** package ‘MetabolicSurv’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘llbayesireg’ -* removing ‘/tmp/workdir/llbayesireg/new/llbayesireg.Rcheck/llbayesireg’ +ERROR: lazy loading failed for package ‘MetabolicSurv’ +* removing ‘/tmp/workdir/MetabolicSurv/new/MetabolicSurv.Rcheck/MetabolicSurv’ ``` ### CRAN ``` -* installing *source* package ‘llbayesireg’ ... -** package ‘llbayesireg’ successfully unpacked and MD5 sums checked +* installing *source* package ‘MetabolicSurv’ ... +** package ‘MetabolicSurv’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘llbayesireg’ -* removing ‘/tmp/workdir/llbayesireg/old/llbayesireg.Rcheck/llbayesireg’ +ERROR: lazy loading failed for package ‘MetabolicSurv’ +* removing ‘/tmp/workdir/MetabolicSurv/old/MetabolicSurv.Rcheck/MetabolicSurv’ ``` -# LorenzRegression +# miWQS
-* Version: 1.0.0 -* GitHub: NA -* Source code: https://github.com/cran/LorenzRegression -* Date/Publication: 2023-02-28 17:32:34 UTC -* Number of recursive dependencies: 63 +* Version: 0.4.4 +* GitHub: https://github.com/phargarten2/miWQS +* Source code: https://github.com/cran/miWQS +* Date/Publication: 2021-04-02 21:50:02 UTC +* Number of recursive dependencies: 151 -Run `revdepcheck::cloud_details(, "LorenzRegression")` for more info +Run `revdepcheck::cloud_details(, "miWQS")` for more info
## In both -* checking whether package ‘LorenzRegression’ can be installed ... ERROR +* checking whether package ‘miWQS’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/LorenzRegression/new/LorenzRegression.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/miWQS/new/miWQS.Rcheck/00install.out’ for details. ``` ## Installation @@ -4500,17 +3931,10 @@ Run `revdepcheck::cloud_details(, "LorenzRegression")` for more info ### Devel ``` -* installing *source* package ‘LorenzRegression’ ... -** package ‘LorenzRegression’ successfully unpacked and MD5 sums checked +* installing *source* package ‘miWQS’ ... +** package ‘miWQS’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c GA_fitness.cpp -o GA_fitness.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c GA_meanrank.cpp -o GA_meanrank.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c PLR_derivative.cpp -o PLR_derivative.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c PLR_loss.cpp -o PLR_loss.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -... +** R ** data *** moving datasets to lazyload DB ** inst @@ -4519,25 +3943,18 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘LorenzRegression’ -* removing ‘/tmp/workdir/LorenzRegression/new/LorenzRegression.Rcheck/LorenzRegression’ +ERROR: lazy loading failed for package ‘miWQS’ +* removing ‘/tmp/workdir/miWQS/new/miWQS.Rcheck/miWQS’ ``` ### CRAN ``` -* installing *source* package ‘LorenzRegression’ ... -** package ‘LorenzRegression’ successfully unpacked and MD5 sums checked +* installing *source* package ‘miWQS’ ... +** package ‘miWQS’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c GA_fitness.cpp -o GA_fitness.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c GA_meanrank.cpp -o GA_meanrank.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c PLR_derivative.cpp -o PLR_derivative.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c PLR_loss.cpp -o PLR_loss.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -... +** R ** data *** moving datasets to lazyload DB ** inst @@ -4546,31 +3963,31 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘LorenzRegression’ -* removing ‘/tmp/workdir/LorenzRegression/old/LorenzRegression.Rcheck/LorenzRegression’ +ERROR: lazy loading failed for package ‘miWQS’ +* removing ‘/tmp/workdir/miWQS/old/miWQS.Rcheck/miWQS’ ``` -# lsirm12pl +# MRZero
-* Version: 1.3.1 +* Version: 0.2.0 * GitHub: NA -* Source code: https://github.com/cran/lsirm12pl -* Date/Publication: 2023-06-22 14:12:35 UTC -* Number of recursive dependencies: 123 +* Source code: https://github.com/cran/MRZero +* Date/Publication: 2024-04-14 09:30:03 UTC +* Number of recursive dependencies: 82 -Run `revdepcheck::cloud_details(, "lsirm12pl")` for more info +Run `revdepcheck::cloud_details(, "MRZero")` for more info
## In both -* checking whether package ‘lsirm12pl’ can be installed ... ERROR +* checking whether package ‘MRZero’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/lsirm12pl/new/lsirm12pl.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/MRZero/new/MRZero.Rcheck/00install.out’ for details. ``` ## Installation @@ -4578,77 +3995,57 @@ Run `revdepcheck::cloud_details(, "lsirm12pl")` for more info ### Devel ``` -* installing *source* package ‘lsirm12pl’ ... -** package ‘lsirm12pl’ successfully unpacked and MD5 sums checked +* installing *source* package ‘MRZero’ ... +** package ‘MRZero’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c log_likelihood.cpp -o log_likelihood.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl.cpp -o lsirm1pl.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl_fixed_gamma.cpp -o lsirm1pl_fixed_gamma.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl_fixed_gamma_mar.cpp -o lsirm1pl_fixed_gamma_mar.o -... ** R -** data -*** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘lsirm12pl’ -* removing ‘/tmp/workdir/lsirm12pl/new/lsirm12pl.Rcheck/lsirm12pl’ +ERROR: lazy loading failed for package ‘MRZero’ +* removing ‘/tmp/workdir/MRZero/new/MRZero.Rcheck/MRZero’ ``` ### CRAN ``` -* installing *source* package ‘lsirm12pl’ ... -** package ‘lsirm12pl’ successfully unpacked and MD5 sums checked +* installing *source* package ‘MRZero’ ... +** package ‘MRZero’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c log_likelihood.cpp -o log_likelihood.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl.cpp -o lsirm1pl.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl_fixed_gamma.cpp -o lsirm1pl_fixed_gamma.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl_fixed_gamma_mar.cpp -o lsirm1pl_fixed_gamma_mar.o -... ** R -** data -*** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘lsirm12pl’ -* removing ‘/tmp/workdir/lsirm12pl/old/lsirm12pl.Rcheck/lsirm12pl’ +ERROR: lazy loading failed for package ‘MRZero’ +* removing ‘/tmp/workdir/MRZero/old/MRZero.Rcheck/MRZero’ ``` -# mbsts +# Multiaovbay
-* Version: 3.0 +* Version: 0.1.0 * GitHub: NA -* Source code: https://github.com/cran/mbsts -* Date/Publication: 2023-01-07 01:10:02 UTC -* Number of recursive dependencies: 82 +* Source code: https://github.com/cran/Multiaovbay +* Date/Publication: 2023-03-17 17:20:02 UTC +* Number of recursive dependencies: 153 -Run `revdepcheck::cloud_details(, "mbsts")` for more info +Run `revdepcheck::cloud_details(, "Multiaovbay")` for more info
## In both -* checking whether package ‘mbsts’ can be installed ... ERROR +* checking whether package ‘Multiaovbay’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/mbsts/new/mbsts.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/Multiaovbay/new/Multiaovbay.Rcheck/00install.out’ for details. ``` ## Installation @@ -4656,59 +4053,57 @@ Run `revdepcheck::cloud_details(, "mbsts")` for more info ### Devel ``` -* installing *source* package ‘mbsts’ ... -** package ‘mbsts’ successfully unpacked and MD5 sums checked +* installing *source* package ‘Multiaovbay’ ... +** package ‘Multiaovbay’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘mbsts’ -* removing ‘/tmp/workdir/mbsts/new/mbsts.Rcheck/mbsts’ +ERROR: lazy loading failed for package ‘Multiaovbay’ +* removing ‘/tmp/workdir/Multiaovbay/new/Multiaovbay.Rcheck/Multiaovbay’ ``` ### CRAN ``` -* installing *source* package ‘mbsts’ ... -** package ‘mbsts’ successfully unpacked and MD5 sums checked +* installing *source* package ‘Multiaovbay’ ... +** package ‘Multiaovbay’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘mbsts’ -* removing ‘/tmp/workdir/mbsts/old/mbsts.Rcheck/mbsts’ +ERROR: lazy loading failed for package ‘Multiaovbay’ +* removing ‘/tmp/workdir/Multiaovbay/old/Multiaovbay.Rcheck/Multiaovbay’ ``` -# MendelianRandomization +# multilevelTools
-* Version: 0.10.0 -* GitHub: NA -* Source code: https://github.com/cran/MendelianRandomization -* Date/Publication: 2024-04-12 10:10:02 UTC -* Number of recursive dependencies: 88 - -Run `revdepcheck::cloud_details(, "MendelianRandomization")` for more info - +* Version: 0.1.1 +* GitHub: https://github.com/JWiley/multilevelTools +* Source code: https://github.com/cran/multilevelTools +* Date/Publication: 2020-03-04 09:50:02 UTC +* Number of recursive dependencies: 168 + +Run `revdepcheck::cloud_details(, "multilevelTools")` for more info +
## In both -* checking whether package ‘MendelianRandomization’ can be installed ... ERROR +* checking whether package ‘multilevelTools’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/MendelianRandomization/new/MendelianRandomization.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/multilevelTools/new/multilevelTools.Rcheck/00install.out’ for details. ``` ## Installation @@ -4716,71 +4111,69 @@ Run `revdepcheck::cloud_details(, "MendelianRandomization")` for more info ### Devel ``` -* installing *source* package ‘MendelianRandomization’ ... -** package ‘MendelianRandomization’ successfully unpacked and MD5 sums checked +* installing *source* package ‘multilevelTools’ ... +** package ‘multilevelTools’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c mvmrcML.cpp -o mvmrcML.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o MendelianRandomization.so RcppExports.o mvmrcML.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/MendelianRandomization/new/MendelianRandomization.Rcheck/00LOCK-MendelianRandomization/00new/MendelianRandomization/libs ** R ** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘MendelianRandomization’ -* removing ‘/tmp/workdir/MendelianRandomization/new/MendelianRandomization.Rcheck/MendelianRandomization’ +ERROR: lazy loading failed for package ‘multilevelTools’ +* removing ‘/tmp/workdir/multilevelTools/new/multilevelTools.Rcheck/multilevelTools’ ``` ### CRAN ``` -* installing *source* package ‘MendelianRandomization’ ... -** package ‘MendelianRandomization’ successfully unpacked and MD5 sums checked +* installing *source* package ‘multilevelTools’ ... +** package ‘multilevelTools’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c mvmrcML.cpp -o mvmrcML.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o MendelianRandomization.so RcppExports.o mvmrcML.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/MendelianRandomization/old/MendelianRandomization.Rcheck/00LOCK-MendelianRandomization/00new/MendelianRandomization/libs ** R ** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘MendelianRandomization’ -* removing ‘/tmp/workdir/MendelianRandomization/old/MendelianRandomization.Rcheck/MendelianRandomization’ +ERROR: lazy loading failed for package ‘multilevelTools’ +* removing ‘/tmp/workdir/multilevelTools/old/multilevelTools.Rcheck/multilevelTools’ ``` -# MetabolicSurv +# multinma
-* Version: 1.1.2 -* GitHub: https://github.com/OlajumokeEvangelina/MetabolicSurv -* Source code: https://github.com/cran/MetabolicSurv -* Date/Publication: 2021-06-11 08:30:02 UTC -* Number of recursive dependencies: 142 +* Version: 0.7.1 +* GitHub: https://github.com/dmphillippo/multinma +* Source code: https://github.com/cran/multinma +* Date/Publication: 2024-06-11 12:20:06 UTC +* Number of recursive dependencies: 152 -Run `revdepcheck::cloud_details(, "MetabolicSurv")` for more info +Run `revdepcheck::cloud_details(, "multinma")` for more info
## In both -* checking whether package ‘MetabolicSurv’ can be installed ... ERROR +* checking whether package ‘multinma’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/MetabolicSurv/new/MetabolicSurv.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/multinma/new/multinma.Rcheck/00install.out’ for details. ``` ## Installation @@ -4788,63 +4181,77 @@ Run `revdepcheck::cloud_details(, "MetabolicSurv")` for more info ### Devel ``` -* installing *source* package ‘MetabolicSurv’ ... -** package ‘MetabolicSurv’ successfully unpacked and MD5 sums checked +* installing *source* package ‘multinma’ ... +** package ‘multinma’ successfully unpacked and MD5 sums checked ** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘MetabolicSurv’ -* removing ‘/tmp/workdir/MetabolicSurv/new/MetabolicSurv.Rcheck/MetabolicSurv’ +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 + + +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_survival_mspline_namespace::model_survival_mspline; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_mspline.o] Error 1 +ERROR: compilation failed for package ‘multinma’ +* removing ‘/tmp/workdir/multinma/new/multinma.Rcheck/multinma’ ``` ### CRAN ``` -* installing *source* package ‘MetabolicSurv’ ... -** package ‘MetabolicSurv’ successfully unpacked and MD5 sums checked +* installing *source* package ‘multinma’ ... +** package ‘multinma’ successfully unpacked and MD5 sums checked ** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘MetabolicSurv’ -* removing ‘/tmp/workdir/MetabolicSurv/old/MetabolicSurv.Rcheck/MetabolicSurv’ +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 + + +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_survival_mspline_namespace::model_survival_mspline; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_mspline.o] Error 1 +ERROR: compilation failed for package ‘multinma’ +* removing ‘/tmp/workdir/multinma/old/multinma.Rcheck/multinma’ ``` -# miWQS +# NCA
-* Version: 0.4.4 -* GitHub: https://github.com/phargarten2/miWQS -* Source code: https://github.com/cran/miWQS -* Date/Publication: 2021-04-02 21:50:02 UTC -* Number of recursive dependencies: 152 +* Version: 4.0.1 +* GitHub: NA +* Source code: https://github.com/cran/NCA +* Date/Publication: 2024-02-23 09:30:15 UTC +* Number of recursive dependencies: 99 -Run `revdepcheck::cloud_details(, "miWQS")` for more info +Run `revdepcheck::cloud_details(, "NCA")` for more info
## In both -* checking whether package ‘miWQS’ can be installed ... ERROR +* checking whether package ‘NCA’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/miWQS/new/miWQS.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/NCA/new/NCA.Rcheck/00install.out’ for details. ``` ## Installation @@ -4852,63 +4259,59 @@ Run `revdepcheck::cloud_details(, "miWQS")` for more info ### Devel ``` -* installing *source* package ‘miWQS’ ... -** package ‘miWQS’ successfully unpacked and MD5 sums checked +* installing *source* package ‘NCA’ ... +** package ‘NCA’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data -*** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘miWQS’ -* removing ‘/tmp/workdir/miWQS/new/miWQS.Rcheck/miWQS’ +ERROR: lazy loading failed for package ‘NCA’ +* removing ‘/tmp/workdir/NCA/new/NCA.Rcheck/NCA’ ``` ### CRAN ``` -* installing *source* package ‘miWQS’ ... -** package ‘miWQS’ successfully unpacked and MD5 sums checked +* installing *source* package ‘NCA’ ... +** package ‘NCA’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data -*** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘miWQS’ -* removing ‘/tmp/workdir/miWQS/old/miWQS.Rcheck/miWQS’ +ERROR: lazy loading failed for package ‘NCA’ +* removing ‘/tmp/workdir/NCA/old/NCA.Rcheck/NCA’ ``` -# mlmts +# netcmc
-* Version: 1.1.1 +* Version: 1.0.2 * GitHub: NA -* Source code: https://github.com/cran/mlmts -* Date/Publication: 2023-01-22 21:30:02 UTC -* Number of recursive dependencies: 241 +* Source code: https://github.com/cran/netcmc +* Date/Publication: 2022-11-08 22:30:15 UTC +* Number of recursive dependencies: 61 -Run `revdepcheck::cloud_details(, "mlmts")` for more info +Run `revdepcheck::cloud_details(, "netcmc")` for more info
## In both -* checking whether package ‘mlmts’ can be installed ... ERROR +* checking whether package ‘netcmc’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/mlmts/new/mlmts.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/netcmc/new/netcmc.Rcheck/00install.out’ for details. ``` ## Installation @@ -4916,63 +4319,77 @@ Run `revdepcheck::cloud_details(, "mlmts")` for more info ### Devel ``` -* installing *source* package ‘mlmts’ ... -** package ‘mlmts’ successfully unpacked and MD5 sums checked +* installing *source* package ‘netcmc’ ... +** package ‘netcmc’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c choleskyDecompositionRcppConversion.cpp -o choleskyDecompositionRcppConversion.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleMatrixMultiplicationRcpp.cpp -o doubleMatrixMultiplicationRcpp.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleVectorMultiplicationRcpp.cpp -o doubleVectorMultiplicationRcpp.o +... +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c vectorVectorTransposeMultiplicationRcpp.cpp -o vectorVectorTransposeMultiplicationRcpp.o +g++ -std=gnu++11 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o netcmc.so RcppExports.o choleskyDecompositionRcppConversion.o doubleMatrixMultiplicationRcpp.o doubleVectorMultiplicationRcpp.o eigenValuesRcppConversion.o getDiagonalMatrix.o getExp.o getExpDividedByOnePlusExp.o getMeanCenteredRandomEffects.o getMultivariateBinomialNetworkLerouxDIC.o getMultivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariateGaussianNetworkLerouxDIC.o getMultivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariatePoissonNetworkLerouxDIC.o getMultivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getNonZeroEntries.o getSubvector.o getSubvectorIndecies.o getSumExpNetwork.o getSumExpNetworkIndecies.o getSumExpNetworkLeroux.o getSumExpNetworkLerouxIndecies.o getSumLogExp.o getSumLogExpIndecies.o getSumVector.o getTripletForm.o getUnivariateBinomialNetworkLerouxDIC.o getUnivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariateGaussianNetworkLerouxDIC.o getUnivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkDIC.o getUnivariatePoissonNetworkFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkLerouxDIC.o getUnivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getVectorMean.o matrixInverseRcppConversion.o matrixMatrixAdditionRcpp.o matrixMatrixSubtractionRcpp.o matrixVectorMultiplicationRcpp.o multivariateBinomialNetworkLerouxAllUpdate.o multivariateBinomialNetworkLerouxBetaUpdate.o multivariateBinomialNetworkLerouxRhoUpdate.o multivariateBinomialNetworkLerouxSingleUpdate.o multivariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o multivariateBinomialNetworkLerouxTauSquaredUpdate.o multivariateBinomialNetworkLerouxURandomEffectsUpdate.o multivariateBinomialNetworkLerouxVRandomEffectsUpdate.o multivariateBinomialNetworkLerouxVarianceCovarianceUUpdate.o multivariateBinomialNetworkRandAllUpdate.o multivariateBinomialNetworkRandSingleUpdate.o multivariateGaussianNetworkLerouxAllMHUpdate.o multivariateGaussianNetworkLerouxBetaUpdate.o multivariateGaussianNetworkLerouxRhoUpdate.o multivariateGaussianNetworkLerouxSigmaSquaredEUpdate.o multivariateGaussianNetworkLerouxSingleMHUpdate.o multivariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o multivariateGaussianNetworkLerouxTauSquaredUpdate.o multivariateGaussianNetworkLerouxURandomEffectsUpdate.o multivariateGaussianNetworkLerouxVarianceCovarianceUUpdate.o multivariateGaussianNetworkRandAllUpdate.o multivariateGaussianNetworkRandSingleUpdate.o multivariateGaussianNetworkRandVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxAllUpdate.o multivariatePoissonNetworkLerouxBetaUpdate.o multivariatePoissonNetworkLerouxRhoUpdate.o multivariatePoissonNetworkLerouxSingleUpdate.o multivariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o multivariatePoissonNetworkLerouxTauSquaredUpdate.o multivariatePoissonNetworkLerouxURandomEffectsUpdate.o multivariatePoissonNetworkLerouxVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxVarianceCovarianceUUpdate.o multivariatePoissonNetworkRandAllUpdate.o multivariatePoissonNetworkRandSingleUpdate.o sumMatrix.o univariateBinomialNetworkLerouxAllUpdate.o univariateBinomialNetworkLerouxBetaUpdate.o univariateBinomialNetworkLerouxRhoUpdate.o univariateBinomialNetworkLerouxSigmaSquaredUpdate.o univariateBinomialNetworkLerouxSingleUpdate.o univariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o univariateBinomialNetworkLerouxTauSquaredUpdate.o univariateBinomialNetworkLerouxURandomEffectsUpdate.o univariateGaussianNetworkLerouxAllMHUpdate.o univariateGaussianNetworkLerouxBetaUpdate.o univariateGaussianNetworkLerouxRhoUpdate.o univariateGaussianNetworkLerouxSigmaSquaredEUpdate.o univariateGaussianNetworkLerouxSigmaSquaredUUpdate.o univariateGaussianNetworkLerouxSingleMHUpdate.o univariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o univariateGaussianNetworkLerouxTauSquaredUpdate.o univariateGaussianNetworkLerouxURandomEffectsUpdate.o univariatePoissonNetworkLerouxAllUpdate.o univariatePoissonNetworkLerouxBetaUpdate.o univariatePoissonNetworkLerouxRhoUpdate.o univariatePoissonNetworkLerouxSigmaSquaredUpdate.o univariatePoissonNetworkLerouxSingleUpdate.o univariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o univariatePoissonNetworkLerouxTauSquaredUpdate.o univariatePoissonNetworkLerouxURandomEffectsUpdate.o vectorTransposeVectorMultiplicationRcpp.o vectorVectorTransposeMultiplicationRcpp.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/netcmc/new/netcmc.Rcheck/00LOCK-netcmc/00new/netcmc/libs ** R -** data -*** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading -Error : package or namespace load failed for ‘quantspec’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): +Error: package or namespace load failed for ‘MCMCpack’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Error: unable to load R code in package ‘mlmts’ Execution halted -ERROR: lazy loading failed for package ‘mlmts’ -* removing ‘/tmp/workdir/mlmts/new/mlmts.Rcheck/mlmts’ +ERROR: lazy loading failed for package ‘netcmc’ +* removing ‘/tmp/workdir/netcmc/new/netcmc.Rcheck/netcmc’ ``` ### CRAN ``` -* installing *source* package ‘mlmts’ ... -** package ‘mlmts’ successfully unpacked and MD5 sums checked +* installing *source* package ‘netcmc’ ... +** package ‘netcmc’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c choleskyDecompositionRcppConversion.cpp -o choleskyDecompositionRcppConversion.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleMatrixMultiplicationRcpp.cpp -o doubleMatrixMultiplicationRcpp.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleVectorMultiplicationRcpp.cpp -o doubleVectorMultiplicationRcpp.o +... +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c vectorVectorTransposeMultiplicationRcpp.cpp -o vectorVectorTransposeMultiplicationRcpp.o +g++ -std=gnu++11 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o netcmc.so RcppExports.o choleskyDecompositionRcppConversion.o doubleMatrixMultiplicationRcpp.o doubleVectorMultiplicationRcpp.o eigenValuesRcppConversion.o getDiagonalMatrix.o getExp.o getExpDividedByOnePlusExp.o getMeanCenteredRandomEffects.o getMultivariateBinomialNetworkLerouxDIC.o getMultivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariateGaussianNetworkLerouxDIC.o getMultivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariatePoissonNetworkLerouxDIC.o getMultivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getNonZeroEntries.o getSubvector.o getSubvectorIndecies.o getSumExpNetwork.o getSumExpNetworkIndecies.o getSumExpNetworkLeroux.o getSumExpNetworkLerouxIndecies.o getSumLogExp.o getSumLogExpIndecies.o getSumVector.o getTripletForm.o getUnivariateBinomialNetworkLerouxDIC.o getUnivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariateGaussianNetworkLerouxDIC.o getUnivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkDIC.o getUnivariatePoissonNetworkFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkLerouxDIC.o getUnivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getVectorMean.o matrixInverseRcppConversion.o matrixMatrixAdditionRcpp.o matrixMatrixSubtractionRcpp.o matrixVectorMultiplicationRcpp.o multivariateBinomialNetworkLerouxAllUpdate.o multivariateBinomialNetworkLerouxBetaUpdate.o multivariateBinomialNetworkLerouxRhoUpdate.o multivariateBinomialNetworkLerouxSingleUpdate.o multivariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o multivariateBinomialNetworkLerouxTauSquaredUpdate.o multivariateBinomialNetworkLerouxURandomEffectsUpdate.o multivariateBinomialNetworkLerouxVRandomEffectsUpdate.o multivariateBinomialNetworkLerouxVarianceCovarianceUUpdate.o multivariateBinomialNetworkRandAllUpdate.o multivariateBinomialNetworkRandSingleUpdate.o multivariateGaussianNetworkLerouxAllMHUpdate.o multivariateGaussianNetworkLerouxBetaUpdate.o multivariateGaussianNetworkLerouxRhoUpdate.o multivariateGaussianNetworkLerouxSigmaSquaredEUpdate.o multivariateGaussianNetworkLerouxSingleMHUpdate.o multivariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o multivariateGaussianNetworkLerouxTauSquaredUpdate.o multivariateGaussianNetworkLerouxURandomEffectsUpdate.o multivariateGaussianNetworkLerouxVarianceCovarianceUUpdate.o multivariateGaussianNetworkRandAllUpdate.o multivariateGaussianNetworkRandSingleUpdate.o multivariateGaussianNetworkRandVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxAllUpdate.o multivariatePoissonNetworkLerouxBetaUpdate.o multivariatePoissonNetworkLerouxRhoUpdate.o multivariatePoissonNetworkLerouxSingleUpdate.o multivariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o multivariatePoissonNetworkLerouxTauSquaredUpdate.o multivariatePoissonNetworkLerouxURandomEffectsUpdate.o multivariatePoissonNetworkLerouxVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxVarianceCovarianceUUpdate.o multivariatePoissonNetworkRandAllUpdate.o multivariatePoissonNetworkRandSingleUpdate.o sumMatrix.o univariateBinomialNetworkLerouxAllUpdate.o univariateBinomialNetworkLerouxBetaUpdate.o univariateBinomialNetworkLerouxRhoUpdate.o univariateBinomialNetworkLerouxSigmaSquaredUpdate.o univariateBinomialNetworkLerouxSingleUpdate.o univariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o univariateBinomialNetworkLerouxTauSquaredUpdate.o univariateBinomialNetworkLerouxURandomEffectsUpdate.o univariateGaussianNetworkLerouxAllMHUpdate.o univariateGaussianNetworkLerouxBetaUpdate.o univariateGaussianNetworkLerouxRhoUpdate.o univariateGaussianNetworkLerouxSigmaSquaredEUpdate.o univariateGaussianNetworkLerouxSigmaSquaredUUpdate.o univariateGaussianNetworkLerouxSingleMHUpdate.o univariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o univariateGaussianNetworkLerouxTauSquaredUpdate.o univariateGaussianNetworkLerouxURandomEffectsUpdate.o univariatePoissonNetworkLerouxAllUpdate.o univariatePoissonNetworkLerouxBetaUpdate.o univariatePoissonNetworkLerouxRhoUpdate.o univariatePoissonNetworkLerouxSigmaSquaredUpdate.o univariatePoissonNetworkLerouxSingleUpdate.o univariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o univariatePoissonNetworkLerouxTauSquaredUpdate.o univariatePoissonNetworkLerouxURandomEffectsUpdate.o vectorTransposeVectorMultiplicationRcpp.o vectorVectorTransposeMultiplicationRcpp.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/netcmc/old/netcmc.Rcheck/00LOCK-netcmc/00new/netcmc/libs ** R -** data -*** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading -Error : package or namespace load failed for ‘quantspec’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): +Error: package or namespace load failed for ‘MCMCpack’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Error: unable to load R code in package ‘mlmts’ Execution halted -ERROR: lazy loading failed for package ‘mlmts’ -* removing ‘/tmp/workdir/mlmts/old/mlmts.Rcheck/mlmts’ +ERROR: lazy loading failed for package ‘netcmc’ +* removing ‘/tmp/workdir/netcmc/old/netcmc.Rcheck/netcmc’ ``` -# MRZero +# NetworkChange
-* Version: 0.2.0 -* GitHub: NA -* Source code: https://github.com/cran/MRZero -* Date/Publication: 2024-04-14 09:30:03 UTC -* Number of recursive dependencies: 82 +* Version: 0.8 +* GitHub: https://github.com/jongheepark/NetworkChange +* Source code: https://github.com/cran/NetworkChange +* Date/Publication: 2022-03-04 07:30:02 UTC +* Number of recursive dependencies: 132 -Run `revdepcheck::cloud_details(, "MRZero")` for more info +Run `revdepcheck::cloud_details(, "NetworkChange")` for more info
## In both -* checking whether package ‘MRZero’ can be installed ... ERROR +* checking whether package ‘NetworkChange’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/MRZero/new/MRZero.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/NetworkChange/new/NetworkChange.Rcheck/00install.out’ for details. ``` ## Installation @@ -4980,57 +4397,57 @@ Run `revdepcheck::cloud_details(, "MRZero")` for more info ### Devel ``` -* installing *source* package ‘MRZero’ ... -** package ‘MRZero’ successfully unpacked and MD5 sums checked +* installing *source* package ‘NetworkChange’ ... +** package ‘NetworkChange’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘MCMCpack’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘MRZero’ -* removing ‘/tmp/workdir/MRZero/new/MRZero.Rcheck/MRZero’ +ERROR: lazy loading failed for package ‘NetworkChange’ +* removing ‘/tmp/workdir/NetworkChange/new/NetworkChange.Rcheck/NetworkChange’ ``` ### CRAN ``` -* installing *source* package ‘MRZero’ ... -** package ‘MRZero’ successfully unpacked and MD5 sums checked +* installing *source* package ‘NetworkChange’ ... +** package ‘NetworkChange’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘MCMCpack’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘MRZero’ -* removing ‘/tmp/workdir/MRZero/old/MRZero.Rcheck/MRZero’ +ERROR: lazy loading failed for package ‘NetworkChange’ +* removing ‘/tmp/workdir/NetworkChange/old/NetworkChange.Rcheck/NetworkChange’ ``` -# Multiaovbay +# nlmeVPC
-* Version: 0.1.0 +* Version: 2.6 * GitHub: NA -* Source code: https://github.com/cran/Multiaovbay -* Date/Publication: 2023-03-17 17:20:02 UTC -* Number of recursive dependencies: 161 +* Source code: https://github.com/cran/nlmeVPC +* Date/Publication: 2022-12-22 05:20:02 UTC +* Number of recursive dependencies: 77 -Run `revdepcheck::cloud_details(, "Multiaovbay")` for more info +Run `revdepcheck::cloud_details(, "nlmeVPC")` for more info
## In both -* checking whether package ‘Multiaovbay’ can be installed ... ERROR +* checking whether package ‘nlmeVPC’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/Multiaovbay/new/Multiaovbay.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/nlmeVPC/new/nlmeVPC.Rcheck/00install.out’ for details. ``` ## Installation @@ -5038,57 +4455,73 @@ Run `revdepcheck::cloud_details(, "Multiaovbay")` for more info ### Devel ``` -* installing *source* package ‘Multiaovbay’ ... -** package ‘Multiaovbay’ successfully unpacked and MD5 sums checked +* installing *source* package ‘nlmeVPC’ ... +** package ‘nlmeVPC’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Misc.cpp -o Misc.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o nlmeVPC.so Misc.o RcppExports.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/nlmeVPC/new/nlmeVPC.Rcheck/00LOCK-nlmeVPC/00new/nlmeVPC/libs ** R +** data ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.0 is required + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘Multiaovbay’ -* removing ‘/tmp/workdir/Multiaovbay/new/Multiaovbay.Rcheck/Multiaovbay’ +ERROR: lazy loading failed for package ‘nlmeVPC’ +* removing ‘/tmp/workdir/nlmeVPC/new/nlmeVPC.Rcheck/nlmeVPC’ ``` ### CRAN ``` -* installing *source* package ‘Multiaovbay’ ... -** package ‘Multiaovbay’ successfully unpacked and MD5 sums checked +* installing *source* package ‘nlmeVPC’ ... +** package ‘nlmeVPC’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Misc.cpp -o Misc.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o nlmeVPC.so Misc.o RcppExports.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/nlmeVPC/old/nlmeVPC.Rcheck/00LOCK-nlmeVPC/00new/nlmeVPC/libs ** R +** data ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.0 is required + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘Multiaovbay’ -* removing ‘/tmp/workdir/Multiaovbay/old/Multiaovbay.Rcheck/Multiaovbay’ +ERROR: lazy loading failed for package ‘nlmeVPC’ +* removing ‘/tmp/workdir/nlmeVPC/old/nlmeVPC.Rcheck/nlmeVPC’ ``` -# multilevelTools +# NMADiagT
-* Version: 0.1.1 -* GitHub: https://github.com/JWiley/multilevelTools -* Source code: https://github.com/cran/multilevelTools -* Date/Publication: 2020-03-04 09:50:02 UTC -* Number of recursive dependencies: 164 +* Version: 0.1.2 +* GitHub: NA +* Source code: https://github.com/cran/NMADiagT +* Date/Publication: 2020-02-26 07:00:02 UTC +* Number of recursive dependencies: 79 -Run `revdepcheck::cloud_details(, "multilevelTools")` for more info +Run `revdepcheck::cloud_details(, "NMADiagT")` for more info
## In both -* checking whether package ‘multilevelTools’ can be installed ... ERROR +* checking whether package ‘NMADiagT’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/multilevelTools/new/multilevelTools.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/NMADiagT/new/NMADiagT.Rcheck/00install.out’ for details. ``` ## Installation @@ -5096,8 +4529,8 @@ Run `revdepcheck::cloud_details(, "multilevelTools")` for more info ### Devel ``` -* installing *source* package ‘multilevelTools’ ... -** package ‘multilevelTools’ successfully unpacked and MD5 sums checked +* installing *source* package ‘NMADiagT’ ... +** package ‘NMADiagT’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst @@ -5106,16 +4539,16 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘multilevelTools’ -* removing ‘/tmp/workdir/multilevelTools/new/multilevelTools.Rcheck/multilevelTools’ +ERROR: lazy loading failed for package ‘NMADiagT’ +* removing ‘/tmp/workdir/NMADiagT/new/NMADiagT.Rcheck/NMADiagT’ ``` ### CRAN ``` -* installing *source* package ‘multilevelTools’ ... -** package ‘multilevelTools’ successfully unpacked and MD5 sums checked +* installing *source* package ‘NMADiagT’ ... +** package ‘NMADiagT’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst @@ -5124,31 +4557,31 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘multilevelTools’ -* removing ‘/tmp/workdir/multilevelTools/old/multilevelTools.Rcheck/multilevelTools’ +ERROR: lazy loading failed for package ‘NMADiagT’ +* removing ‘/tmp/workdir/NMADiagT/old/NMADiagT.Rcheck/NMADiagT’ ``` -# multinma +# optweight
-* Version: 0.7.0 -* GitHub: https://github.com/dmphillippo/multinma -* Source code: https://github.com/cran/multinma -* Date/Publication: 2024-05-07 15:40:02 UTC -* Number of recursive dependencies: 152 +* Version: 0.2.5 +* GitHub: NA +* Source code: https://github.com/cran/optweight +* Date/Publication: 2019-09-16 15:40:02 UTC +* Number of recursive dependencies: 55 -Run `revdepcheck::cloud_details(, "multinma")` for more info +Run `revdepcheck::cloud_details(, "optweight")` for more info
## In both -* checking whether package ‘multinma’ can be installed ... ERROR +* checking whether package ‘optweight’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/multinma/new/multinma.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/optweight/new/optweight.Rcheck/00install.out’ for details. ``` ## Installation @@ -5156,77 +4589,57 @@ Run `revdepcheck::cloud_details(, "multinma")` for more info ### Devel ``` -* installing *source* package ‘multinma’ ... -** package ‘multinma’ successfully unpacked and MD5 sums checked +* installing *source* package ‘optweight’ ... +** package ‘optweight’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_survival_mspline_namespace::model_survival_mspline; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_mspline.o] Error 1 -ERROR: compilation failed for package ‘multinma’ -* removing ‘/tmp/workdir/multinma/new/multinma.Rcheck/multinma’ +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘optweight’ +* removing ‘/tmp/workdir/optweight/new/optweight.Rcheck/optweight’ ``` ### CRAN ``` -* installing *source* package ‘multinma’ ... -** package ‘multinma’ successfully unpacked and MD5 sums checked +* installing *source* package ‘optweight’ ... +** package ‘optweight’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_survival_mspline_namespace::model_survival_mspline; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_mspline.o] Error 1 -ERROR: compilation failed for package ‘multinma’ -* removing ‘/tmp/workdir/multinma/old/multinma.Rcheck/multinma’ +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘optweight’ +* removing ‘/tmp/workdir/optweight/old/optweight.Rcheck/optweight’ ``` -# NCA +# OVtool
-* Version: 4.0.1 +* Version: 1.0.3 * GitHub: NA -* Source code: https://github.com/cran/NCA -* Date/Publication: 2024-02-23 09:30:15 UTC -* Number of recursive dependencies: 99 +* Source code: https://github.com/cran/OVtool +* Date/Publication: 2021-11-02 08:10:07 UTC +* Number of recursive dependencies: 157 -Run `revdepcheck::cloud_details(, "NCA")` for more info +Run `revdepcheck::cloud_details(, "OVtool")` for more info
## In both -* checking whether package ‘NCA’ can be installed ... ERROR +* checking whether package ‘OVtool’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/NCA/new/NCA.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/OVtool/new/OVtool.Rcheck/00install.out’ for details. ``` ## Installation @@ -5234,59 +4647,61 @@ Run `revdepcheck::cloud_details(, "NCA")` for more info ### Devel ``` -* installing *source* package ‘NCA’ ... -** package ‘NCA’ successfully unpacked and MD5 sums checked +* installing *source* package ‘OVtool’ ... +** package ‘OVtool’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data +*** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘twang’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘NCA’ -* removing ‘/tmp/workdir/NCA/new/NCA.Rcheck/NCA’ +ERROR: lazy loading failed for package ‘OVtool’ +* removing ‘/tmp/workdir/OVtool/new/OVtool.Rcheck/OVtool’ ``` ### CRAN ``` -* installing *source* package ‘NCA’ ... -** package ‘NCA’ successfully unpacked and MD5 sums checked +* installing *source* package ‘OVtool’ ... +** package ‘OVtool’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data +*** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘twang’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘NCA’ -* removing ‘/tmp/workdir/NCA/old/NCA.Rcheck/NCA’ +ERROR: lazy loading failed for package ‘OVtool’ +* removing ‘/tmp/workdir/OVtool/old/OVtool.Rcheck/OVtool’ ``` -# netcmc +# paths
-* Version: 1.0.2 +* Version: 0.1.1 * GitHub: NA -* Source code: https://github.com/cran/netcmc -* Date/Publication: 2022-11-08 22:30:15 UTC -* Number of recursive dependencies: 61 +* Source code: https://github.com/cran/paths +* Date/Publication: 2021-06-18 08:40:02 UTC +* Number of recursive dependencies: 102 -Run `revdepcheck::cloud_details(, "netcmc")` for more info +Run `revdepcheck::cloud_details(, "paths")` for more info
## In both -* checking whether package ‘netcmc’ can be installed ... ERROR +* checking whether package ‘paths’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/netcmc/new/netcmc.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/paths/new/paths.Rcheck/00install.out’ for details. ``` ## Installation @@ -5294,77 +4709,63 @@ Run `revdepcheck::cloud_details(, "netcmc")` for more info ### Devel ``` -* installing *source* package ‘netcmc’ ... -** package ‘netcmc’ successfully unpacked and MD5 sums checked +* installing *source* package ‘paths’ ... +** package ‘paths’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c choleskyDecompositionRcppConversion.cpp -o choleskyDecompositionRcppConversion.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleMatrixMultiplicationRcpp.cpp -o doubleMatrixMultiplicationRcpp.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleVectorMultiplicationRcpp.cpp -o doubleVectorMultiplicationRcpp.o -... -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c vectorVectorTransposeMultiplicationRcpp.cpp -o vectorVectorTransposeMultiplicationRcpp.o -g++ -std=gnu++11 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o netcmc.so RcppExports.o choleskyDecompositionRcppConversion.o doubleMatrixMultiplicationRcpp.o doubleVectorMultiplicationRcpp.o eigenValuesRcppConversion.o getDiagonalMatrix.o getExp.o getExpDividedByOnePlusExp.o getMeanCenteredRandomEffects.o getMultivariateBinomialNetworkLerouxDIC.o getMultivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariateGaussianNetworkLerouxDIC.o getMultivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariatePoissonNetworkLerouxDIC.o getMultivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getNonZeroEntries.o getSubvector.o getSubvectorIndecies.o getSumExpNetwork.o getSumExpNetworkIndecies.o getSumExpNetworkLeroux.o getSumExpNetworkLerouxIndecies.o getSumLogExp.o getSumLogExpIndecies.o getSumVector.o getTripletForm.o getUnivariateBinomialNetworkLerouxDIC.o getUnivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariateGaussianNetworkLerouxDIC.o getUnivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkDIC.o getUnivariatePoissonNetworkFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkLerouxDIC.o getUnivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getVectorMean.o matrixInverseRcppConversion.o matrixMatrixAdditionRcpp.o matrixMatrixSubtractionRcpp.o matrixVectorMultiplicationRcpp.o multivariateBinomialNetworkLerouxAllUpdate.o multivariateBinomialNetworkLerouxBetaUpdate.o multivariateBinomialNetworkLerouxRhoUpdate.o multivariateBinomialNetworkLerouxSingleUpdate.o multivariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o multivariateBinomialNetworkLerouxTauSquaredUpdate.o multivariateBinomialNetworkLerouxURandomEffectsUpdate.o multivariateBinomialNetworkLerouxVRandomEffectsUpdate.o multivariateBinomialNetworkLerouxVarianceCovarianceUUpdate.o multivariateBinomialNetworkRandAllUpdate.o multivariateBinomialNetworkRandSingleUpdate.o multivariateGaussianNetworkLerouxAllMHUpdate.o multivariateGaussianNetworkLerouxBetaUpdate.o multivariateGaussianNetworkLerouxRhoUpdate.o multivariateGaussianNetworkLerouxSigmaSquaredEUpdate.o multivariateGaussianNetworkLerouxSingleMHUpdate.o multivariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o multivariateGaussianNetworkLerouxTauSquaredUpdate.o multivariateGaussianNetworkLerouxURandomEffectsUpdate.o multivariateGaussianNetworkLerouxVarianceCovarianceUUpdate.o multivariateGaussianNetworkRandAllUpdate.o multivariateGaussianNetworkRandSingleUpdate.o multivariateGaussianNetworkRandVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxAllUpdate.o multivariatePoissonNetworkLerouxBetaUpdate.o multivariatePoissonNetworkLerouxRhoUpdate.o multivariatePoissonNetworkLerouxSingleUpdate.o multivariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o multivariatePoissonNetworkLerouxTauSquaredUpdate.o multivariatePoissonNetworkLerouxURandomEffectsUpdate.o multivariatePoissonNetworkLerouxVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxVarianceCovarianceUUpdate.o multivariatePoissonNetworkRandAllUpdate.o multivariatePoissonNetworkRandSingleUpdate.o sumMatrix.o univariateBinomialNetworkLerouxAllUpdate.o univariateBinomialNetworkLerouxBetaUpdate.o univariateBinomialNetworkLerouxRhoUpdate.o univariateBinomialNetworkLerouxSigmaSquaredUpdate.o univariateBinomialNetworkLerouxSingleUpdate.o univariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o univariateBinomialNetworkLerouxTauSquaredUpdate.o univariateBinomialNetworkLerouxURandomEffectsUpdate.o univariateGaussianNetworkLerouxAllMHUpdate.o univariateGaussianNetworkLerouxBetaUpdate.o univariateGaussianNetworkLerouxRhoUpdate.o univariateGaussianNetworkLerouxSigmaSquaredEUpdate.o univariateGaussianNetworkLerouxSigmaSquaredUUpdate.o univariateGaussianNetworkLerouxSingleMHUpdate.o univariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o univariateGaussianNetworkLerouxTauSquaredUpdate.o univariateGaussianNetworkLerouxURandomEffectsUpdate.o univariatePoissonNetworkLerouxAllUpdate.o univariatePoissonNetworkLerouxBetaUpdate.o univariatePoissonNetworkLerouxRhoUpdate.o univariatePoissonNetworkLerouxSigmaSquaredUpdate.o univariatePoissonNetworkLerouxSingleUpdate.o univariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o univariatePoissonNetworkLerouxTauSquaredUpdate.o univariatePoissonNetworkLerouxURandomEffectsUpdate.o vectorTransposeVectorMultiplicationRcpp.o vectorVectorTransposeMultiplicationRcpp.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/netcmc/new/netcmc.Rcheck/00LOCK-netcmc/00new/netcmc/libs ** R +** data +*** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘MCMCpack’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘netcmc’ -* removing ‘/tmp/workdir/netcmc/new/netcmc.Rcheck/netcmc’ +ERROR: lazy loading failed for package ‘paths’ +* removing ‘/tmp/workdir/paths/new/paths.Rcheck/paths’ ``` ### CRAN ``` -* installing *source* package ‘netcmc’ ... -** package ‘netcmc’ successfully unpacked and MD5 sums checked +* installing *source* package ‘paths’ ... +** package ‘paths’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c choleskyDecompositionRcppConversion.cpp -o choleskyDecompositionRcppConversion.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleMatrixMultiplicationRcpp.cpp -o doubleMatrixMultiplicationRcpp.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleVectorMultiplicationRcpp.cpp -o doubleVectorMultiplicationRcpp.o -... -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c vectorVectorTransposeMultiplicationRcpp.cpp -o vectorVectorTransposeMultiplicationRcpp.o -g++ -std=gnu++11 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o netcmc.so RcppExports.o choleskyDecompositionRcppConversion.o doubleMatrixMultiplicationRcpp.o doubleVectorMultiplicationRcpp.o eigenValuesRcppConversion.o getDiagonalMatrix.o getExp.o getExpDividedByOnePlusExp.o getMeanCenteredRandomEffects.o getMultivariateBinomialNetworkLerouxDIC.o getMultivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariateGaussianNetworkLerouxDIC.o getMultivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariatePoissonNetworkLerouxDIC.o getMultivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getNonZeroEntries.o getSubvector.o getSubvectorIndecies.o getSumExpNetwork.o getSumExpNetworkIndecies.o getSumExpNetworkLeroux.o getSumExpNetworkLerouxIndecies.o getSumLogExp.o getSumLogExpIndecies.o getSumVector.o getTripletForm.o getUnivariateBinomialNetworkLerouxDIC.o getUnivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariateGaussianNetworkLerouxDIC.o getUnivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkDIC.o getUnivariatePoissonNetworkFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkLerouxDIC.o getUnivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getVectorMean.o matrixInverseRcppConversion.o matrixMatrixAdditionRcpp.o matrixMatrixSubtractionRcpp.o matrixVectorMultiplicationRcpp.o multivariateBinomialNetworkLerouxAllUpdate.o multivariateBinomialNetworkLerouxBetaUpdate.o multivariateBinomialNetworkLerouxRhoUpdate.o multivariateBinomialNetworkLerouxSingleUpdate.o multivariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o multivariateBinomialNetworkLerouxTauSquaredUpdate.o multivariateBinomialNetworkLerouxURandomEffectsUpdate.o multivariateBinomialNetworkLerouxVRandomEffectsUpdate.o multivariateBinomialNetworkLerouxVarianceCovarianceUUpdate.o multivariateBinomialNetworkRandAllUpdate.o multivariateBinomialNetworkRandSingleUpdate.o multivariateGaussianNetworkLerouxAllMHUpdate.o multivariateGaussianNetworkLerouxBetaUpdate.o multivariateGaussianNetworkLerouxRhoUpdate.o multivariateGaussianNetworkLerouxSigmaSquaredEUpdate.o multivariateGaussianNetworkLerouxSingleMHUpdate.o multivariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o multivariateGaussianNetworkLerouxTauSquaredUpdate.o multivariateGaussianNetworkLerouxURandomEffectsUpdate.o multivariateGaussianNetworkLerouxVarianceCovarianceUUpdate.o multivariateGaussianNetworkRandAllUpdate.o multivariateGaussianNetworkRandSingleUpdate.o multivariateGaussianNetworkRandVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxAllUpdate.o multivariatePoissonNetworkLerouxBetaUpdate.o multivariatePoissonNetworkLerouxRhoUpdate.o multivariatePoissonNetworkLerouxSingleUpdate.o multivariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o multivariatePoissonNetworkLerouxTauSquaredUpdate.o multivariatePoissonNetworkLerouxURandomEffectsUpdate.o multivariatePoissonNetworkLerouxVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxVarianceCovarianceUUpdate.o multivariatePoissonNetworkRandAllUpdate.o multivariatePoissonNetworkRandSingleUpdate.o sumMatrix.o univariateBinomialNetworkLerouxAllUpdate.o univariateBinomialNetworkLerouxBetaUpdate.o univariateBinomialNetworkLerouxRhoUpdate.o univariateBinomialNetworkLerouxSigmaSquaredUpdate.o univariateBinomialNetworkLerouxSingleUpdate.o univariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o univariateBinomialNetworkLerouxTauSquaredUpdate.o univariateBinomialNetworkLerouxURandomEffectsUpdate.o univariateGaussianNetworkLerouxAllMHUpdate.o univariateGaussianNetworkLerouxBetaUpdate.o univariateGaussianNetworkLerouxRhoUpdate.o univariateGaussianNetworkLerouxSigmaSquaredEUpdate.o univariateGaussianNetworkLerouxSigmaSquaredUUpdate.o univariateGaussianNetworkLerouxSingleMHUpdate.o univariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o univariateGaussianNetworkLerouxTauSquaredUpdate.o univariateGaussianNetworkLerouxURandomEffectsUpdate.o univariatePoissonNetworkLerouxAllUpdate.o univariatePoissonNetworkLerouxBetaUpdate.o univariatePoissonNetworkLerouxRhoUpdate.o univariatePoissonNetworkLerouxSigmaSquaredUpdate.o univariatePoissonNetworkLerouxSingleUpdate.o univariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o univariatePoissonNetworkLerouxTauSquaredUpdate.o univariatePoissonNetworkLerouxURandomEffectsUpdate.o vectorTransposeVectorMultiplicationRcpp.o vectorVectorTransposeMultiplicationRcpp.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/netcmc/old/netcmc.Rcheck/00LOCK-netcmc/00new/netcmc/libs ** R +** data +*** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘MCMCpack’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘netcmc’ -* removing ‘/tmp/workdir/netcmc/old/netcmc.Rcheck/netcmc’ +ERROR: lazy loading failed for package ‘paths’ +* removing ‘/tmp/workdir/paths/old/paths.Rcheck/paths’ ``` -# NetworkChange +# PLMIX
-* Version: 0.8 -* GitHub: https://github.com/jongheepark/NetworkChange -* Source code: https://github.com/cran/NetworkChange -* Date/Publication: 2022-03-04 07:30:02 UTC -* Number of recursive dependencies: 132 +* Version: 2.1.1 +* GitHub: NA +* Source code: https://github.com/cran/PLMIX +* Date/Publication: 2019-09-04 11:50:02 UTC +* Number of recursive dependencies: 138 -Run `revdepcheck::cloud_details(, "NetworkChange")` for more info +Run `revdepcheck::cloud_details(, "PLMIX")` for more info
## In both -* checking whether package ‘NetworkChange’ can be installed ... ERROR +* checking whether package ‘PLMIX’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/NetworkChange/new/NetworkChange.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/PLMIX/new/PLMIX.Rcheck/00install.out’ for details. ``` ## Installation @@ -5372,57 +4773,77 @@ Run `revdepcheck::cloud_details(, "NetworkChange")` for more info ### Devel ``` -* installing *source* package ‘NetworkChange’ ... -** package ‘NetworkChange’ successfully unpacked and MD5 sums checked +* installing *source* package ‘PLMIX’ ... +** package ‘PLMIX’ successfully unpacked and MD5 sums checked ** using staged installation -** R +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompProbZpartial.cpp -o CompProbZpartial.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompRateP.cpp -o CompRateP.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompRateYpartial.cpp -o CompRateYpartial.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c Estep.cpp -o Estep.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c PLMIXsim.cpp -o PLMIXsim.o +... ** data +*** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘MCMCpack’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘NetworkChange’ -* removing ‘/tmp/workdir/NetworkChange/new/NetworkChange.Rcheck/NetworkChange’ +ERROR: lazy loading failed for package ‘PLMIX’ +* removing ‘/tmp/workdir/PLMIX/new/PLMIX.Rcheck/PLMIX’ ``` ### CRAN ``` -* installing *source* package ‘NetworkChange’ ... -** package ‘NetworkChange’ successfully unpacked and MD5 sums checked +* installing *source* package ‘PLMIX’ ... +** package ‘PLMIX’ successfully unpacked and MD5 sums checked ** using staged installation -** R +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompProbZpartial.cpp -o CompProbZpartial.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompRateP.cpp -o CompRateP.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompRateYpartial.cpp -o CompRateYpartial.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c Estep.cpp -o Estep.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c PLMIXsim.cpp -o PLMIXsim.o +... ** data +*** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘MCMCpack’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘NetworkChange’ -* removing ‘/tmp/workdir/NetworkChange/old/NetworkChange.Rcheck/NetworkChange’ +ERROR: lazy loading failed for package ‘PLMIX’ +* removing ‘/tmp/workdir/PLMIX/old/PLMIX.Rcheck/PLMIX’ ``` -# nlmeVPC +# popstudy
-* Version: 2.6 +* Version: 1.0.1 * GitHub: NA -* Source code: https://github.com/cran/nlmeVPC -* Date/Publication: 2022-12-22 05:20:02 UTC -* Number of recursive dependencies: 91 +* Source code: https://github.com/cran/popstudy +* Date/Publication: 2023-10-17 23:50:02 UTC +* Number of recursive dependencies: 240 -Run `revdepcheck::cloud_details(, "nlmeVPC")` for more info +Run `revdepcheck::cloud_details(, "popstudy")` for more info
## In both -* checking whether package ‘nlmeVPC’ can be installed ... ERROR +* checking whether package ‘popstudy’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/nlmeVPC/new/nlmeVPC.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/popstudy/new/popstudy.Rcheck/00install.out’ for details. ``` ## Installation @@ -5430,73 +4851,63 @@ Run `revdepcheck::cloud_details(, "nlmeVPC")` for more info ### Devel ``` -* installing *source* package ‘nlmeVPC’ ... -** package ‘nlmeVPC’ successfully unpacked and MD5 sums checked +* installing *source* package ‘popstudy’ ... +** package ‘popstudy’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Misc.cpp -o Misc.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++11 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o nlmeVPC.so Misc.o RcppExports.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/nlmeVPC/new/nlmeVPC.Rcheck/00LOCK-nlmeVPC/00new/nlmeVPC/libs ** R ** data +*** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘nlmeVPC’ -* removing ‘/tmp/workdir/nlmeVPC/new/nlmeVPC.Rcheck/nlmeVPC’ +ERROR: lazy loading failed for package ‘popstudy’ +* removing ‘/tmp/workdir/popstudy/new/popstudy.Rcheck/popstudy’ ``` ### CRAN ``` -* installing *source* package ‘nlmeVPC’ ... -** package ‘nlmeVPC’ successfully unpacked and MD5 sums checked +* installing *source* package ‘popstudy’ ... +** package ‘popstudy’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Misc.cpp -o Misc.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++11 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o nlmeVPC.so Misc.o RcppExports.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/nlmeVPC/old/nlmeVPC.Rcheck/00LOCK-nlmeVPC/00new/nlmeVPC/libs ** R ** data +*** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘nlmeVPC’ -* removing ‘/tmp/workdir/nlmeVPC/old/nlmeVPC.Rcheck/nlmeVPC’ +ERROR: lazy loading failed for package ‘popstudy’ +* removing ‘/tmp/workdir/popstudy/old/popstudy.Rcheck/popstudy’ ``` -# NMADiagT +# pould
-* Version: 0.1.2 +* Version: 1.0.1 * GitHub: NA -* Source code: https://github.com/cran/NMADiagT -* Date/Publication: 2020-02-26 07:00:02 UTC -* Number of recursive dependencies: 79 +* Source code: https://github.com/cran/pould +* Date/Publication: 2020-10-16 13:50:03 UTC +* Number of recursive dependencies: 104 -Run `revdepcheck::cloud_details(, "NMADiagT")` for more info +Run `revdepcheck::cloud_details(, "pould")` for more info
## In both -* checking whether package ‘NMADiagT’ can be installed ... ERROR +* checking whether package ‘pould’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/NMADiagT/new/NMADiagT.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/pould/new/pould.Rcheck/00install.out’ for details. ``` ## Installation @@ -5504,59 +4915,63 @@ Run `revdepcheck::cloud_details(, "NMADiagT")` for more info ### Devel ``` -* installing *source* package ‘NMADiagT’ ... -** package ‘NMADiagT’ successfully unpacked and MD5 sums checked +* installing *source* package ‘pould’ ... +** package ‘pould’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘NMADiagT’ -* removing ‘/tmp/workdir/NMADiagT/new/NMADiagT.Rcheck/NMADiagT’ +ERROR: lazy loading failed for package ‘pould’ +* removing ‘/tmp/workdir/pould/new/pould.Rcheck/pould’ ``` ### CRAN ``` -* installing *source* package ‘NMADiagT’ ... -** package ‘NMADiagT’ successfully unpacked and MD5 sums checked +* installing *source* package ‘pould’ ... +** package ‘pould’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘NMADiagT’ -* removing ‘/tmp/workdir/NMADiagT/old/NMADiagT.Rcheck/NMADiagT’ +ERROR: lazy loading failed for package ‘pould’ +* removing ‘/tmp/workdir/pould/old/pould.Rcheck/pould’ ``` -# optweight +# powerly
-* Version: 0.2.5 -* GitHub: NA -* Source code: https://github.com/cran/optweight -* Date/Publication: 2019-09-16 15:40:02 UTC -* Number of recursive dependencies: 55 +* Version: 1.8.6 +* GitHub: https://github.com/mihaiconstantin/powerly +* Source code: https://github.com/cran/powerly +* Date/Publication: 2022-09-09 14:10:01 UTC +* Number of recursive dependencies: 181 -Run `revdepcheck::cloud_details(, "optweight")` for more info +Run `revdepcheck::cloud_details(, "powerly")` for more info
## In both -* checking whether package ‘optweight’ can be installed ... ERROR +* checking whether package ‘powerly’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/optweight/new/optweight.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/powerly/new/powerly.Rcheck/00install.out’ for details. ``` ## Installation @@ -5564,57 +4979,69 @@ Run `revdepcheck::cloud_details(, "optweight")` for more info ### Devel ``` -* installing *source* package ‘optweight’ ... -** package ‘optweight’ successfully unpacked and MD5 sums checked +* installing *source* package ‘powerly’ ... +** package ‘powerly’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘optweight’ -* removing ‘/tmp/workdir/optweight/new/optweight.Rcheck/optweight’ +ERROR: lazy loading failed for package ‘powerly’ +* removing ‘/tmp/workdir/powerly/new/powerly.Rcheck/powerly’ ``` ### CRAN ``` -* installing *source* package ‘optweight’ ... -** package ‘optweight’ successfully unpacked and MD5 sums checked +* installing *source* package ‘powerly’ ... +** package ‘powerly’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘optweight’ -* removing ‘/tmp/workdir/optweight/old/optweight.Rcheck/optweight’ +ERROR: lazy loading failed for package ‘powerly’ +* removing ‘/tmp/workdir/powerly/old/powerly.Rcheck/powerly’ ``` -# OVtool +# pre
-* Version: 1.0.3 -* GitHub: NA -* Source code: https://github.com/cran/OVtool -* Date/Publication: 2021-11-02 08:10:07 UTC -* Number of recursive dependencies: 158 +* Version: 1.0.7 +* GitHub: https://github.com/marjoleinF/pre +* Source code: https://github.com/cran/pre +* Date/Publication: 2024-01-12 19:30:02 UTC +* Number of recursive dependencies: 151 -Run `revdepcheck::cloud_details(, "OVtool")` for more info +Run `revdepcheck::cloud_details(, "pre")` for more info
## In both -* checking whether package ‘OVtool’ can be installed ... ERROR +* checking whether package ‘pre’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/OVtool/new/OVtool.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/pre/new/pre.Rcheck/00install.out’ for details. ``` ## Installation @@ -5622,125 +5049,139 @@ Run `revdepcheck::cloud_details(, "OVtool")` for more info ### Devel ``` -* installing *source* package ‘OVtool’ ... -** package ‘OVtool’ successfully unpacked and MD5 sums checked +* installing *source* package ‘pre’ ... +** package ‘pre’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘twang’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘OVtool’ -* removing ‘/tmp/workdir/OVtool/new/OVtool.Rcheck/OVtool’ +ERROR: lazy loading failed for package ‘pre’ +* removing ‘/tmp/workdir/pre/new/pre.Rcheck/pre’ ``` ### CRAN ``` -* installing *source* package ‘OVtool’ ... -** package ‘OVtool’ successfully unpacked and MD5 sums checked +* installing *source* package ‘pre’ ... +** package ‘pre’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘twang’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘OVtool’ -* removing ‘/tmp/workdir/OVtool/old/OVtool.Rcheck/OVtool’ +ERROR: lazy loading failed for package ‘pre’ +* removing ‘/tmp/workdir/pre/old/pre.Rcheck/pre’ ``` -# paths +# ProFAST
-* Version: 0.1.1 -* GitHub: NA -* Source code: https://github.com/cran/paths -* Date/Publication: 2021-06-18 08:40:02 UTC -* Number of recursive dependencies: 103 +* Version: 1.4 +* GitHub: https://github.com/feiyoung/ProFAST +* Source code: https://github.com/cran/ProFAST +* Date/Publication: 2024-03-18 08:10:06 UTC +* Number of recursive dependencies: 245 -Run `revdepcheck::cloud_details(, "paths")` for more info +Run `revdepcheck::cloud_details(, "ProFAST")` for more info
-## In both - -* checking whether package ‘paths’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/paths/new/paths.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘paths’ ... -** package ‘paths’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘paths’ -* removing ‘/tmp/workdir/paths/new/paths.Rcheck/paths’ +* using log directory ‘/tmp/workdir/ProFAST/new/ProFAST.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘ProFAST/DESCRIPTION’ ... OK +... +* this is package ‘ProFAST’ version ‘1.4’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'DR.SC', 'PRECAST' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` ### CRAN ``` -* installing *source* package ‘paths’ ... -** package ‘paths’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘paths’ -* removing ‘/tmp/workdir/paths/old/paths.Rcheck/paths’ +* using log directory ‘/tmp/workdir/ProFAST/old/ProFAST.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘ProFAST/DESCRIPTION’ ... OK +... +* this is package ‘ProFAST’ version ‘1.4’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'DR.SC', 'PRECAST' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` -# PLMIX +# psbcSpeedUp
-* Version: 2.1.1 -* GitHub: NA -* Source code: https://github.com/cran/PLMIX -* Date/Publication: 2019-09-04 11:50:02 UTC -* Number of recursive dependencies: 151 +* Version: 2.0.7 +* GitHub: https://github.com/ocbe-uio/psbcSpeedUp +* Source code: https://github.com/cran/psbcSpeedUp +* Date/Publication: 2024-07-01 09:00:02 UTC +* Number of recursive dependencies: 129 -Run `revdepcheck::cloud_details(, "PLMIX")` for more info +Run `revdepcheck::cloud_details(, "psbcSpeedUp")` for more info
## In both -* checking whether package ‘PLMIX’ can be installed ... ERROR +* checking whether package ‘psbcSpeedUp’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/PLMIX/new/PLMIX.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/psbcSpeedUp/new/psbcSpeedUp.Rcheck/00install.out’ for details. ``` ## Installation @@ -5748,16 +5189,16 @@ Run `revdepcheck::cloud_details(, "PLMIX")` for more info ### Devel ``` -* installing *source* package ‘PLMIX’ ... -** package ‘PLMIX’ successfully unpacked and MD5 sums checked +* installing *source* package ‘psbcSpeedUp’ ... +** package ‘psbcSpeedUp’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompProbZpartial.cpp -o CompProbZpartial.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompRateP.cpp -o CompRateP.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompRateYpartial.cpp -o CompRateYpartial.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c Estep.cpp -o Estep.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c PLMIXsim.cpp -o PLMIXsim.o +checking whether the C++ compiler works... yes +checking for C++ compiler default output file name... a.out +checking for suffix of executables... +checking whether we are cross compiling... no +checking for suffix of object files... o +checking whether the compiler supports GNU C++... yes +checking whether g++ -std=gnu++17 accepts -g... yes ... ** data *** moving datasets to lazyload DB @@ -5767,24 +5208,24 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘PLMIX’ -* removing ‘/tmp/workdir/PLMIX/new/PLMIX.Rcheck/PLMIX’ +ERROR: lazy loading failed for package ‘psbcSpeedUp’ +* removing ‘/tmp/workdir/psbcSpeedUp/new/psbcSpeedUp.Rcheck/psbcSpeedUp’ ``` ### CRAN ``` -* installing *source* package ‘PLMIX’ ... -** package ‘PLMIX’ successfully unpacked and MD5 sums checked +* installing *source* package ‘psbcSpeedUp’ ... +** package ‘psbcSpeedUp’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompProbZpartial.cpp -o CompProbZpartial.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompRateP.cpp -o CompRateP.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompRateYpartial.cpp -o CompRateYpartial.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c Estep.cpp -o Estep.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c PLMIXsim.cpp -o PLMIXsim.o +checking whether the C++ compiler works... yes +checking for C++ compiler default output file name... a.out +checking for suffix of executables... +checking whether we are cross compiling... no +checking for suffix of object files... o +checking whether the compiler supports GNU C++... yes +checking whether g++ -std=gnu++17 accepts -g... yes ... ** data *** moving datasets to lazyload DB @@ -5794,31 +5235,31 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘PLMIX’ -* removing ‘/tmp/workdir/PLMIX/old/PLMIX.Rcheck/PLMIX’ +ERROR: lazy loading failed for package ‘psbcSpeedUp’ +* removing ‘/tmp/workdir/psbcSpeedUp/old/psbcSpeedUp.Rcheck/psbcSpeedUp’ ``` -# popstudy +# pscore
-* Version: 1.0.1 -* GitHub: NA -* Source code: https://github.com/cran/popstudy -* Date/Publication: 2023-10-17 23:50:02 UTC -* Number of recursive dependencies: 236 +* Version: 0.4.0 +* GitHub: https://github.com/JWiley/score-project +* Source code: https://github.com/cran/pscore +* Date/Publication: 2022-05-13 22:30:02 UTC +* Number of recursive dependencies: 169 -Run `revdepcheck::cloud_details(, "popstudy")` for more info +Run `revdepcheck::cloud_details(, "pscore")` for more info
## In both -* checking whether package ‘popstudy’ can be installed ... ERROR +* checking whether package ‘pscore’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/popstudy/new/popstudy.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/pscore/new/pscore.Rcheck/00install.out’ for details. ``` ## Installation @@ -5826,63 +5267,71 @@ Run `revdepcheck::cloud_details(, "popstudy")` for more info ### Devel ``` -* installing *source* package ‘popstudy’ ... -** package ‘popstudy’ successfully unpacked and MD5 sums checked +* installing *source* package ‘pscore’ ... +** package ‘pscore’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘popstudy’ -* removing ‘/tmp/workdir/popstudy/new/popstudy.Rcheck/popstudy’ +ERROR: lazy loading failed for package ‘pscore’ +* removing ‘/tmp/workdir/pscore/new/pscore.Rcheck/pscore’ ``` ### CRAN ``` -* installing *source* package ‘popstudy’ ... -** package ‘popstudy’ successfully unpacked and MD5 sums checked +* installing *source* package ‘pscore’ ... +** package ‘pscore’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘popstudy’ -* removing ‘/tmp/workdir/popstudy/old/popstudy.Rcheck/popstudy’ +ERROR: lazy loading failed for package ‘pscore’ +* removing ‘/tmp/workdir/pscore/old/pscore.Rcheck/pscore’ ``` -# pould +# psfmi
-* Version: 1.0.1 -* GitHub: NA -* Source code: https://github.com/cran/pould -* Date/Publication: 2020-10-16 13:50:03 UTC -* Number of recursive dependencies: 104 +* Version: 1.4.0 +* GitHub: https://github.com/mwheymans/psfmi +* Source code: https://github.com/cran/psfmi +* Date/Publication: 2023-06-17 22:40:02 UTC +* Number of recursive dependencies: 164 -Run `revdepcheck::cloud_details(, "pould")` for more info +Run `revdepcheck::cloud_details(, "psfmi")` for more info
## In both -* checking whether package ‘pould’ can be installed ... ERROR +* checking whether package ‘psfmi’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/pould/new/pould.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/psfmi/new/psfmi.Rcheck/00install.out’ for details. ``` ## Installation @@ -5890,8 +5339,8 @@ Run `revdepcheck::cloud_details(, "pould")` for more info ### Devel ``` -* installing *source* package ‘pould’ ... -** package ‘pould’ successfully unpacked and MD5 sums checked +* installing *source* package ‘psfmi’ ... +** package ‘psfmi’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data @@ -5902,16 +5351,16 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘pould’ -* removing ‘/tmp/workdir/pould/new/pould.Rcheck/pould’ +ERROR: lazy loading failed for package ‘psfmi’ +* removing ‘/tmp/workdir/psfmi/new/psfmi.Rcheck/psfmi’ ``` ### CRAN ``` -* installing *source* package ‘pould’ ... -** package ‘pould’ successfully unpacked and MD5 sums checked +* installing *source* package ‘psfmi’ ... +** package ‘psfmi’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data @@ -5922,31 +5371,31 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘pould’ -* removing ‘/tmp/workdir/pould/old/pould.Rcheck/pould’ +ERROR: lazy loading failed for package ‘psfmi’ +* removing ‘/tmp/workdir/psfmi/old/psfmi.Rcheck/psfmi’ ``` -# powerly +# qPCRtools
-* Version: 1.8.6 -* GitHub: https://github.com/mihaiconstantin/powerly -* Source code: https://github.com/cran/powerly -* Date/Publication: 2022-09-09 14:10:01 UTC -* Number of recursive dependencies: 176 +* Version: 1.0.1 +* GitHub: https://github.com/lixiang117423/qPCRtools +* Source code: https://github.com/cran/qPCRtools +* Date/Publication: 2023-11-02 13:10:05 UTC +* Number of recursive dependencies: 106 -Run `revdepcheck::cloud_details(, "powerly")` for more info +Run `revdepcheck::cloud_details(, "qPCRtools")` for more info
## In both -* checking whether package ‘powerly’ can be installed ... ERROR +* checking whether package ‘qPCRtools’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/powerly/new/powerly.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/qPCRtools/new/qPCRtools.Rcheck/00install.out’ for details. ``` ## Installation @@ -5954,59 +5403,59 @@ Run `revdepcheck::cloud_details(, "powerly")` for more info ### Devel ``` -* installing *source* package ‘powerly’ ... -** package ‘powerly’ successfully unpacked and MD5 sums checked +* installing *source* package ‘qPCRtools’ ... +** package ‘qPCRtools’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘powerly’ -* removing ‘/tmp/workdir/powerly/new/powerly.Rcheck/powerly’ +ERROR: lazy loading failed for package ‘qPCRtools’ +* removing ‘/tmp/workdir/qPCRtools/new/qPCRtools.Rcheck/qPCRtools’ ``` ### CRAN ``` -* installing *source* package ‘powerly’ ... -** package ‘powerly’ successfully unpacked and MD5 sums checked +* installing *source* package ‘qPCRtools’ ... +** package ‘qPCRtools’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘powerly’ -* removing ‘/tmp/workdir/powerly/old/powerly.Rcheck/powerly’ +ERROR: lazy loading failed for package ‘qPCRtools’ +* removing ‘/tmp/workdir/qPCRtools/old/qPCRtools.Rcheck/qPCRtools’ ``` -# pre +# qreport
-* Version: 1.0.7 -* GitHub: https://github.com/marjoleinF/pre -* Source code: https://github.com/cran/pre -* Date/Publication: 2024-01-12 19:30:02 UTC -* Number of recursive dependencies: 152 +* Version: 1.0-1 +* GitHub: NA +* Source code: https://github.com/cran/qreport +* Date/Publication: 2024-05-26 21:50:03 UTC +* Number of recursive dependencies: 77 -Run `revdepcheck::cloud_details(, "pre")` for more info +Run `revdepcheck::cloud_details(, "qreport")` for more info
## In both -* checking whether package ‘pre’ can be installed ... ERROR +* checking whether package ‘qreport’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/pre/new/pre.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/qreport/new/qreport.Rcheck/00install.out’ for details. ``` ## Installation @@ -6014,215 +5463,135 @@ Run `revdepcheck::cloud_details(, "pre")` for more info ### Devel ``` -* installing *source* package ‘pre’ ... -** package ‘pre’ successfully unpacked and MD5 sums checked +* installing *source* package ‘qreport’ ... +** package ‘qreport’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data -*** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘pre’ -* removing ‘/tmp/workdir/pre/new/pre.Rcheck/pre’ +ERROR: lazy loading failed for package ‘qreport’ +* removing ‘/tmp/workdir/qreport/new/qreport.Rcheck/qreport’ ``` ### CRAN ``` -* installing *source* package ‘pre’ ... -** package ‘pre’ successfully unpacked and MD5 sums checked +* installing *source* package ‘qreport’ ... +** package ‘qreport’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data -*** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘pre’ -* removing ‘/tmp/workdir/pre/old/pre.Rcheck/pre’ +ERROR: lazy loading failed for package ‘qreport’ +* removing ‘/tmp/workdir/qreport/old/qreport.Rcheck/qreport’ ``` -# PRECAST +# qris
-* Version: 1.6.5 -* GitHub: https://github.com/feiyoung/PRECAST -* Source code: https://github.com/cran/PRECAST -* Date/Publication: 2024-03-19 08:30:02 UTC -* Number of recursive dependencies: 225 +* Version: 1.1.1 +* GitHub: https://github.com/Kyuhyun07/qris +* Source code: https://github.com/cran/qris +* Date/Publication: 2024-03-05 14:40:03 UTC +* Number of recursive dependencies: 55 -Run `revdepcheck::cloud_details(, "PRECAST")` for more info +Run `revdepcheck::cloud_details(, "qris")` for more info
-## Error before installation +## In both -### Devel - -``` -* using log directory ‘/tmp/workdir/PRECAST/new/PRECAST.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘PRECAST/DESCRIPTION’ ... OK -... -* this is package ‘PRECAST’ version ‘1.6.5’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'Seurat', 'DR.SC' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/PRECAST/old/PRECAST.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘PRECAST/DESCRIPTION’ ... OK -... -* this is package ‘PRECAST’ version ‘1.6.5’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'Seurat', 'DR.SC' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -# ProFAST - -
- -* Version: 1.4 -* GitHub: https://github.com/feiyoung/ProFAST -* Source code: https://github.com/cran/ProFAST -* Date/Publication: 2024-03-18 08:10:06 UTC -* Number of recursive dependencies: 253 - -Run `revdepcheck::cloud_details(, "ProFAST")` for more info - -
+* checking whether package ‘qris’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/qris/new/qris.Rcheck/00install.out’ for details. + ``` -## Error before installation +## Installation ### Devel ``` -* using log directory ‘/tmp/workdir/ProFAST/new/ProFAST.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘ProFAST/DESCRIPTION’ ... OK +* installing *source* package ‘qris’ ... +** package ‘qris’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Amat.cpp -o Amat.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c ghat.cpp -o ghat.o ... -* this is package ‘ProFAST’ version ‘1.4’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'DR.SC', 'PRECAST', 'Seurat' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - +installing to /tmp/workdir/qris/new/qris.Rcheck/00LOCK-qris/00new/qris/libs +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘qris’ +* removing ‘/tmp/workdir/qris/new/qris.Rcheck/qris’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/ProFAST/old/ProFAST.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘ProFAST/DESCRIPTION’ ... OK +* installing *source* package ‘qris’ ... +** package ‘qris’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Amat.cpp -o Amat.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c ghat.cpp -o ghat.o ... -* this is package ‘ProFAST’ version ‘1.4’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'DR.SC', 'PRECAST', 'Seurat' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - +installing to /tmp/workdir/qris/old/qris.Rcheck/00LOCK-qris/00new/qris/libs +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘qris’ +* removing ‘/tmp/workdir/qris/old/qris.Rcheck/qris’ ``` -# pscore +# qte
-* Version: 0.4.0 -* GitHub: https://github.com/JWiley/score-project -* Source code: https://github.com/cran/pscore -* Date/Publication: 2022-05-13 22:30:02 UTC -* Number of recursive dependencies: 165 +* Version: 1.3.1 +* GitHub: NA +* Source code: https://github.com/cran/qte +* Date/Publication: 2022-09-01 14:30:02 UTC +* Number of recursive dependencies: 87 -Run `revdepcheck::cloud_details(, "pscore")` for more info +Run `revdepcheck::cloud_details(, "qte")` for more info
## In both -* checking whether package ‘pscore’ can be installed ... ERROR +* checking whether package ‘qte’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/pscore/new/pscore.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/qte/new/qte.Rcheck/00install.out’ for details. ``` ## Installation @@ -6230,61 +5599,63 @@ Run `revdepcheck::cloud_details(, "pscore")` for more info ### Devel ``` -* installing *source* package ‘pscore’ ... -** package ‘pscore’ successfully unpacked and MD5 sums checked +* installing *source* package ‘qte’ ... +** package ‘qte’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘pscore’ -* removing ‘/tmp/workdir/pscore/new/pscore.Rcheck/pscore’ +ERROR: lazy loading failed for package ‘qte’ +* removing ‘/tmp/workdir/qte/new/qte.Rcheck/qte’ ``` ### CRAN ``` -* installing *source* package ‘pscore’ ... -** package ‘pscore’ successfully unpacked and MD5 sums checked +* installing *source* package ‘qte’ ... +** package ‘qte’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘pscore’ -* removing ‘/tmp/workdir/pscore/old/pscore.Rcheck/pscore’ +ERROR: lazy loading failed for package ‘qte’ +* removing ‘/tmp/workdir/qte/old/qte.Rcheck/qte’ ``` -# psfmi +# quid
-* Version: 1.4.0 -* GitHub: https://github.com/mwheymans/psfmi -* Source code: https://github.com/cran/psfmi -* Date/Publication: 2023-06-17 22:40:02 UTC -* Number of recursive dependencies: 160 +* Version: 0.0.1 +* GitHub: NA +* Source code: https://github.com/cran/quid +* Date/Publication: 2021-12-09 09:00:02 UTC +* Number of recursive dependencies: 95 -Run `revdepcheck::cloud_details(, "psfmi")` for more info +Run `revdepcheck::cloud_details(, "quid")` for more info
## In both -* checking whether package ‘psfmi’ can be installed ... ERROR +* checking whether package ‘quid’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/psfmi/new/psfmi.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/quid/new/quid.Rcheck/00install.out’ for details. ``` ## Installation @@ -6292,8 +5663,8 @@ Run `revdepcheck::cloud_details(, "psfmi")` for more info ### Devel ``` -* installing *source* package ‘psfmi’ ... -** package ‘psfmi’ successfully unpacked and MD5 sums checked +* installing *source* package ‘quid’ ... +** package ‘quid’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data @@ -6304,16 +5675,16 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘psfmi’ -* removing ‘/tmp/workdir/psfmi/new/psfmi.Rcheck/psfmi’ +ERROR: lazy loading failed for package ‘quid’ +* removing ‘/tmp/workdir/quid/new/quid.Rcheck/quid’ ``` ### CRAN ``` -* installing *source* package ‘psfmi’ ... -** package ‘psfmi’ successfully unpacked and MD5 sums checked +* installing *source* package ‘quid’ ... +** package ‘quid’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data @@ -6324,31 +5695,31 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘psfmi’ -* removing ‘/tmp/workdir/psfmi/old/psfmi.Rcheck/psfmi’ +ERROR: lazy loading failed for package ‘quid’ +* removing ‘/tmp/workdir/quid/old/quid.Rcheck/quid’ ``` -# qreport +# RATest
-* Version: 1.0-0 -* GitHub: NA -* Source code: https://github.com/cran/qreport -* Date/Publication: 2023-09-12 22:10:02 UTC -* Number of recursive dependencies: 77 +* Version: 0.1.10 +* GitHub: https://github.com/ignaciomsarmiento/RATest +* Source code: https://github.com/cran/RATest +* Date/Publication: 2022-09-29 04:30:02 UTC +* Number of recursive dependencies: 54 -Run `revdepcheck::cloud_details(, "qreport")` for more info +Run `revdepcheck::cloud_details(, "RATest")` for more info
## In both -* checking whether package ‘qreport’ can be installed ... ERROR +* checking whether package ‘RATest’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/qreport/new/qreport.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/RATest/new/RATest.Rcheck/00install.out’ for details. ``` ## Installation @@ -6356,57 +5727,63 @@ Run `revdepcheck::cloud_details(, "qreport")` for more info ### Devel ``` -* installing *source* package ‘qreport’ ... -** package ‘qreport’ successfully unpacked and MD5 sums checked +* installing *source* package ‘RATest’ ... +** package ‘RATest’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘qreport’ -* removing ‘/tmp/workdir/qreport/new/qreport.Rcheck/qreport’ +ERROR: lazy loading failed for package ‘RATest’ +* removing ‘/tmp/workdir/RATest/new/RATest.Rcheck/RATest’ ``` ### CRAN ``` -* installing *source* package ‘qreport’ ... -** package ‘qreport’ successfully unpacked and MD5 sums checked +* installing *source* package ‘RATest’ ... +** package ‘RATest’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** byte-compile and prepare package for lazy loading +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘qreport’ -* removing ‘/tmp/workdir/qreport/old/qreport.Rcheck/qreport’ +ERROR: lazy loading failed for package ‘RATest’ +* removing ‘/tmp/workdir/RATest/old/RATest.Rcheck/RATest’ ``` -# qris +# RcmdrPlugin.RiskDemo
-* Version: 1.1.1 -* GitHub: https://github.com/Kyuhyun07/qris -* Source code: https://github.com/cran/qris -* Date/Publication: 2024-03-05 14:40:03 UTC -* Number of recursive dependencies: 55 +* Version: 3.2 +* GitHub: NA +* Source code: https://github.com/cran/RcmdrPlugin.RiskDemo +* Date/Publication: 2024-02-06 09:20:02 UTC +* Number of recursive dependencies: 200 -Run `revdepcheck::cloud_details(, "qris")` for more info +Run `revdepcheck::cloud_details(, "RcmdrPlugin.RiskDemo")` for more info
## In both -* checking whether package ‘qris’ can be installed ... ERROR +* checking whether package ‘RcmdrPlugin.RiskDemo’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/qris/new/qris.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/RcmdrPlugin.RiskDemo/new/RcmdrPlugin.RiskDemo.Rcheck/00install.out’ for details. ``` ## Installation @@ -6414,77 +5791,71 @@ Run `revdepcheck::cloud_details(, "qris")` for more info ### Devel ``` -* installing *source* package ‘qris’ ... -** package ‘qris’ successfully unpacked and MD5 sums checked +* installing *source* package ‘RcmdrPlugin.RiskDemo’ ... +** package ‘RcmdrPlugin.RiskDemo’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Amat.cpp -o Amat.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c ghat.cpp -o ghat.o -... -installing to /tmp/workdir/qris/new/qris.Rcheck/00LOCK-qris/00new/qris/libs ** R +** data ** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘qris’ -* removing ‘/tmp/workdir/qris/new/qris.Rcheck/qris’ +ERROR: lazy loading failed for package ‘RcmdrPlugin.RiskDemo’ +* removing ‘/tmp/workdir/RcmdrPlugin.RiskDemo/new/RcmdrPlugin.RiskDemo.Rcheck/RcmdrPlugin.RiskDemo’ ``` ### CRAN ``` -* installing *source* package ‘qris’ ... -** package ‘qris’ successfully unpacked and MD5 sums checked +* installing *source* package ‘RcmdrPlugin.RiskDemo’ ... +** package ‘RcmdrPlugin.RiskDemo’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Amat.cpp -o Amat.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c ghat.cpp -o ghat.o -... -installing to /tmp/workdir/qris/old/qris.Rcheck/00LOCK-qris/00new/qris/libs ** R +** data ** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘qris’ -* removing ‘/tmp/workdir/qris/old/qris.Rcheck/qris’ +ERROR: lazy loading failed for package ‘RcmdrPlugin.RiskDemo’ +* removing ‘/tmp/workdir/RcmdrPlugin.RiskDemo/old/RcmdrPlugin.RiskDemo.Rcheck/RcmdrPlugin.RiskDemo’ ``` -# qte +# rddtools
-* Version: 1.3.1 -* GitHub: NA -* Source code: https://github.com/cran/qte -* Date/Publication: 2022-09-01 14:30:02 UTC -* Number of recursive dependencies: 87 +* Version: 1.6.0 +* GitHub: https://github.com/bquast/rddtools +* Source code: https://github.com/cran/rddtools +* Date/Publication: 2022-01-10 12:42:49 UTC +* Number of recursive dependencies: 106 -Run `revdepcheck::cloud_details(, "qte")` for more info +Run `revdepcheck::cloud_details(, "rddtools")` for more info
## In both -* checking whether package ‘qte’ can be installed ... ERROR +* checking whether package ‘rddtools’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/qte/new/qte.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/rddtools/new/rddtools.Rcheck/00install.out’ for details. ``` ## Installation @@ -6492,63 +5863,59 @@ Run `revdepcheck::cloud_details(, "qte")` for more info ### Devel ``` -* installing *source* package ‘qte’ ... -** package ‘qte’ successfully unpacked and MD5 sums checked +* installing *source* package ‘rddtools’ ... +** package ‘rddtools’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘qte’ -* removing ‘/tmp/workdir/qte/new/qte.Rcheck/qte’ +ERROR: lazy loading failed for package ‘rddtools’ +* removing ‘/tmp/workdir/rddtools/new/rddtools.Rcheck/rddtools’ ``` ### CRAN ``` -* installing *source* package ‘qte’ ... -** package ‘qte’ successfully unpacked and MD5 sums checked +* installing *source* package ‘rddtools’ ... +** package ‘rddtools’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘qte’ -* removing ‘/tmp/workdir/qte/old/qte.Rcheck/qte’ +ERROR: lazy loading failed for package ‘rddtools’ +* removing ‘/tmp/workdir/rddtools/old/rddtools.Rcheck/rddtools’ ``` -# quid +# riskRegression
-* Version: 0.0.1 -* GitHub: NA -* Source code: https://github.com/cran/quid -* Date/Publication: 2021-12-09 09:00:02 UTC -* Number of recursive dependencies: 95 +* Version: 2023.12.21 +* GitHub: https://github.com/tagteam/riskRegression +* Source code: https://github.com/cran/riskRegression +* Date/Publication: 2023-12-19 17:00:02 UTC +* Number of recursive dependencies: 186 -Run `revdepcheck::cloud_details(, "quid")` for more info +Run `revdepcheck::cloud_details(, "riskRegression")` for more info
## In both -* checking whether package ‘quid’ can be installed ... ERROR +* checking whether package ‘riskRegression’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/quid/new/quid.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/riskRegression/new/riskRegression.Rcheck/00install.out’ for details. ``` ## Installation @@ -6556,63 +5923,82 @@ Run `revdepcheck::cloud_details(, "quid")` for more info ### Devel ``` -* installing *source* package ‘quid’ ... -** package ‘quid’ successfully unpacked and MD5 sums checked +* installing *source* package ‘riskRegression’ ... +** package ‘riskRegression’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c IC-Nelson-Aalen-cens-time.cpp -o IC-Nelson-Aalen-cens-time.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c aucCVFun.cpp -o aucCVFun.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c baseHaz.cpp -o baseHaz.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c calcSeCSC.cpp -o calcSeCSC.o +... ** R ** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘quid’ -* removing ‘/tmp/workdir/quid/new/quid.Rcheck/quid’ +ERROR: lazy loading failed for package ‘riskRegression’ +* removing ‘/tmp/workdir/riskRegression/new/riskRegression.Rcheck/riskRegression’ ``` ### CRAN ``` -* installing *source* package ‘quid’ ... -** package ‘quid’ successfully unpacked and MD5 sums checked +* installing *source* package ‘riskRegression’ ... +** package ‘riskRegression’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c IC-Nelson-Aalen-cens-time.cpp -o IC-Nelson-Aalen-cens-time.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c aucCVFun.cpp -o aucCVFun.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c baseHaz.cpp -o baseHaz.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c calcSeCSC.cpp -o calcSeCSC.o +... ** R ** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘quid’ -* removing ‘/tmp/workdir/quid/old/quid.Rcheck/quid’ +ERROR: lazy loading failed for package ‘riskRegression’ +* removing ‘/tmp/workdir/riskRegression/old/riskRegression.Rcheck/riskRegression’ ``` -# RATest +# rms
-* Version: 0.1.10 -* GitHub: https://github.com/ignaciomsarmiento/RATest -* Source code: https://github.com/cran/RATest -* Date/Publication: 2022-09-29 04:30:02 UTC -* Number of recursive dependencies: 54 +* Version: 6.8-1 +* GitHub: https://github.com/harrelfe/rms +* Source code: https://github.com/cran/rms +* Date/Publication: 2024-05-27 12:00:02 UTC +* Number of recursive dependencies: 145 -Run `revdepcheck::cloud_details(, "RATest")` for more info +Run `revdepcheck::cloud_details(, "rms")` for more info
## In both -* checking whether package ‘RATest’ can be installed ... ERROR +* checking whether package ‘rms’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/RATest/new/RATest.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/rms/new/rms.Rcheck/00install.out’ for details. + ``` + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘rmsb’ ``` ## Installation @@ -6620,63 +6006,77 @@ Run `revdepcheck::cloud_details(, "RATest")` for more info ### Devel ``` -* installing *source* package ‘RATest’ ... -** package ‘RATest’ successfully unpacked and MD5 sums checked +* installing *source* package ‘rms’ ... +** package ‘rms’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o +gfortran -fpic -g -O2 -c lrmfit.f -o lrmfit.o +gfortran -fpic -g -O2 -c mlmats.f -o mlmats.o +gfortran -fpic -g -O2 -c ormuv.f -o ormuv.o +... ** R -** data -*** moving datasets to lazyload DB +** demo ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘RATest’ -* removing ‘/tmp/workdir/RATest/new/RATest.Rcheck/RATest’ +ERROR: lazy loading failed for package ‘rms’ +* removing ‘/tmp/workdir/rms/new/rms.Rcheck/rms’ ``` ### CRAN ``` -* installing *source* package ‘RATest’ ... -** package ‘RATest’ successfully unpacked and MD5 sums checked +* installing *source* package ‘rms’ ... +** package ‘rms’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o +gfortran -fpic -g -O2 -c lrmfit.f -o lrmfit.o +gfortran -fpic -g -O2 -c mlmats.f -o mlmats.o +gfortran -fpic -g -O2 -c ormuv.f -o ormuv.o +... ** R -** data -*** moving datasets to lazyload DB +** demo ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘RATest’ -* removing ‘/tmp/workdir/RATest/old/RATest.Rcheck/RATest’ +ERROR: lazy loading failed for package ‘rms’ +* removing ‘/tmp/workdir/rms/old/rms.Rcheck/rms’ ``` -# RcmdrPlugin.RiskDemo +# rmsb
-* Version: 3.2 +* Version: 1.1-1 * GitHub: NA -* Source code: https://github.com/cran/RcmdrPlugin.RiskDemo -* Date/Publication: 2024-02-06 09:20:02 UTC -* Number of recursive dependencies: 208 +* Source code: https://github.com/cran/rmsb +* Date/Publication: 2024-07-08 11:10:03 UTC +* Number of recursive dependencies: 135 -Run `revdepcheck::cloud_details(, "RcmdrPlugin.RiskDemo")` for more info +Run `revdepcheck::cloud_details(, "rmsb")` for more info
## In both -* checking whether package ‘RcmdrPlugin.RiskDemo’ can be installed ... ERROR +* checking whether package ‘rmsb’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/RcmdrPlugin.RiskDemo/new/RcmdrPlugin.RiskDemo.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/rmsb/new/rmsb.Rcheck/00install.out’ for details. ``` ## Installation @@ -6684,61 +6084,51 @@ Run `revdepcheck::cloud_details(, "RcmdrPlugin.RiskDemo")` for more info ### Devel ``` -* installing *source* package ‘RcmdrPlugin.RiskDemo’ ... -** package ‘RcmdrPlugin.RiskDemo’ successfully unpacked and MD5 sums checked +* installing *source* package ‘rmsb’ ... +** package ‘rmsb’ successfully unpacked and MD5 sums checked ** using staged installation -** R -** data -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error in loadNamespace(x) : there is no package called ‘rstantools’ +Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted -ERROR: lazy loading failed for package ‘RcmdrPlugin.RiskDemo’ -* removing ‘/tmp/workdir/RcmdrPlugin.RiskDemo/new/RcmdrPlugin.RiskDemo.Rcheck/RcmdrPlugin.RiskDemo’ +ERROR: configuration failed for package ‘rmsb’ +* removing ‘/tmp/workdir/rmsb/new/rmsb.Rcheck/rmsb’ ``` ### CRAN ``` -* installing *source* package ‘RcmdrPlugin.RiskDemo’ ... -** package ‘RcmdrPlugin.RiskDemo’ successfully unpacked and MD5 sums checked +* installing *source* package ‘rmsb’ ... +** package ‘rmsb’ successfully unpacked and MD5 sums checked ** using staged installation -** R -** data -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error in loadNamespace(x) : there is no package called ‘rstantools’ +Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted -ERROR: lazy loading failed for package ‘RcmdrPlugin.RiskDemo’ -* removing ‘/tmp/workdir/RcmdrPlugin.RiskDemo/old/RcmdrPlugin.RiskDemo.Rcheck/RcmdrPlugin.RiskDemo’ +ERROR: configuration failed for package ‘rmsb’ +* removing ‘/tmp/workdir/rmsb/old/rmsb.Rcheck/rmsb’ ``` -# rddtools +# robmed
-* Version: 1.6.0 -* GitHub: https://github.com/bquast/rddtools -* Source code: https://github.com/cran/rddtools -* Date/Publication: 2022-01-10 12:42:49 UTC -* Number of recursive dependencies: 102 +* Version: 1.0.2 +* GitHub: https://github.com/aalfons/robmed +* Source code: https://github.com/cran/robmed +* Date/Publication: 2023-06-16 23:00:02 UTC +* Number of recursive dependencies: 60 -Run `revdepcheck::cloud_details(, "rddtools")` for more info +Run `revdepcheck::cloud_details(, "robmed")` for more info
## In both -* checking whether package ‘rddtools’ can be installed ... ERROR +* checking whether package ‘robmed’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/rddtools/new/rddtools.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/robmed/new/robmed.Rcheck/00install.out’ for details. ``` ## Installation @@ -6746,59 +6136,63 @@ Run `revdepcheck::cloud_details(, "rddtools")` for more info ### Devel ``` -* installing *source* package ‘rddtools’ ... -** package ‘rddtools’ successfully unpacked and MD5 sums checked +* installing *source* package ‘robmed’ ... +** package ‘robmed’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘rddtools’ -* removing ‘/tmp/workdir/rddtools/new/rddtools.Rcheck/rddtools’ +ERROR: lazy loading failed for package ‘robmed’ +* removing ‘/tmp/workdir/robmed/new/robmed.Rcheck/robmed’ ``` ### CRAN ``` -* installing *source* package ‘rddtools’ ... -** package ‘rddtools’ successfully unpacked and MD5 sums checked +* installing *source* package ‘robmed’ ... +** package ‘robmed’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘rddtools’ -* removing ‘/tmp/workdir/rddtools/old/rddtools.Rcheck/rddtools’ +ERROR: lazy loading failed for package ‘robmed’ +* removing ‘/tmp/workdir/robmed/old/robmed.Rcheck/robmed’ ``` -# riskRegression +# robmedExtra
-* Version: 2023.12.21 -* GitHub: https://github.com/tagteam/riskRegression -* Source code: https://github.com/cran/riskRegression -* Date/Publication: 2023-12-19 17:00:02 UTC -* Number of recursive dependencies: 186 +* Version: 0.1.0 +* GitHub: https://github.com/aalfons/robmedExtra +* Source code: https://github.com/cran/robmedExtra +* Date/Publication: 2023-06-02 14:40:02 UTC +* Number of recursive dependencies: 96 -Run `revdepcheck::cloud_details(, "riskRegression")` for more info +Run `revdepcheck::cloud_details(, "robmedExtra")` for more info
## In both -* checking whether package ‘riskRegression’ can be installed ... ERROR +* checking whether package ‘robmedExtra’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/riskRegression/new/riskRegression.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/robmedExtra/new/robmedExtra.Rcheck/00install.out’ for details. ``` ## Installation @@ -6806,158 +6200,119 @@ Run `revdepcheck::cloud_details(, "riskRegression")` for more info ### Devel ``` -* installing *source* package ‘riskRegression’ ... -** package ‘riskRegression’ successfully unpacked and MD5 sums checked +* installing *source* package ‘robmedExtra’ ... +** package ‘robmedExtra’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c IC-Nelson-Aalen-cens-time.cpp -o IC-Nelson-Aalen-cens-time.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c aucCVFun.cpp -o aucCVFun.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c baseHaz.cpp -o baseHaz.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c calcSeCSC.cpp -o calcSeCSC.o -... ** R -** data ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘robmed’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘riskRegression’ -* removing ‘/tmp/workdir/riskRegression/new/riskRegression.Rcheck/riskRegression’ +ERROR: lazy loading failed for package ‘robmedExtra’ +* removing ‘/tmp/workdir/robmedExtra/new/robmedExtra.Rcheck/robmedExtra’ ``` ### CRAN ``` -* installing *source* package ‘riskRegression’ ... -** package ‘riskRegression’ successfully unpacked and MD5 sums checked +* installing *source* package ‘robmedExtra’ ... +** package ‘robmedExtra’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c IC-Nelson-Aalen-cens-time.cpp -o IC-Nelson-Aalen-cens-time.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c aucCVFun.cpp -o aucCVFun.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c baseHaz.cpp -o baseHaz.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c calcSeCSC.cpp -o calcSeCSC.o -... ** R -** data ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘robmed’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘riskRegression’ -* removing ‘/tmp/workdir/riskRegression/old/riskRegression.Rcheck/riskRegression’ +ERROR: lazy loading failed for package ‘robmedExtra’ +* removing ‘/tmp/workdir/robmedExtra/old/robmedExtra.Rcheck/robmedExtra’ ``` -# rliger +# RPPanalyzer
-* Version: 2.0.1 -* GitHub: https://github.com/welch-lab/liger -* Source code: https://github.com/cran/rliger -* Date/Publication: 2024-04-04 23:20:02 UTC -* Number of recursive dependencies: 218 +* Version: 1.4.9 +* GitHub: NA +* Source code: https://github.com/cran/RPPanalyzer +* Date/Publication: 2024-01-25 11:00:02 UTC +* Number of recursive dependencies: 82 -Run `revdepcheck::cloud_details(, "rliger")` for more info +Run `revdepcheck::cloud_details(, "RPPanalyzer")` for more info
-## Error before installation - -### Devel +## In both -``` -* using log directory ‘/tmp/workdir/rliger/new/rliger.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘rliger/DESCRIPTION’ ... OK -... - [ FAIL 1 | WARN 0 | SKIP 5 | PASS 1234 ] - Error: Test failures - Execution halted -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘liger-vignette.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 2 ERRORs, 2 NOTEs +* checking whether package ‘RPPanalyzer’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/RPPanalyzer/new/RPPanalyzer.Rcheck/00install.out’ for details. + ``` +## Installation +### Devel +``` +* installing *source* package ‘RPPanalyzer’ ... +** package ‘RPPanalyzer’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘RPPanalyzer’ +* removing ‘/tmp/workdir/RPPanalyzer/new/RPPanalyzer.Rcheck/RPPanalyzer’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/rliger/old/rliger.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘rliger/DESCRIPTION’ ... OK -... - [ FAIL 1 | WARN 0 | SKIP 5 | PASS 1234 ] - Error: Test failures - Execution halted -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘liger-vignette.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 2 ERRORs, 2 NOTEs - - - +* installing *source* package ‘RPPanalyzer’ ... +** package ‘RPPanalyzer’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘RPPanalyzer’ +* removing ‘/tmp/workdir/RPPanalyzer/old/RPPanalyzer.Rcheck/RPPanalyzer’ ``` -# rms +# RQdeltaCT
-* Version: 6.8-0 -* GitHub: https://github.com/harrelfe/rms -* Source code: https://github.com/cran/rms -* Date/Publication: 2024-03-11 16:20:02 UTC -* Number of recursive dependencies: 154 +* Version: 1.3.0 +* GitHub: NA +* Source code: https://github.com/cran/RQdeltaCT +* Date/Publication: 2024-04-17 15:50:02 UTC +* Number of recursive dependencies: 165 -Run `revdepcheck::cloud_details(, "rms")` for more info +Run `revdepcheck::cloud_details(, "RQdeltaCT")` for more info
## In both -* checking whether package ‘rms’ can be installed ... ERROR +* checking whether package ‘RQdeltaCT’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/rms/new/rms.Rcheck/00install.out’ for details. - ``` - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘rmsb’ + See ‘/tmp/workdir/RQdeltaCT/new/RQdeltaCT.Rcheck/00install.out’ for details. ``` ## Installation @@ -6965,77 +6320,68 @@ Run `revdepcheck::cloud_details(, "rms")` for more info ### Devel ``` -* installing *source* package ‘rms’ ... -** package ‘rms’ successfully unpacked and MD5 sums checked +* installing *source* package ‘RQdeltaCT’ ... +** package ‘RQdeltaCT’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o -gfortran -fpic -g -O2 -c lrmfit.f -o lrmfit.o -gfortran -fpic -g -O2 -c mlmats.f -o mlmats.o -gfortran -fpic -g -O2 -c ormuv.f -o ormuv.o -... ** R -** demo +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘rms’ -* removing ‘/tmp/workdir/rms/new/rms.Rcheck/rms’ +ERROR: lazy loading failed for package ‘RQdeltaCT’ +* removing ‘/tmp/workdir/RQdeltaCT/new/RQdeltaCT.Rcheck/RQdeltaCT’ ``` ### CRAN ``` -* installing *source* package ‘rms’ ... -** package ‘rms’ successfully unpacked and MD5 sums checked +* installing *source* package ‘RQdeltaCT’ ... +** package ‘RQdeltaCT’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o -gfortran -fpic -g -O2 -c lrmfit.f -o lrmfit.o -gfortran -fpic -g -O2 -c mlmats.f -o mlmats.o -gfortran -fpic -g -O2 -c ormuv.f -o ormuv.o -... ** R -** demo +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘rms’ -* removing ‘/tmp/workdir/rms/old/rms.Rcheck/rms’ +ERROR: lazy loading failed for package ‘RQdeltaCT’ +* removing ‘/tmp/workdir/RQdeltaCT/old/RQdeltaCT.Rcheck/RQdeltaCT’ ``` -# rmsb +# scCustomize
-* Version: 1.1-0 -* GitHub: NA -* Source code: https://github.com/cran/rmsb -* Date/Publication: 2024-03-12 15:50:02 UTC -* Number of recursive dependencies: 144 +* Version: 2.1.2 +* GitHub: https://github.com/samuel-marsh/scCustomize +* Source code: https://github.com/cran/scCustomize +* Date/Publication: 2024-02-28 19:40:02 UTC +* Number of recursive dependencies: 267 -Run `revdepcheck::cloud_details(, "rmsb")` for more info +Run `revdepcheck::cloud_details(, "scCustomize")` for more info
## In both -* checking whether package ‘rmsb’ can be installed ... ERROR +* checking whether package ‘scCustomize’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/rmsb/new/rmsb.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/scCustomize/new/scCustomize.Rcheck/00install.out’ for details. + ``` + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘Nebulosa’ ``` ## Installation @@ -7043,51 +6389,59 @@ Run `revdepcheck::cloud_details(, "rmsb")` for more info ### Devel ``` -* installing *source* package ‘rmsb’ ... -** package ‘rmsb’ successfully unpacked and MD5 sums checked +* installing *source* package ‘scCustomize’ ... +** package ‘scCustomize’ successfully unpacked and MD5 sums checked ** using staged installation -Error in loadNamespace(x) : there is no package called ‘rstantools’ -Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required Execution halted -ERROR: configuration failed for package ‘rmsb’ -* removing ‘/tmp/workdir/rmsb/new/rmsb.Rcheck/rmsb’ +ERROR: lazy loading failed for package ‘scCustomize’ +* removing ‘/tmp/workdir/scCustomize/new/scCustomize.Rcheck/scCustomize’ ``` ### CRAN ``` -* installing *source* package ‘rmsb’ ... -** package ‘rmsb’ successfully unpacked and MD5 sums checked +* installing *source* package ‘scCustomize’ ... +** package ‘scCustomize’ successfully unpacked and MD5 sums checked ** using staged installation -Error in loadNamespace(x) : there is no package called ‘rstantools’ -Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required Execution halted -ERROR: configuration failed for package ‘rmsb’ -* removing ‘/tmp/workdir/rmsb/old/rmsb.Rcheck/rmsb’ +ERROR: lazy loading failed for package ‘scCustomize’ +* removing ‘/tmp/workdir/scCustomize/old/scCustomize.Rcheck/scCustomize’ ``` -# robmed +# SCdeconR
-* Version: 1.0.2 -* GitHub: https://github.com/aalfons/robmed -* Source code: https://github.com/cran/robmed -* Date/Publication: 2023-06-16 23:00:02 UTC -* Number of recursive dependencies: 60 +* Version: 1.0.0 +* GitHub: https://github.com/Liuy12/SCdeconR +* Source code: https://github.com/cran/SCdeconR +* Date/Publication: 2024-03-22 19:20:02 UTC +* Number of recursive dependencies: 236 -Run `revdepcheck::cloud_details(, "robmed")` for more info +Run `revdepcheck::cloud_details(, "SCdeconR")` for more info
## In both -* checking whether package ‘robmed’ can be installed ... ERROR +* checking whether package ‘SCdeconR’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/robmed/new/robmed.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/SCdeconR/new/SCdeconR.Rcheck/00install.out’ for details. ``` ## Installation @@ -7095,63 +6449,57 @@ Run `revdepcheck::cloud_details(, "robmed")` for more info ### Devel ``` -* installing *source* package ‘robmed’ ... -** package ‘robmed’ successfully unpacked and MD5 sums checked +* installing *source* package ‘SCdeconR’ ... +** package ‘SCdeconR’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required Execution halted -ERROR: lazy loading failed for package ‘robmed’ -* removing ‘/tmp/workdir/robmed/new/robmed.Rcheck/robmed’ +ERROR: lazy loading failed for package ‘SCdeconR’ +* removing ‘/tmp/workdir/SCdeconR/new/SCdeconR.Rcheck/SCdeconR’ ``` ### CRAN ``` -* installing *source* package ‘robmed’ ... -** package ‘robmed’ successfully unpacked and MD5 sums checked +* installing *source* package ‘SCdeconR’ ... +** package ‘SCdeconR’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required Execution halted -ERROR: lazy loading failed for package ‘robmed’ -* removing ‘/tmp/workdir/robmed/old/robmed.Rcheck/robmed’ +ERROR: lazy loading failed for package ‘SCdeconR’ +* removing ‘/tmp/workdir/SCdeconR/old/SCdeconR.Rcheck/SCdeconR’ ``` -# robmedExtra +# scGate
-* Version: 0.1.0 -* GitHub: https://github.com/aalfons/robmedExtra -* Source code: https://github.com/cran/robmedExtra -* Date/Publication: 2023-06-02 14:40:02 UTC -* Number of recursive dependencies: 96 +* Version: 1.6.2 +* GitHub: https://github.com/carmonalab/scGate +* Source code: https://github.com/cran/scGate +* Date/Publication: 2024-04-23 08:50:02 UTC +* Number of recursive dependencies: 179 -Run `revdepcheck::cloud_details(, "robmedExtra")` for more info +Run `revdepcheck::cloud_details(, "scGate")` for more info
## In both -* checking whether package ‘robmedExtra’ can be installed ... ERROR +* checking whether package ‘scGate’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/robmedExtra/new/robmedExtra.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/scGate/new/scGate.Rcheck/00install.out’ for details. ``` ## Installation @@ -7159,57 +6507,71 @@ Run `revdepcheck::cloud_details(, "robmedExtra")` for more info ### Devel ``` -* installing *source* package ‘robmedExtra’ ... -** package ‘robmedExtra’ successfully unpacked and MD5 sums checked +* installing *source* package ‘scGate’ ... +** package ‘scGate’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB +Warning: namespace ‘Seurat’ is not available and has been replaced +by .GlobalEnv when processing object ‘query.seurat’ +Warning: namespace ‘Seurat’ is not available and has been replaced +by .GlobalEnv when processing object ‘query.seurat’ ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘robmed’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘robmedExtra’ -* removing ‘/tmp/workdir/robmedExtra/new/robmedExtra.Rcheck/robmedExtra’ +ERROR: lazy loading failed for package ‘scGate’ +* removing ‘/tmp/workdir/scGate/new/scGate.Rcheck/scGate’ ``` ### CRAN ``` -* installing *source* package ‘robmedExtra’ ... -** package ‘robmedExtra’ successfully unpacked and MD5 sums checked +* installing *source* package ‘scGate’ ... +** package ‘scGate’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB +Warning: namespace ‘Seurat’ is not available and has been replaced +by .GlobalEnv when processing object ‘query.seurat’ +Warning: namespace ‘Seurat’ is not available and has been replaced +by .GlobalEnv when processing object ‘query.seurat’ ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘robmed’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘robmedExtra’ -* removing ‘/tmp/workdir/robmedExtra/old/robmedExtra.Rcheck/robmedExtra’ +ERROR: lazy loading failed for package ‘scGate’ +* removing ‘/tmp/workdir/scGate/old/scGate.Rcheck/scGate’ ``` -# RPPanalyzer +# SCIntRuler
-* Version: 1.4.9 -* GitHub: NA -* Source code: https://github.com/cran/RPPanalyzer -* Date/Publication: 2024-01-25 11:00:02 UTC -* Number of recursive dependencies: 82 +* Version: 0.99.6 +* GitHub: https://github.com/yuelyu21/SCIntRuler +* Source code: https://github.com/cran/SCIntRuler +* Date/Publication: 2024-07-12 15:20:08 UTC +* Number of recursive dependencies: 202 -Run `revdepcheck::cloud_details(, "RPPanalyzer")` for more info +Run `revdepcheck::cloud_details(, "SCIntRuler")` for more info
## In both -* checking whether package ‘RPPanalyzer’ can be installed ... ERROR +* checking whether package ‘SCIntRuler’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/RPPanalyzer/new/RPPanalyzer.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/SCIntRuler/new/SCIntRuler.Rcheck/00install.out’ for details. ``` ## Installation @@ -7217,61 +6579,77 @@ Run `revdepcheck::cloud_details(, "RPPanalyzer")` for more info ### Devel ``` -* installing *source* package ‘RPPanalyzer’ ... -** package ‘RPPanalyzer’ successfully unpacked and MD5 sums checked +* installing *source* package ‘SCIntRuler’ ... +** package ‘SCIntRuler’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c crossdist.cpp -o crossdist.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o SCIntRuler.so RcppExports.o crossdist.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/SCIntRuler/new/SCIntRuler.Rcheck/00LOCK-SCIntRuler/00new/SCIntRuler/libs ** R +... ** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘RPPanalyzer’ -* removing ‘/tmp/workdir/RPPanalyzer/new/RPPanalyzer.Rcheck/RPPanalyzer’ +ERROR: lazy loading failed for package ‘SCIntRuler’ +* removing ‘/tmp/workdir/SCIntRuler/new/SCIntRuler.Rcheck/SCIntRuler’ ``` ### CRAN ``` -* installing *source* package ‘RPPanalyzer’ ... -** package ‘RPPanalyzer’ successfully unpacked and MD5 sums checked +* installing *source* package ‘SCIntRuler’ ... +** package ‘SCIntRuler’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c crossdist.cpp -o crossdist.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o SCIntRuler.so RcppExports.o crossdist.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/SCIntRuler/old/SCIntRuler.Rcheck/00LOCK-SCIntRuler/00new/SCIntRuler/libs ** R +... ** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘RPPanalyzer’ -* removing ‘/tmp/workdir/RPPanalyzer/old/RPPanalyzer.Rcheck/RPPanalyzer’ +ERROR: lazy loading failed for package ‘SCIntRuler’ +* removing ‘/tmp/workdir/SCIntRuler/old/SCIntRuler.Rcheck/SCIntRuler’ ``` -# rstanarm +# scMappR
-* Version: 2.32.1 -* GitHub: https://github.com/stan-dev/rstanarm -* Source code: https://github.com/cran/rstanarm -* Date/Publication: 2024-01-18 23:00:03 UTC -* Number of recursive dependencies: 138 +* Version: 1.0.11 +* GitHub: NA +* Source code: https://github.com/cran/scMappR +* Date/Publication: 2023-06-30 08:40:08 UTC +* Number of recursive dependencies: 234 -Run `revdepcheck::cloud_details(, "rstanarm")` for more info +Run `revdepcheck::cloud_details(, "scMappR")` for more info
## In both -* checking whether package ‘rstanarm’ can be installed ... ERROR +* checking whether package ‘scMappR’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/rstanarm/new/rstanarm.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/scMappR/new/scMappR.Rcheck/00install.out’ for details. ``` ## Installation @@ -7279,662 +6657,118 @@ Run `revdepcheck::cloud_details(, "rstanarm")` for more info ### Devel ``` -* installing *source* package ‘rstanarm’ ... -** package ‘rstanarm’ successfully unpacked and MD5 sums checked +* installing *source* package ‘scMappR’ ... +** package ‘scMappR’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 -"/opt/R/4.3.1/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/bernoulli.stan -Wrote C++ file "stan_files/bernoulli.cc" - - -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stan_files/bernoulli.o] Error 1 -rm stan_files/bernoulli.cc -ERROR: compilation failed for package ‘rstanarm’ -* removing ‘/tmp/workdir/rstanarm/new/rstanarm.Rcheck/rstanarm’ +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘scMappR’ +* removing ‘/tmp/workdir/scMappR/new/scMappR.Rcheck/scMappR’ ``` ### CRAN ``` -* installing *source* package ‘rstanarm’ ... -** package ‘rstanarm’ successfully unpacked and MD5 sums checked +* installing *source* package ‘scMappR’ ... +** package ‘scMappR’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 -"/opt/R/4.3.1/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/bernoulli.stan -Wrote C++ file "stan_files/bernoulli.cc" - - -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stan_files/bernoulli.o] Error 1 -rm stan_files/bernoulli.cc -ERROR: compilation failed for package ‘rstanarm’ -* removing ‘/tmp/workdir/rstanarm/old/rstanarm.Rcheck/rstanarm’ +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘scMappR’ +* removing ‘/tmp/workdir/scMappR/old/scMappR.Rcheck/scMappR’ ``` -# scCustomize +# scpi
-* Version: 2.1.2 -* GitHub: https://github.com/samuel-marsh/scCustomize -* Source code: https://github.com/cran/scCustomize -* Date/Publication: 2024-02-28 19:40:02 UTC -* Number of recursive dependencies: 274 +* Version: 2.2.5 +* GitHub: NA +* Source code: https://github.com/cran/scpi +* Date/Publication: 2023-11-01 06:10:07 UTC +* Number of recursive dependencies: 98 -Run `revdepcheck::cloud_details(, "scCustomize")` for more info +Run `revdepcheck::cloud_details(, "scpi")` for more info
-## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/scCustomize/new/scCustomize.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scCustomize/DESCRIPTION’ ... OK -... -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'Seurat', 'SeuratObject' - -Package suggested but not available for checking: ‘Nebulosa’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/scCustomize/old/scCustomize.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scCustomize/DESCRIPTION’ ... OK -... -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'Seurat', 'SeuratObject' - -Package suggested but not available for checking: ‘Nebulosa’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -# SCdeconR - -
- -* Version: 1.0.0 -* GitHub: https://github.com/Liuy12/SCdeconR -* Source code: https://github.com/cran/SCdeconR -* Date/Publication: 2024-03-22 19:20:02 UTC -* Number of recursive dependencies: 235 - -Run `revdepcheck::cloud_details(, "SCdeconR")` for more info +## In both -
+* checking whether package ‘scpi’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/scpi/new/scpi.Rcheck/00install.out’ for details. + ``` -## Error before installation +## Installation ### Devel ``` -* using log directory ‘/tmp/workdir/SCdeconR/new/SCdeconR.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘SCdeconR/DESCRIPTION’ ... OK -... -* this is package ‘SCdeconR’ version ‘1.0.0’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/SCdeconR/old/SCdeconR.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘SCdeconR/DESCRIPTION’ ... OK -... -* this is package ‘SCdeconR’ version ‘1.0.0’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -# scDiffCom - -
- -* Version: 1.0.0 -* GitHub: NA -* Source code: https://github.com/cran/scDiffCom -* Date/Publication: 2023-11-03 18:40:02 UTC -* Number of recursive dependencies: 259 - -Run `revdepcheck::cloud_details(, "scDiffCom")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/scDiffCom/new/scDiffCom.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scDiffCom/DESCRIPTION’ ... OK -... -* this is package ‘scDiffCom’ version ‘1.0.0’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/scDiffCom/old/scDiffCom.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scDiffCom/DESCRIPTION’ ... OK -... -* this is package ‘scDiffCom’ version ‘1.0.0’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -# scGate - -
- -* Version: 1.6.2 -* GitHub: https://github.com/carmonalab/scGate -* Source code: https://github.com/cran/scGate -* Date/Publication: 2024-04-23 08:50:02 UTC -* Number of recursive dependencies: 178 - -Run `revdepcheck::cloud_details(, "scGate")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/scGate/new/scGate.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scGate/DESCRIPTION’ ... OK -... -* this is package ‘scGate’ version ‘1.6.2’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/scGate/old/scGate.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scGate/DESCRIPTION’ ... OK -... -* this is package ‘scGate’ version ‘1.6.2’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -# scMappR - -
- -* Version: 1.0.11 -* GitHub: NA -* Source code: https://github.com/cran/scMappR -* Date/Publication: 2023-06-30 08:40:08 UTC -* Number of recursive dependencies: 233 - -Run `revdepcheck::cloud_details(, "scMappR")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/scMappR/new/scMappR.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scMappR/DESCRIPTION’ ... OK -... -* this is package ‘scMappR’ version ‘1.0.11’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/scMappR/old/scMappR.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scMappR/DESCRIPTION’ ... OK -... -* this is package ‘scMappR’ version ‘1.0.11’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -# SCORPIUS - -
- -* Version: 1.0.9 -* GitHub: https://github.com/rcannood/SCORPIUS -* Source code: https://github.com/cran/SCORPIUS -* Date/Publication: 2023-08-07 17:30:05 UTC -* Number of recursive dependencies: 202 - -Run `revdepcheck::cloud_details(, "SCORPIUS")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/SCORPIUS/new/SCORPIUS.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘SCORPIUS/DESCRIPTION’ ... OK -... -Run `reticulate::py_last_error()` for details. -Execution halted - - ‘anndata.Rmd’ using ‘UTF-8’... failed - ‘ginhoux.Rmd’ using ‘UTF-8’... OK - ‘simulated-data.Rmd’ using ‘UTF-8’... OK - ‘singlecellexperiment.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 ERROR, 1 NOTE - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/SCORPIUS/old/SCORPIUS.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘SCORPIUS/DESCRIPTION’ ... OK -... -Run `reticulate::py_last_error()` for details. -Execution halted - - ‘anndata.Rmd’ using ‘UTF-8’... failed - ‘ginhoux.Rmd’ using ‘UTF-8’... OK - ‘simulated-data.Rmd’ using ‘UTF-8’... OK - ‘singlecellexperiment.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 ERROR, 1 NOTE - - - - - -``` -# scpoisson - -
- -* Version: 0.0.1 -* GitHub: NA -* Source code: https://github.com/cran/scpoisson -* Date/Publication: 2022-08-17 06:50:02 UTC -* Number of recursive dependencies: 203 - -Run `revdepcheck::cloud_details(, "scpoisson")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/scpoisson/new/scpoisson.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scpoisson/DESCRIPTION’ ... OK -... -* this is package ‘scpoisson’ version ‘0.0.1’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'Seurat', 'SeuratObject' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/scpoisson/old/scpoisson.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scpoisson/DESCRIPTION’ ... OK -... -* this is package ‘scpoisson’ version ‘0.0.1’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'Seurat', 'SeuratObject' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -# SCpubr - -
- -* Version: 2.0.2 -* GitHub: https://github.com/enblacar/SCpubr -* Source code: https://github.com/cran/SCpubr -* Date/Publication: 2023-10-11 09:50:02 UTC -* Number of recursive dependencies: 306 - -Run `revdepcheck::cloud_details(, "SCpubr")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/SCpubr/new/SCpubr.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘SCpubr/DESCRIPTION’ ... OK -... -* checking for unstated dependencies in ‘tests’ ... OK -* checking tests ... OK - Running ‘testthat.R’ -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... NONE - ‘reference_manual.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 2 NOTEs - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/SCpubr/old/SCpubr.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘SCpubr/DESCRIPTION’ ... OK +* installing *source* package ‘scpi’ ... +** package ‘scpi’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Warning in .recacheSubclasses(def@className, def, env) : + undefined subclass "pcorMatrix" of class "ConstVal"; definition not updated +Warning in .recacheSubclasses(def@className, def, env) : ... -* checking for unstated dependencies in ‘tests’ ... OK -* checking tests ... OK - Running ‘testthat.R’ -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... NONE - ‘reference_manual.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 2 NOTEs +Warning in .recacheSubclasses(def@className, def, env) : + undefined subclass "pcorMatrix" of class "ConstValORExpr"; definition not updated +Warning in .recacheSubclasses(def@className, def, env) : + undefined subclass "pcorMatrix" of class "ConstValORNULL"; definition not updated +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘scpi’ +* removing ‘/tmp/workdir/scpi/new/scpi.Rcheck/scpi’ +``` +### CRAN +``` +* installing *source* package ‘scpi’ ... +** package ‘scpi’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Warning in .recacheSubclasses(def@className, def, env) : + undefined subclass "pcorMatrix" of class "ConstVal"; definition not updated +Warning in .recacheSubclasses(def@className, def, env) : +... +Warning in .recacheSubclasses(def@className, def, env) : + undefined subclass "pcorMatrix" of class "ConstValORExpr"; definition not updated +Warning in .recacheSubclasses(def@className, def, env) : + undefined subclass "pcorMatrix" of class "ConstValORNULL"; definition not updated +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘scpi’ +* removing ‘/tmp/workdir/scpi/old/scpi.Rcheck/scpi’ ``` @@ -7946,71 +6780,73 @@ Status: 2 NOTEs * GitHub: NA * Source code: https://github.com/cran/scRNAstat * Date/Publication: 2021-09-22 08:10:02 UTC -* Number of recursive dependencies: 155 +* Number of recursive dependencies: 156 Run `revdepcheck::cloud_details(, "scRNAstat")` for more info -## Error before installation +## In both + +* checking whether package ‘scRNAstat’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/scRNAstat/new/scRNAstat.Rcheck/00install.out’ for details. + ``` + +## Installation ### Devel ``` -* using log directory ‘/tmp/workdir/scRNAstat/new/scRNAstat.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scRNAstat/DESCRIPTION’ ... OK +* installing *source* package ‘scRNAstat’ ... +** package ‘scRNAstat’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +Warning: namespace ‘Seurat’ is not available and has been replaced +by .GlobalEnv when processing object ‘AJ064_small_last_sce’ +Warning: namespace ‘SeuratObject’ is not available and has been replaced +by .GlobalEnv when processing object ‘AJ064_small_last_sce’ ... -* this is package ‘scRNAstat’ version ‘0.1.1’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - +by .GlobalEnv when processing object ‘AJ064_small_last_sce’ +Warning: namespace ‘DBI’ is not available and has been replaced +by .GlobalEnv when processing object ‘AJ064_small_last_sce’ +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘scRNAstat’ +* removing ‘/tmp/workdir/scRNAstat/new/scRNAstat.Rcheck/scRNAstat’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/scRNAstat/old/scRNAstat.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scRNAstat/DESCRIPTION’ ... OK +* installing *source* package ‘scRNAstat’ ... +** package ‘scRNAstat’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +Warning: namespace ‘Seurat’ is not available and has been replaced +by .GlobalEnv when processing object ‘AJ064_small_last_sce’ +Warning: namespace ‘SeuratObject’ is not available and has been replaced +by .GlobalEnv when processing object ‘AJ064_small_last_sce’ ... -* this is package ‘scRNAstat’ version ‘0.1.1’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - +by .GlobalEnv when processing object ‘AJ064_small_last_sce’ +Warning: namespace ‘DBI’ is not available and has been replaced +by .GlobalEnv when processing object ‘AJ064_small_last_sce’ +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘scRNAstat’ +* removing ‘/tmp/workdir/scRNAstat/old/scRNAstat.Rcheck/scRNAstat’ ``` @@ -8086,7 +6922,7 @@ ERROR: lazy loading failed for package ‘sectorgap’ * GitHub: NA * Source code: https://github.com/cran/SEERaBomb * Date/Publication: 2019-12-12 18:50:03 UTC -* Number of recursive dependencies: 184 +* Number of recursive dependencies: 185 Run `revdepcheck::cloud_details(, "SEERaBomb")` for more info @@ -8160,22 +6996,222 @@ ERROR: lazy loading failed for package ‘SEERaBomb’
-* Version: 0.2.0 -* GitHub: NA -* Source code: https://github.com/cran/semicmprskcoxmsm -* Date/Publication: 2022-04-29 23:40:02 UTC -* Number of recursive dependencies: 70 +* Version: 0.2.0 +* GitHub: NA +* Source code: https://github.com/cran/semicmprskcoxmsm +* Date/Publication: 2022-04-29 23:40:02 UTC +* Number of recursive dependencies: 70 + +Run `revdepcheck::cloud_details(, "semicmprskcoxmsm")` for more info + +
+ +## In both + +* checking whether package ‘semicmprskcoxmsm’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/semicmprskcoxmsm/new/semicmprskcoxmsm.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘semicmprskcoxmsm’ ... +** package ‘semicmprskcoxmsm’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘semicmprskcoxmsm’ +* removing ‘/tmp/workdir/semicmprskcoxmsm/new/semicmprskcoxmsm.Rcheck/semicmprskcoxmsm’ + + +``` +### CRAN + +``` +* installing *source* package ‘semicmprskcoxmsm’ ... +** package ‘semicmprskcoxmsm’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘semicmprskcoxmsm’ +* removing ‘/tmp/workdir/semicmprskcoxmsm/old/semicmprskcoxmsm.Rcheck/semicmprskcoxmsm’ + + +``` +# SensMap + +
+ +* Version: 0.7 +* GitHub: https://github.com/IbtihelRebhi/SensMap +* Source code: https://github.com/cran/SensMap +* Date/Publication: 2022-07-04 19:00:02 UTC +* Number of recursive dependencies: 145 + +Run `revdepcheck::cloud_details(, "SensMap")` for more info + +
+ +## In both + +* checking whether package ‘SensMap’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/SensMap/new/SensMap.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘SensMap’ ... +** package ‘SensMap’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘SensMap’ +* removing ‘/tmp/workdir/SensMap/new/SensMap.Rcheck/SensMap’ + + +``` +### CRAN + +``` +* installing *source* package ‘SensMap’ ... +** package ‘SensMap’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘SensMap’ +* removing ‘/tmp/workdir/SensMap/old/SensMap.Rcheck/SensMap’ + + +``` +# Seurat + +
+ +* Version: 5.1.0 +* GitHub: https://github.com/satijalab/seurat +* Source code: https://github.com/cran/Seurat +* Date/Publication: 2024-05-10 17:23:17 UTC +* Number of recursive dependencies: 266 + +Run `revdepcheck::cloud_details(, "Seurat")` for more info + +
+ +## In both + +* checking whether package ‘Seurat’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/Seurat/new/Seurat.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘Seurat’ ... +** package ‘Seurat’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c ModularityOptimizer.cpp -o ModularityOptimizer.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RModularityOptimizer.cpp -o RModularityOptimizer.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required +Execution halted +ERROR: lazy loading failed for package ‘Seurat’ +* removing ‘/tmp/workdir/Seurat/new/Seurat.Rcheck/Seurat’ + + +``` +### CRAN + +``` +* installing *source* package ‘Seurat’ ... +** package ‘Seurat’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c ModularityOptimizer.cpp -o ModularityOptimizer.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RModularityOptimizer.cpp -o RModularityOptimizer.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required +Execution halted +ERROR: lazy loading failed for package ‘Seurat’ +* removing ‘/tmp/workdir/Seurat/old/Seurat.Rcheck/Seurat’ + + +``` +# shinyTempSignal + +
+ +* Version: 0.0.8 +* GitHub: https://github.com/YuLab-SMU/shinyTempSignal +* Source code: https://github.com/cran/shinyTempSignal +* Date/Publication: 2024-03-06 08:00:02 UTC +* Number of recursive dependencies: 137 -Run `revdepcheck::cloud_details(, "semicmprskcoxmsm")` for more info +Run `revdepcheck::cloud_details(, "shinyTempSignal")` for more info
## In both -* checking whether package ‘semicmprskcoxmsm’ can be installed ... ERROR +* checking whether package ‘shinyTempSignal’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/semicmprskcoxmsm/new/semicmprskcoxmsm.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/shinyTempSignal/new/shinyTempSignal.Rcheck/00install.out’ for details. ``` ## Installation @@ -8183,57 +7219,59 @@ Run `revdepcheck::cloud_details(, "semicmprskcoxmsm")` for more info ### Devel ``` -* installing *source* package ‘semicmprskcoxmsm’ ... -** package ‘semicmprskcoxmsm’ successfully unpacked and MD5 sums checked +* installing *source* package ‘shinyTempSignal’ ... +** package ‘shinyTempSignal’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘semicmprskcoxmsm’ -* removing ‘/tmp/workdir/semicmprskcoxmsm/new/semicmprskcoxmsm.Rcheck/semicmprskcoxmsm’ +ERROR: lazy loading failed for package ‘shinyTempSignal’ +* removing ‘/tmp/workdir/shinyTempSignal/new/shinyTempSignal.Rcheck/shinyTempSignal’ ``` ### CRAN ``` -* installing *source* package ‘semicmprskcoxmsm’ ... -** package ‘semicmprskcoxmsm’ successfully unpacked and MD5 sums checked +* installing *source* package ‘shinyTempSignal’ ... +** package ‘shinyTempSignal’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘semicmprskcoxmsm’ -* removing ‘/tmp/workdir/semicmprskcoxmsm/old/semicmprskcoxmsm.Rcheck/semicmprskcoxmsm’ +ERROR: lazy loading failed for package ‘shinyTempSignal’ +* removing ‘/tmp/workdir/shinyTempSignal/old/shinyTempSignal.Rcheck/shinyTempSignal’ ``` -# SensMap +# sievePH
-* Version: 0.7 -* GitHub: https://github.com/IbtihelRebhi/SensMap -* Source code: https://github.com/cran/SensMap -* Date/Publication: 2022-07-04 19:00:02 UTC -* Number of recursive dependencies: 146 +* Version: 1.1 +* GitHub: https://github.com/mjuraska/sievePH +* Source code: https://github.com/cran/sievePH +* Date/Publication: 2024-05-17 23:40:02 UTC +* Number of recursive dependencies: 72 -Run `revdepcheck::cloud_details(, "SensMap")` for more info +Run `revdepcheck::cloud_details(, "sievePH")` for more info
## In both -* checking whether package ‘SensMap’ can be installed ... ERROR +* checking whether package ‘sievePH’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/SensMap/new/SensMap.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/sievePH/new/sievePH.Rcheck/00install.out’ for details. ``` ## Installation @@ -8241,40 +7279,46 @@ Run `revdepcheck::cloud_details(, "SensMap")` for more info ### Devel ``` -* installing *source* package ‘SensMap’ ... -** package ‘SensMap’ successfully unpacked and MD5 sums checked +* installing *source* package ‘sievePH’ ... +** package ‘sievePH’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c kernel_sievePH_utils.cpp -o kernel_sievePH_utils.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o sievePH.so RcppExports.o kernel_sievePH_utils.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/sievePH/new/sievePH.Rcheck/00LOCK-sievePH/00new/sievePH/libs ** R -** data -*** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘SensMap’ -* removing ‘/tmp/workdir/SensMap/new/SensMap.Rcheck/SensMap’ +ERROR: lazy loading failed for package ‘sievePH’ +* removing ‘/tmp/workdir/sievePH/new/sievePH.Rcheck/sievePH’ ``` ### CRAN ``` -* installing *source* package ‘SensMap’ ... -** package ‘SensMap’ successfully unpacked and MD5 sums checked +* installing *source* package ‘sievePH’ ... +** package ‘sievePH’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c kernel_sievePH_utils.cpp -o kernel_sievePH_utils.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o sievePH.so RcppExports.o kernel_sievePH_utils.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/sievePH/old/sievePH.Rcheck/00LOCK-sievePH/00new/sievePH/libs ** R -** data -*** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘SensMap’ -* removing ‘/tmp/workdir/SensMap/old/SensMap.Rcheck/SensMap’ +ERROR: lazy loading failed for package ‘sievePH’ +* removing ‘/tmp/workdir/sievePH/old/sievePH.Rcheck/sievePH’ ``` @@ -8286,71 +7330,73 @@ ERROR: lazy loading failed for package ‘SensMap’ * GitHub: https://github.com/stuart-lab/signac * Source code: https://github.com/cran/Signac * Date/Publication: 2024-04-04 02:42:57 UTC -* Number of recursive dependencies: 249 +* Number of recursive dependencies: 250 Run `revdepcheck::cloud_details(, "Signac")` for more info -## Error before installation +## In both + +* checking whether package ‘Signac’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/Signac/new/Signac.Rcheck/00install.out’ for details. + ``` + +## Installation ### Devel ``` -* using log directory ‘/tmp/workdir/Signac/new/Signac.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘Signac/DESCRIPTION’ ... OK +* installing *source* package ‘Signac’ ... +** package ‘Signac’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c filter.cpp -o filter.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c group.cpp -o group.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c split.cpp -o split.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c validate.cpp -o validate.o ... -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘SeuratObject’ - -Package suggested but not available for checking: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘Signac’ +* removing ‘/tmp/workdir/Signac/new/Signac.Rcheck/Signac’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/Signac/old/Signac.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘Signac/DESCRIPTION’ ... OK +* installing *source* package ‘Signac’ ... +** package ‘Signac’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c filter.cpp -o filter.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c group.cpp -o group.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c split.cpp -o split.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c validate.cpp -o validate.o ... -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘SeuratObject’ - -Package suggested but not available for checking: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘Signac’ +* removing ‘/tmp/workdir/Signac/old/Signac.Rcheck/Signac’ ``` @@ -8362,7 +7408,7 @@ Status: 1 ERROR * GitHub: https://github.com/arcaldwell49/SimplyAgree * Source code: https://github.com/cran/SimplyAgree * Date/Publication: 2024-03-21 14:20:06 UTC -* Number of recursive dependencies: 111 +* Number of recursive dependencies: 115 Run `revdepcheck::cloud_details(, "SimplyAgree")` for more info @@ -8389,6 +7435,11 @@ Run `revdepcheck::cloud_details(, "SimplyAgree")` for more info *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace @@ -8409,6 +7460,11 @@ ERROR: lazy loading failed for package ‘SimplyAgree’ *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace @@ -8550,7 +7606,7 @@ ERROR: lazy loading failed for package ‘SNPassoc’ * GitHub: NA * Source code: https://github.com/cran/snplinkage * Date/Publication: 2023-05-04 08:10:02 UTC -* Number of recursive dependencies: 146 +* Number of recursive dependencies: 145 Run `revdepcheck::cloud_details(, "snplinkage")` for more info @@ -8626,94 +7682,18 @@ Status: 1 ERROR * GitHub: https://github.com/constantAmateur/SoupX * Source code: https://github.com/cran/SoupX * Date/Publication: 2022-11-01 14:00:03 UTC -* Number of recursive dependencies: 200 +* Number of recursive dependencies: 201 Run `revdepcheck::cloud_details(, "SoupX")` for more info -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/SoupX/new/SoupX.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘SoupX/DESCRIPTION’ ... OK -... -* this is package ‘SoupX’ version ‘1.6.2’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/SoupX/old/SoupX.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘SoupX/DESCRIPTION’ ... OK -... -* this is package ‘SoupX’ version ‘1.6.2’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -# SpaDES.core - -
- -* Version: 2.0.5 -* GitHub: https://github.com/PredictiveEcology/SpaDES.core -* Source code: https://github.com/cran/SpaDES.core -* Date/Publication: 2024-04-25 17:20:02 UTC -* Number of recursive dependencies: 136 - -Run `revdepcheck::cloud_details(, "SpaDES.core")` for more info - -
- ## In both -* checking whether package ‘SpaDES.core’ can be installed ... ERROR +* checking whether package ‘SoupX’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/SpaDES.core/new/SpaDES.core.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/SoupX/new/SoupX.Rcheck/00install.out’ for details. ``` ## Installation @@ -8721,38 +7701,40 @@ Run `revdepcheck::cloud_details(, "SpaDES.core")` for more info ### Devel ``` -* installing *source* package ‘SpaDES.core’ ... -** package ‘SpaDES.core’ successfully unpacked and MD5 sums checked +* installing *source* package ‘SoupX’ ... +** package ‘SoupX’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Creating a new generic function for ‘citation’ in package ‘SpaDES.core’ -Error in get(x, envir = ns, inherits = FALSE) : - object '.addingToMemoisedMsg' not found -Error: unable to load R code in package ‘SpaDES.core’ +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘SpaDES.core’ -* removing ‘/tmp/workdir/SpaDES.core/new/SpaDES.core.Rcheck/SpaDES.core’ +ERROR: lazy loading failed for package ‘SoupX’ +* removing ‘/tmp/workdir/SoupX/new/SoupX.Rcheck/SoupX’ ``` ### CRAN ``` -* installing *source* package ‘SpaDES.core’ ... -** package ‘SpaDES.core’ successfully unpacked and MD5 sums checked +* installing *source* package ‘SoupX’ ... +** package ‘SoupX’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Creating a new generic function for ‘citation’ in package ‘SpaDES.core’ -Error in get(x, envir = ns, inherits = FALSE) : - object '.addingToMemoisedMsg' not found -Error: unable to load R code in package ‘SpaDES.core’ +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘SpaDES.core’ -* removing ‘/tmp/workdir/SpaDES.core/old/SpaDES.core.Rcheck/SpaDES.core’ +ERROR: lazy loading failed for package ‘SoupX’ +* removing ‘/tmp/workdir/SoupX/old/SoupX.Rcheck/SoupX’ ``` @@ -8797,112 +7779,36 @@ installing to /tmp/workdir/sparsereg/new/sparsereg.Rcheck/00LOCK-sparsereg/00new ** R ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘sparsereg’ -* removing ‘/tmp/workdir/sparsereg/new/sparsereg.Rcheck/sparsereg’ - - -``` -### CRAN - -``` -* installing *source* package ‘sparsereg’ ... -** package ‘sparsereg’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c makeinter.cpp -o makeinter.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c makethreeinter.cpp -o makethreeinter.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c subgroup.cpp -o subgroup.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o sparsereg.so RcppExports.o makeinter.o makethreeinter.o subgroup.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/sparsereg/old/sparsereg.Rcheck/00LOCK-sparsereg/00new/sparsereg/libs -** R -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘sparsereg’ -* removing ‘/tmp/workdir/sparsereg/old/sparsereg.Rcheck/sparsereg’ - - -``` -# SPECK - -
- -* Version: 1.0.0 -* GitHub: NA -* Source code: https://github.com/cran/SPECK -* Date/Publication: 2023-11-17 17:30:02 UTC -* Number of recursive dependencies: 161 - -Run `revdepcheck::cloud_details(, "SPECK")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/SPECK/new/SPECK.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘SPECK/DESCRIPTION’ ... OK -... -Package required but not available: ‘Seurat’ - -Package required and available but unsuitable version: ‘Matrix’ - -Package suggested but not available for checking: ‘SeuratObject’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘sparsereg’ +* removing ‘/tmp/workdir/sparsereg/new/sparsereg.Rcheck/sparsereg’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/SPECK/old/SPECK.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘SPECK/DESCRIPTION’ ... OK -... -Package required but not available: ‘Seurat’ - -Package required and available but unsuitable version: ‘Matrix’ - -Package suggested but not available for checking: ‘SeuratObject’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - +* installing *source* package ‘sparsereg’ ... +** package ‘sparsereg’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c makeinter.cpp -o makeinter.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c makethreeinter.cpp -o makethreeinter.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c subgroup.cpp -o subgroup.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o sparsereg.so RcppExports.o makeinter.o makethreeinter.o subgroup.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/sparsereg/old/sparsereg.Rcheck/00LOCK-sparsereg/00new/sparsereg/libs +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘sparsereg’ +* removing ‘/tmp/workdir/sparsereg/old/sparsereg.Rcheck/sparsereg’ ``` @@ -8986,7 +7892,7 @@ ERROR: lazy loading failed for package ‘spikeSlabGAM’ * GitHub: https://github.com/StatsWithR/statsr * Source code: https://github.com/cran/statsr * Date/Publication: 2021-01-22 20:40:03 UTC -* Number of recursive dependencies: 98 +* Number of recursive dependencies: 97 Run `revdepcheck::cloud_details(, "statsr")` for more info @@ -9048,7 +7954,7 @@ ERROR: lazy loading failed for package ‘statsr’ * GitHub: NA * Source code: https://github.com/cran/streamDAG * Date/Publication: 2023-10-06 18:50:02 UTC -* Number of recursive dependencies: 133 +* Number of recursive dependencies: 132 Run `revdepcheck::cloud_details(, "streamDAG")` for more info @@ -9326,7 +8232,7 @@ ERROR: lazy loading failed for package ‘tempted’ * GitHub: https://github.com/YuLab-SMU/tidydr * Source code: https://github.com/cran/tidydr * Date/Publication: 2023-03-08 09:20:02 UTC -* Number of recursive dependencies: 71 +* Number of recursive dependencies: 74 Run `revdepcheck::cloud_details(, "tidydr")` for more info @@ -9388,7 +8294,7 @@ ERROR: lazy loading failed for package ‘tidydr’ * GitHub: NA * Source code: https://github.com/cran/tidyEdSurvey * Date/Publication: 2024-05-14 20:20:03 UTC -* Number of recursive dependencies: 107 +* Number of recursive dependencies: 111 Run `revdepcheck::cloud_details(, "tidyEdSurvey")` for more info @@ -9412,8 +8318,13 @@ Run `revdepcheck::cloud_details(, "tidyEdSurvey")` for more info ** using staged installation ** R ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘EdSurvey’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1.1 is required +Error: package or namespace load failed for ‘EdSurvey’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +In addition: Warning message: +In check_dep_version() : ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Execution halted ERROR: lazy loading failed for package ‘tidyEdSurvey’ * removing ‘/tmp/workdir/tidyEdSurvey/new/tidyEdSurvey.Rcheck/tidyEdSurvey’ @@ -9428,8 +8339,13 @@ ERROR: lazy loading failed for package ‘tidyEdSurvey’ ** using staged installation ** R ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘EdSurvey’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1.1 is required +Error: package or namespace load failed for ‘EdSurvey’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +In addition: Warning message: +In check_dep_version() : ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Execution halted ERROR: lazy loading failed for package ‘tidyEdSurvey’ * removing ‘/tmp/workdir/tidyEdSurvey/old/tidyEdSurvey.Rcheck/tidyEdSurvey’ @@ -9444,71 +8360,57 @@ ERROR: lazy loading failed for package ‘tidyEdSurvey’ * GitHub: https://github.com/stemangiola/tidyseurat * Source code: https://github.com/cran/tidyseurat * Date/Publication: 2024-01-10 04:50:02 UTC -* Number of recursive dependencies: 206 +* Number of recursive dependencies: 207 Run `revdepcheck::cloud_details(, "tidyseurat")` for more info -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/tidyseurat/new/tidyseurat.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘tidyseurat/DESCRIPTION’ ... OK -... -* this is package ‘tidyseurat’ version ‘0.8.0’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'SeuratObject', 'Seurat' +## In both -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR +* checking whether package ‘tidyseurat’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/tidyseurat/new/tidyseurat.Rcheck/00install.out’ for details. + ``` +## Installation +### Devel +``` +* installing *source* package ‘tidyseurat’ ... +** package ‘tidyseurat’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Execution halted +ERROR: lazy loading failed for package ‘tidyseurat’ +* removing ‘/tmp/workdir/tidyseurat/new/tidyseurat.Rcheck/tidyseurat’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/tidyseurat/old/tidyseurat.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘tidyseurat/DESCRIPTION’ ... OK -... -* this is package ‘tidyseurat’ version ‘0.8.0’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'SeuratObject', 'Seurat' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - +* installing *source* package ‘tidyseurat’ ... +** package ‘tidyseurat’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Execution halted +ERROR: lazy loading failed for package ‘tidyseurat’ +* removing ‘/tmp/workdir/tidyseurat/old/tidyseurat.Rcheck/tidyseurat’ ``` @@ -9575,82 +8477,6 @@ ERROR: lazy loading failed for package ‘tidyvpc’ * removing ‘/tmp/workdir/tidyvpc/old/tidyvpc.Rcheck/tidyvpc’ -``` -# treefit - -
- -* Version: 1.0.2 -* GitHub: https://github.com/hayamizu-lab/treefit-r -* Source code: https://github.com/cran/treefit -* Date/Publication: 2022-01-18 07:50:02 UTC -* Number of recursive dependencies: 159 - -Run `revdepcheck::cloud_details(, "treefit")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/treefit/new/treefit.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘treefit/DESCRIPTION’ ... OK -... - - When sourcing ‘working-with-seurat.R’: -Error: there is no package called ‘Seurat’ -Execution halted - - ‘treefit.Rmd’ using ‘UTF-8’... OK - ‘working-with-seurat.Rmd’ using ‘UTF-8’... failed -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 WARNING, 1 NOTE - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/treefit/old/treefit.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘treefit/DESCRIPTION’ ... OK -... - - When sourcing ‘working-with-seurat.R’: -Error: there is no package called ‘Seurat’ -Execution halted - - ‘treefit.Rmd’ using ‘UTF-8’... OK - ‘working-with-seurat.Rmd’ using ‘UTF-8’... failed -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 WARNING, 1 NOTE - - - - - ``` # TriDimRegression @@ -9856,26 +8682,26 @@ ERROR: lazy loading failed for package ‘twang’ ``` -# valse +# vdg
-* Version: 0.1-0 +* Version: 1.2.3 * GitHub: NA -* Source code: https://github.com/cran/valse -* Date/Publication: 2021-05-31 08:00:02 UTC -* Number of recursive dependencies: 55 +* Source code: https://github.com/cran/vdg +* Date/Publication: 2024-04-23 13:00:02 UTC +* Number of recursive dependencies: 45 -Run `revdepcheck::cloud_details(, "valse")` for more info +Run `revdepcheck::cloud_details(, "vdg")` for more info
## In both -* checking whether package ‘valse’ can be installed ... ERROR +* checking whether package ‘vdg’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/valse/new/valse.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/vdg/new/vdg.Rcheck/00install.out’ for details. ``` ## Installation @@ -9883,77 +8709,71 @@ Run `revdepcheck::cloud_details(, "valse")` for more info ### Devel ``` -* installing *source* package ‘valse’ ... -** package ‘valse’ successfully unpacked and MD5 sums checked +* installing *source* package ‘vdg’ ... +** package ‘vdg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c EMGLLF.c -o EMGLLF.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c EMGrank.c -o EMGrank.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c a.EMGLLF.c -o a.EMGLLF.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c a.EMGrank.c -o a.EMGrank.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c valse_init.c -o valse_init.o -... -*** installing help indices -** building package indices -** testing if installed package can be loaded from temporary location -Error: package or namespace load failed for ‘valse’ in dyn.load(file, DLLpath = DLLpath, ...): - unable to load shared object '/tmp/workdir/valse/new/valse.Rcheck/00LOCK-valse/00new/valse/libs/valse.so': - /tmp/workdir/valse/new/valse.Rcheck/00LOCK-valse/00new/valse/libs/valse.so: undefined symbol: gsl_permutation_free -Error: loading failed +using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +gfortran -fpic -g -O2 -c FDS.f -o FDS.o +gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o vdg.so FDS.o -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/vdg/new/vdg.Rcheck/00LOCK-vdg/00new/vdg/libs +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘quantreg’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: loading failed -* removing ‘/tmp/workdir/valse/new/valse.Rcheck/valse’ +ERROR: lazy loading failed for package ‘vdg’ +* removing ‘/tmp/workdir/vdg/new/vdg.Rcheck/vdg’ ``` ### CRAN ``` -* installing *source* package ‘valse’ ... -** package ‘valse’ successfully unpacked and MD5 sums checked +* installing *source* package ‘vdg’ ... +** package ‘vdg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c EMGLLF.c -o EMGLLF.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c EMGrank.c -o EMGrank.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c a.EMGLLF.c -o a.EMGLLF.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c a.EMGrank.c -o a.EMGrank.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c valse_init.c -o valse_init.o -... -*** installing help indices -** building package indices -** testing if installed package can be loaded from temporary location -Error: package or namespace load failed for ‘valse’ in dyn.load(file, DLLpath = DLLpath, ...): - unable to load shared object '/tmp/workdir/valse/old/valse.Rcheck/00LOCK-valse/00new/valse/libs/valse.so': - /tmp/workdir/valse/old/valse.Rcheck/00LOCK-valse/00new/valse/libs/valse.so: undefined symbol: gsl_permutation_free -Error: loading failed +using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +gfortran -fpic -g -O2 -c FDS.f -o FDS.o +gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o vdg.so FDS.o -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/vdg/old/vdg.Rcheck/00LOCK-vdg/00new/vdg/libs +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘quantreg’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: loading failed -* removing ‘/tmp/workdir/valse/old/valse.Rcheck/valse’ +ERROR: lazy loading failed for package ‘vdg’ +* removing ‘/tmp/workdir/vdg/old/vdg.Rcheck/vdg’ ``` -# vdg +# visa
-* Version: 1.2.3 -* GitHub: NA -* Source code: https://github.com/cran/vdg -* Date/Publication: 2024-04-23 13:00:02 UTC -* Number of recursive dependencies: 45 +* Version: 0.1.0 +* GitHub: https://github.com/kang-yu/visa +* Source code: https://github.com/cran/visa +* Date/Publication: 2021-04-20 07:20:02 UTC +* Number of recursive dependencies: 140 -Run `revdepcheck::cloud_details(, "vdg")` for more info +Run `revdepcheck::cloud_details(, "visa")` for more info
## In both -* checking whether package ‘vdg’ can be installed ... ERROR +* checking whether package ‘visa’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/vdg/new/vdg.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/visa/new/visa.Rcheck/00install.out’ for details. ``` ## Installation @@ -9961,48 +8781,40 @@ Run `revdepcheck::cloud_details(, "vdg")` for more info ### Devel ``` -* installing *source* package ‘vdg’ ... -** package ‘vdg’ successfully unpacked and MD5 sums checked +* installing *source* package ‘visa’ ... +** package ‘visa’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -gfortran -fpic -g -O2 -c FDS.f -o FDS.o -gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o vdg.so FDS.o -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/vdg/new/vdg.Rcheck/00LOCK-vdg/00new/vdg/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘quantreg’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘vdg’ -* removing ‘/tmp/workdir/vdg/new/vdg.Rcheck/vdg’ +ERROR: lazy loading failed for package ‘visa’ +* removing ‘/tmp/workdir/visa/new/visa.Rcheck/visa’ ``` ### CRAN ``` -* installing *source* package ‘vdg’ ... -** package ‘vdg’ successfully unpacked and MD5 sums checked +* installing *source* package ‘visa’ ... +** package ‘visa’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -gfortran -fpic -g -O2 -c FDS.f -o FDS.o -gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o vdg.so FDS.o -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/vdg/old/vdg.Rcheck/00LOCK-vdg/00new/vdg/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘quantreg’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘vdg’ -* removing ‘/tmp/workdir/vdg/old/vdg.Rcheck/vdg’ +ERROR: lazy loading failed for package ‘visa’ +* removing ‘/tmp/workdir/visa/old/visa.Rcheck/visa’ ``` @@ -10014,7 +8826,7 @@ ERROR: lazy loading failed for package ‘vdg’ * GitHub: https://github.com/fawda123/WRTDStidal * Source code: https://github.com/cran/WRTDStidal * Date/Publication: 2023-10-20 09:00:11 UTC -* Number of recursive dependencies: 140 +* Number of recursive dependencies: 139 Run `revdepcheck::cloud_details(, "WRTDStidal")` for more info diff --git a/revdep/problems.md b/revdep/problems.md index 1280d2fbbb..8e2e437056 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,2640 +1,1317 @@ -# asmbPLS +# activAnalyzer (patchwork) -
+# actxps (thematic) -* Version: 1.0.0 -* GitHub: NA -* Source code: https://github.com/cran/asmbPLS -* Date/Publication: 2023-04-17 09:50:05 UTC -* Number of recursive dependencies: 100 +# AeRobiology (unknown) -Run `revdepcheck::cloud_details(, "asmbPLS")` for more info +``` +#
+# +# * Version: 2.0.1 +# * GitHub: NA +# * Source code: https://github.com/cran/AeRobiology +# * Date/Publication: 2019-06-03 06:20:03 UTC +# * Number of recursive dependencies: 98 +# +# Run `revdepcheck::cloud_details(, "AeRobiology")` for more info +# +#
+# +# ## Newly broken +# +# * checking re-building of vignette outputs ... NOTE +# ``` +# Error(s) in re-building vignettes: +# --- re-building ‘my-vignette.Rmd’ using rmarkdown +# ``` +# +# ## In both +# +# * checking running R code from vignettes ... ERROR +# ``` +# Errors in running code in vignettes: +# when running code in ‘my-vignette.Rmd’ +# ... +# + export.plot = FALSE, export.result = FALSE, n.types = 3, +# + y.start = 2011, y.end = .... [TRUNCATED] +# +# > iplot_abundance(munich_pollen, interpolation = FALSE, +# + export.plot = FALSE, export.result = FALSE, n.types = 3, +# + y.start = 2011, y.end = .... [TRUNCATED] +# +# When sourcing ‘my-vignette.R’: +# Error: subscript out of bounds +# Execution halted +# +# ‘my-vignette.Rmd’ using ‘UTF-8’... failed +# ``` +``` -
+# agricolaeplotr (missing labels) -## Newly broken +# AnalysisLin (plotly) -* checking whether package ‘asmbPLS’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘asmbPLS’ - See ‘/tmp/workdir/asmbPLS/new/asmbPLS.Rcheck/00install.out’ for details. - ``` +# animbook (plotly) -## In both - -* checking installed package size ... NOTE - ``` - installed size is 19.7Mb - sub-directories of 1Mb or more: - data 2.1Mb - libs 16.5Mb - ``` - -# bdl - -
- -* Version: 1.0.5 -* GitHub: https://github.com/statisticspoland/R_Package_to_API_BDL -* Source code: https://github.com/cran/bdl -* Date/Publication: 2023-02-24 15:00:02 UTC -* Number of recursive dependencies: 144 - -Run `revdepcheck::cloud_details(, "bdl")` for more info - -
- -## Newly broken - -* checking whether package ‘bdl’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘bdl’ - See ‘/tmp/workdir/bdl/new/bdl.Rcheck/00install.out’ for details. - ``` - -# bdscale - -
- -* Version: 2.0.0 -* GitHub: https://github.com/dvmlls/bdscale -* Source code: https://github.com/cran/bdscale -* Date/Publication: 2016-03-17 13:27:37 -* Number of recursive dependencies: 63 - -Run `revdepcheck::cloud_details(, "bdscale")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘bdscale.Rmd’ - ... - > options <- as.Date(c("2014-08-15", "2014-09-19")) - - > plot + geom_vline(xintercept = as.numeric(options), - + size = 2, alpha = 0.25) + ggtitle("calendar dates, option expiry") - Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. - ℹ Please use `linewidth` instead. - - When sourcing ‘bdscale.R’: - Error: `transform_date()` works with objects of class only - Execution halted - - ‘bdscale.Rmd’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘bdscale.Rmd’ using rmarkdown - ``` - -# biclustermd - -
- -* Version: 0.2.3 -* GitHub: https://github.com/jreisner/biclustermd -* Source code: https://github.com/cran/biclustermd -* Date/Publication: 2021-06-17 15:10:06 UTC -* Number of recursive dependencies: 84 - -Run `revdepcheck::cloud_details(, "biclustermd")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(biclustermd) - Loading required package: ggplot2 - Loading required package: tidyr - - Attaching package: 'tidyr' - - ... - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 67 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure ('test-autoplot_biclustermd.R:6:3'): autoplot_biclustermd() correctly plots cluster lines ── - ap$data[[3]]$xintercept[-1] not equal to cumsum(colSums(sbc$P)) + 0.5. - Classes differ: 'mapped_discrete'/'numeric' is not 'numeric' - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 67 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘nycflights13’ - All declared Imports should be used. - ``` - -# brolgar - -
- -* Version: 1.0.1 -* GitHub: https://github.com/njtierney/brolgar -* Source code: https://github.com/cran/brolgar -* Date/Publication: 2024-05-10 14:50:34 UTC -* Number of recursive dependencies: 101 - -Run `revdepcheck::cloud_details(, "brolgar")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘brolgar-Ex.R’ failed - The error most likely occurred in: - - > ### Name: facet_sample - > ### Title: Facet data into groups to facilitate exploration - > ### Aliases: facet_sample - > - > ### ** Examples - > - > library(ggplot2) - > ggplot(heights, - + aes(x = year, - + y = height_cm, - + group = country)) + - + geom_line() + - + facet_sample() - Error in if (params$as.table) { : argument is of length zero - Calls: ... -> setup -> -> compute_layout - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘getting-started.Rmd’ - ... - > set.seed(2019 - 7 - 23 - 1936) - - > library(ggplot2) - - > ggplot(wages, aes(x = xp, y = ln_wages, group = id)) + - + geom_line() + facet_strata() - - ... - Error: argument is of length zero - Execution halted - - ‘exploratory-modelling.Rmd’ using ‘UTF-8’... OK - ‘finding-features.Rmd’ using ‘UTF-8’... OK - ‘getting-started.Rmd’ using ‘UTF-8’... failed - ‘id-interesting-obs.Rmd’ using ‘UTF-8’... OK - ‘longitudinal-data-structures.Rmd’ using ‘UTF-8’... OK - ‘mixed-effects-models.Rmd’ using ‘UTF-8’... failed - ‘visualisation-gallery.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘exploratory-modelling.Rmd’ using rmarkdown - ``` - -# bSi - -
- -* Version: 1.0.0 -* GitHub: NA -* Source code: https://github.com/cran/bSi -* Date/Publication: 2024-01-24 15:52:57 UTC -* Number of recursive dependencies: 99 - -Run `revdepcheck::cloud_details(, "bSi")` for more info - -
- -## Newly broken - -* checking whether package ‘bSi’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘bSi’ - See ‘/tmp/workdir/bSi/new/bSi.Rcheck/00install.out’ for details. - ``` - -# CausalImpact - -
- -* Version: 1.3.0 -* GitHub: NA -* Source code: https://github.com/cran/CausalImpact -* Date/Publication: 2022-11-09 08:40:40 UTC -* Number of recursive dependencies: 77 - -Run `revdepcheck::cloud_details(, "CausalImpact")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘CausalImpact_import_test.R’ - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > # Copyright 2014-2022 Google Inc. All rights reserved. - > # - > # Licensed under the Apache License, Version 2.0 (the "License"); - > # you may not use this file except in compliance with the License. - > # You may obtain a copy of the License at - > # - ... - 20. └─base::lapply(df[aesthetics], self$transform) - 21. └─ggplot2 (local) FUN(X[[i]], ...) - 22. └─ggplot2 (local) transform(..., self = self) - 23. └─transformation$transform(x) - 24. └─cli::cli_abort("{.fun transform_date} works with objects of class {.cls Date} only") - 25. └─rlang::abort(...) - - [ FAIL 2 | WARN 1 | SKIP 0 | PASS 739 ] - Error: Test failures - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘CausalImpact.Rmd’ - ... - - > impact <- CausalImpact(data, pre.period, post.period) - - > q <- plot(impact) + theme_bw(base_size = 11) - - > suppressWarnings(plot(q)) - - When sourcing ‘CausalImpact.R’: - Error: `transform_date()` works with objects of class only - Execution halted - - ‘CausalImpact.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘CausalImpact.Rmd’ using rmarkdown - ``` - -# ClusROC - -
- -* Version: 1.0.2 -* GitHub: https://github.com/toduckhanh/ClusROC -* Source code: https://github.com/cran/ClusROC -* Date/Publication: 2022-11-17 15:00:02 UTC -* Number of recursive dependencies: 107 - -Run `revdepcheck::cloud_details(, "ClusROC")` for more info - -
- -## Newly broken - -* checking whether package ‘ClusROC’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘ClusROC’ - See ‘/tmp/workdir/ClusROC/new/ClusROC.Rcheck/00install.out’ for details. - ``` - -# clustEff - -
- -* Version: 0.3.1 -* GitHub: NA -* Source code: https://github.com/cran/clustEff -* Date/Publication: 2024-01-23 08:52:55 UTC -* Number of recursive dependencies: 136 - -Run `revdepcheck::cloud_details(, "clustEff")` for more info - -
- -## Newly broken - -* checking whether package ‘clustEff’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘clustEff’ - See ‘/tmp/workdir/clustEff/new/clustEff.Rcheck/00install.out’ for details. - ``` - -# CLVTools - -
- -* Version: 0.10.0 -* GitHub: https://github.com/bachmannpatrick/CLVTools -* Source code: https://github.com/cran/CLVTools -* Date/Publication: 2023-10-23 20:10:02 UTC -* Number of recursive dependencies: 85 - -Run `revdepcheck::cloud_details(, "CLVTools")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘CLVTools.Rmd’ - ... - 248: 39.95483 2.336902 - 249: 34.28958 38.969738 - 250: 47.35500 7.284870 - - > plot(clv.apparel) - Plotting from 2005-01-03 until 2006-07-16. - - When sourcing ‘CLVTools.R’: - Error: `transform_date()` works with objects of class only - Execution halted - - ‘CLVTools.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘CLVTools.Rmd’ using rmarkdown - - Quitting from lines 270-272 [plot-actual] (CLVTools.Rmd) - Error: processing vignette 'CLVTools.Rmd' failed with diagnostics: - `transform_date()` works with objects of class only - --- failed re-building ‘CLVTools.Rmd’ - - SUMMARY: processing the following file failed: - ‘CLVTools.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 17.4Mb - sub-directories of 1Mb or more: - libs 15.5Mb - ``` - -# coda4microbiome - -
- -* Version: 0.2.3 -* GitHub: https://github.com/malucalle/coda4microbiome -* Source code: https://github.com/cran/coda4microbiome -* Date/Publication: 2024-02-21 08:30:06 UTC -* Number of recursive dependencies: 136 - -Run `revdepcheck::cloud_details(, "coda4microbiome")` for more info - -
- -## Newly broken - -* checking whether package ‘coda4microbiome’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘coda4microbiome’ - See ‘/tmp/workdir/coda4microbiome/new/coda4microbiome.Rcheck/00install.out’ for details. - ``` - -# CompAREdesign - -
- -* Version: 2.3.1 -* GitHub: NA -* Source code: https://github.com/cran/CompAREdesign -* Date/Publication: 2024-02-15 13:00:02 UTC -* Number of recursive dependencies: 90 - -Run `revdepcheck::cloud_details(, "CompAREdesign")` for more info - -
- -## Newly broken - -* checking whether package ‘CompAREdesign’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘CompAREdesign’ - See ‘/tmp/workdir/CompAREdesign/new/CompAREdesign.Rcheck/00install.out’ for details. - ``` - -# covidcast - -
- -* Version: 0.5.2 -* GitHub: https://github.com/cmu-delphi/covidcast -* Source code: https://github.com/cran/covidcast -* Date/Publication: 2023-07-12 23:40:06 UTC -* Number of recursive dependencies: 93 - -Run `revdepcheck::cloud_details(, "covidcast")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(covidcast) - We encourage COVIDcast API users to register on our mailing list: - https://lists.andrew.cmu.edu/mailman/listinfo/delphi-covidcast-api - We'll send announcements about new data sources, package updates, - server maintenance, and new features. - > - ... - • plot/default-county-choropleth.svg - • plot/default-hrr-choropleth-with-include.svg - • plot/default-msa-choropleth-with-include.svg - • plot/default-state-choropleth-with-include.svg - • plot/default-state-choropleth-with-range.svg - • plot/state-choropleth-with-no-metadata.svg - • plot/state-line-graph-with-range.svg - • plot/state-line-graph-with-stderrs.svg - Error: Test failures - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘plotting-signals.Rmd’ - ... - > plot(inum, choro_col = colors, choro_params = list(breaks = breaks), - + title = "New COVID cases (7-day trailing average) on 2020-07-14") - - When sourcing ‘plotting-signals.R’: - Error: Problem while setting up geom aesthetics. - ℹ Error occurred in the 5th layer. - Caused by error in `check_aesthetics()`: - ! Aesthetics must be either length 1 or the same as the data (3078). - ✖ Fix the following mappings: `fill`. - Execution halted - - ‘correlation-utils.Rmd’ using ‘UTF-8’... OK - ‘covidcast.Rmd’ using ‘UTF-8’... OK - ‘external-data.Rmd’ using ‘UTF-8’... OK - ‘multi-signals.Rmd’ using ‘UTF-8’... OK - ‘plotting-signals.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘correlation-utils.Rmd’ using rmarkdown - --- finished re-building ‘correlation-utils.Rmd’ - - --- re-building ‘covidcast.Rmd’ using rmarkdown - ``` - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 20 marked UTF-8 strings - ``` - -# Coxmos - -
- -* Version: 1.0.2 -* GitHub: https://github.com/BiostatOmics/Coxmos -* Source code: https://github.com/cran/Coxmos -* Date/Publication: 2024-03-25 20:32:38 UTC -* Number of recursive dependencies: 204 - -Run `revdepcheck::cloud_details(, "Coxmos")` for more info - -
- -## Newly broken - -* checking Rd files ... WARNING - ``` - prepare_Rd: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘survminer’ - ``` - -## In both - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘Coxmos-pipeline.Rmd’ - ... - Warning in data("X_proteomic") : data set ‘X_proteomic’ not found - - > data("Y_proteomic") - Warning in data("Y_proteomic") : data set ‘Y_proteomic’ not found - - > X <- X_proteomic - - When sourcing ‘Coxmos-pipeline.R’: - Error: object 'X_proteomic' not found - Execution halted - - ‘Coxmos-MO-pipeline.Rmd’ using ‘UTF-8’... OK - ‘Coxmos-pipeline.Rmd’ using ‘UTF-8’... failed - ``` - -* checking installed package size ... NOTE - ``` - installed size is 6.5Mb - sub-directories of 1Mb or more: - data 2.1Mb - doc 2.9Mb - ``` - -# csa - -
- -* Version: 0.7.1 -* GitHub: https://github.com/imarkonis/csa -* Source code: https://github.com/cran/csa -* Date/Publication: 2023-10-24 13:40:11 UTC -* Number of recursive dependencies: 95 - -Run `revdepcheck::cloud_details(, "csa")` for more info - -
- -## Newly broken - -* checking whether package ‘csa’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘csa’ - See ‘/tmp/workdir/csa/new/csa.Rcheck/00install.out’ for details. - ``` - -# deeptime - -
- -* Version: 1.1.1 -* GitHub: https://github.com/willgearty/deeptime -* Source code: https://github.com/cran/deeptime -* Date/Publication: 2024-03-08 17:10:10 UTC -* Number of recursive dependencies: 181 - -Run `revdepcheck::cloud_details(, "deeptime")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘deeptime-Ex.R’ failed - The error most likely occurred in: - - > ### Name: facet_wrap_color - > ### Title: Wrap a 1d ribbon of panels into 2d with colored strips - > ### Aliases: facet_wrap_color FacetWrapColor - > ### Keywords: datasets - > - > ### ** Examples - > - ... - 6. │ └─ggplot2 (local) setup(..., self = self) - 7. │ └─self$facet$compute_layout(data, self$facet_params) - 8. │ └─ggplot2 (local) compute_layout(..., self = self) - 9. │ └─ggplot2:::wrap_layout(id, dims, params$dir) - 10. │ └─ggplot2:::data_frame0(...) - 11. │ └─vctrs::data_frame(..., .name_repair = "minimal") - 12. └─vctrs:::stop_recycle_incompatible_size(...) - 13. └─vctrs:::stop_vctrs(...) - 14. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(deeptime) - > - > test_check("deeptime") - Scale for y is already present. - Adding another scale for y, which will replace the existing scale. - Scale for y is already present. - ... - • gggeo_scale/gggeo-scale-top-new.svg - • gggeo_scale/gggeo-scale-top-old.svg - • points_range/geom-points-range-aes-new.svg - • points_range/geom-points-range-aes-old.svg - • points_range/geom-points-range-bg-new.svg - • points_range/geom-points-range-bg-old.svg - • points_range/geom-points-range-h-new.svg - • points_range/geom-points-range-h-old.svg - Error: Test failures - Execution halted - ``` - -# DEGRE - -
- -* Version: 0.2.0 -* GitHub: NA -* Source code: https://github.com/cran/DEGRE -* Date/Publication: 2022-11-02 09:32:57 UTC -* Number of recursive dependencies: 89 - -Run `revdepcheck::cloud_details(, "DEGRE")` for more info - -
- -## Newly broken - -* checking whether package ‘DEGRE’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘DEGRE’ - See ‘/tmp/workdir/DEGRE/new/DEGRE.Rcheck/00install.out’ for details. - ``` - -# did - -
- -* Version: 2.1.2 -* GitHub: https://github.com/bcallaway11/did -* Source code: https://github.com/cran/did -* Date/Publication: 2022-07-20 16:00:05 UTC -* Number of recursive dependencies: 125 - -Run `revdepcheck::cloud_details(, "did")` for more info - -
- -## Newly broken - -* checking whether package ‘did’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘did’ - See ‘/tmp/workdir/did/new/did.Rcheck/00install.out’ for details. - ``` - -## In both - -* checking running R code from vignettes ... WARNING - ``` - Errors in running code in vignettes: - when running code in ‘TWFE.Rmd’ - ... - - > knitr::opts_chunk$set(collapse = TRUE, comment = "#>", - + echo = TRUE, eval = FALSE) - - > library(tidyverse) - - When sourcing ‘TWFE.R’: - ... - - When sourcing ‘pre-testing.R’: - Error: cannot open the connection - Execution halted - - ‘TWFE.Rmd’ using ‘UTF-8’... failed - ‘did-basics.Rmd’ using ‘UTF-8’... OK - ‘extensions.Rmd’ using ‘UTF-8’... failed - ‘multi-period-did.Rmd’ using ‘UTF-8’... OK - ‘pre-testing.Rmd’ using ‘UTF-8’... failed - ``` - -# EpiCurve - -
- -* Version: 2.4-2 -* GitHub: https://github.com/IamKDO/EpiCurve -* Source code: https://github.com/cran/EpiCurve -* Date/Publication: 2021-07-14 16:20:05 UTC -* Number of recursive dependencies: 56 - -Run `revdepcheck::cloud_details(, "EpiCurve")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘EpiCurve.Rmd’ - ... - |2016-11-06 | 6.60| 116| - |2016-11-07 | 7.68| 141| - |2016-11-07 | 10.08| 126| - - > EpiCurve(DF, date = "UTS", period = "day", colors = "#9900ef", - + xlabel = sprintf("From %s to %s", min(DF$UTS), max(DF$UTS))) - - When sourcing ‘EpiCurve.R’: - Error: `transform_date()` works with objects of class only - Execution halted - - ‘EpiCurve.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘EpiCurve.Rmd’ using rmarkdown - - Quitting from lines 103-106 [unnamed-chunk-3] (EpiCurve.Rmd) - Error: processing vignette 'EpiCurve.Rmd' failed with diagnostics: - `transform_date()` works with objects of class only - --- failed re-building ‘EpiCurve.Rmd’ - - SUMMARY: processing the following file failed: - ‘EpiCurve.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘tibble’ - All declared Imports should be used. - ``` - -# epiR - -
- -* Version: 2.0.74 -* GitHub: NA -* Source code: https://github.com/cran/epiR -* Date/Publication: 2024-04-27 12:30:02 UTC -* Number of recursive dependencies: 125 - -Run `revdepcheck::cloud_details(, "epiR")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘epiR_descriptive.Rmd’ - ... - + geom_histogram(binwidth = 7, colour = "gray", fill = "dark blue", - + li .... [TRUNCATED] - - > ggplot(data = dat.df, aes(x = as.Date(odate))) + theme_bw() + - + geom_histogram(binwidth = 7, colour = "gray", fill = "dark blue", - + li .... [TRUNCATED] - - When sourcing ‘epiR_descriptive.R’: - Error: `transform_date()` works with objects of class only - Execution halted - - ‘epiR_descriptive.Rmd’... failed - ‘epiR_measures_of_association.Rmd’... OK - ‘epiR_sample_size.Rmd’... OK - ‘epiR_surveillance.Rmd’... OK - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘epiR_descriptive.Rmd’ using rmarkdown - ``` - -# FuncNN - -
- -* Version: 1.0 -* GitHub: https://github.com/b-thi/FuncNN -* Source code: https://github.com/cran/FuncNN -* Date/Publication: 2020-09-15 09:40:15 UTC -* Number of recursive dependencies: 170 - -Run `revdepcheck::cloud_details(, "FuncNN")` for more info - -
- -## Newly broken - -* checking whether package ‘FuncNN’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘FuncNN’ - See ‘/tmp/workdir/FuncNN/new/FuncNN.Rcheck/00install.out’ for details. - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘foreach’ - All declared Imports should be used. - ``` - -# geostan - -
- -* Version: 0.6.1 -* GitHub: https://github.com/ConnorDonegan/geostan -* Source code: https://github.com/cran/geostan -* Date/Publication: 2024-05-10 22:23:01 UTC -* Number of recursive dependencies: 108 - -Run `revdepcheck::cloud_details(, "geostan")` for more info - -
+# ANN2 (missing labels) -## Newly broken +# aplot (patchwork) -* checking whether package ‘geostan’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/geostan/new/geostan.Rcheck/00install.out’ for details. - ``` +# applicable (missing labels) -## Newly fixed +# ASRgenomics (factoextra) -* checking installed package size ... NOTE - ``` - installed size is 129.8Mb - sub-directories of 1Mb or more: - libs 127.6Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘RcppParallel’ ‘rstantools’ - All declared Imports should be used. - ``` - -* checking for GNU extensions in Makefiles ... NOTE - ``` - GNU make is a SystemRequirements. - ``` - -## Installation - -### Devel +# autoplotly (plotly) -``` -* installing *source* package ‘geostan’ ... -** package ‘geostan’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -stanExports_foundation.cc:32:1: fatal error: error writing to /tmp/cccy6wQ6.s: Cannot allocate memory - 32 | } - | ^ -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_foundation.o] Error 1 -ERROR: compilation failed for package ‘geostan’ -* removing ‘/tmp/workdir/geostan/new/geostan.Rcheck/geostan’ +# autoReg (patchwork) + +# bartMan (ggnewscale) + +# bayesAB (missing labels) + +# BayesGrowth (ggdist) + +# BayesianReasoning (missing labels) + +# BayesMallows (missing labels) + +# bayesplot (missing labels) + +# bayestestR (patchwork) + +# beastt (ggdist) +# besthr (patchwork) +# biclustermd (xintercept/yintercept class) + +# biodosetools (missing labels) + +# boxly (plotly) + +# braidReports (annotation_logticks) + +# breathtestcore (plot slots) + +# brolgar (facet params: as.table) + +# cartograflow (plotly) + +# cartographr (unknown) + +``` +#
+# +# * Version: 0.2.2 +# * GitHub: https://github.com/da-wi/cartographr +# * Source code: https://github.com/cran/cartographr +# * Date/Publication: 2024-06-28 14:50:09 UTC +# * Number of recursive dependencies: 99 +# +# Run `revdepcheck::cloud_details(, "cartographr")` for more info +# +#
+# +# ## Newly broken +# +# * checking tests ... ERROR +# ``` +# Running ‘testthat.R’ +# Running the tests in ‘tests/testthat.R’ failed. +# Complete output: +# > # This file is part of the standard setup for testthat. +# > # It is recommended that you do not modify it. +# > # +# > # Where should you do additional test configuration? +# > # Learn more about the roles of various files in: +# > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview +# > # * https://testthat.r-lib.org/articles/special-files.html +# ... +# 21. │ └─base::stop(...) +# 22. └─base::.handleSimpleError(...) +# 23. └─rlang (local) h(simpleError(msg, call)) +# 24. └─handlers[[1L]](cnd) +# 25. └─cli::cli_abort(...) +# 26. └─rlang::abort(...) +# +# [ FAIL 1 | WARN 0 | SKIP 0 | PASS 106 ] +# Error: Test failures +# Execution halted +# ``` +# +# ## In both +# +# * checking installed package size ... NOTE +# ``` +# installed size is 5.3Mb +# sub-directories of 1Mb or more: +# data 3.5Mb +# ``` ``` -### CRAN +# cats (plotly) + +# cheem (plotly) + +# chillR (patchwork) + +# chronicle (plotly) + +# circhelp (patchwork) + +# clifro (missing labels) + +# clinDataReview (plotly) + +# clinUtils (plotly) + +# CohortPlat (plotly) + +# CoreMicrobiomeR (plotly) + +# correlationfunnel (plotly) + +# corrViz (plotly) + +# countfitteR (missing labels) + +# covidcast (unknown) + +``` +#
+# +# * Version: 0.5.2 +# * GitHub: https://github.com/cmu-delphi/covidcast +# * Source code: https://github.com/cran/covidcast +# * Date/Publication: 2023-07-12 23:40:06 UTC +# * Number of recursive dependencies: 93 +# +# Run `revdepcheck::cloud_details(, "covidcast")` for more info +# +#
+# +# ## Newly broken +# +# * checking tests ... ERROR +# ``` +# Running ‘testthat.R’ +# Running the tests in ‘tests/testthat.R’ failed. +# Complete output: +# > library(testthat) +# > library(covidcast) +# We encourage COVIDcast API users to register on our mailing list: +# https://lists.andrew.cmu.edu/mailman/listinfo/delphi-covidcast-api +# We'll send announcements about new data sources, package updates, +# server maintenance, and new features. +# > +# ... +# • plot/default-county-choropleth.svg +# • plot/default-hrr-choropleth-with-include.svg +# • plot/default-msa-choropleth-with-include.svg +# • plot/default-state-choropleth-with-include.svg +# • plot/default-state-choropleth-with-range.svg +# • plot/state-choropleth-with-no-metadata.svg +# • plot/state-line-graph-with-range.svg +# • plot/state-line-graph-with-stderrs.svg +# Error: Test failures +# Execution halted +# ``` +# +# * checking running R code from vignettes ... ERROR +# ``` +# Errors in running code in vignettes: +# when running code in ‘plotting-signals.Rmd’ +# ... +# > knitr::opts_chunk$set(fig.width = 6, fig.height = 4) +# +# > plot(dv) +# +# When sourcing ‘plotting-signals.R’: +# Error: Problem while setting up geom aesthetics. +# ℹ Error occurred in the 6th layer. +# Caused by error in `$<-.data.frame`: +# ! replacement has 1 row, data has 0 +# Execution halted +# +# ‘correlation-utils.Rmd’ using ‘UTF-8’... OK +# ‘covidcast.Rmd’ using ‘UTF-8’... OK +# ‘external-data.Rmd’ using ‘UTF-8’... OK +# ‘multi-signals.Rmd’ using ‘UTF-8’... OK +# ‘plotting-signals.Rmd’ using ‘UTF-8’... failed +# ``` +# +# * checking re-building of vignette outputs ... NOTE +# ``` +# Error(s) in re-building vignettes: +# --- re-building ‘correlation-utils.Rmd’ using rmarkdown +# --- finished re-building ‘correlation-utils.Rmd’ +# +# --- re-building ‘covidcast.Rmd’ using rmarkdown +# ``` +# +# ## In both +# +# * checking data for non-ASCII characters ... NOTE +# ``` +# Note: found 20 marked UTF-8 strings +# ``` ``` -* installing *source* package ‘geostan’ ... -** package ‘geostan’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -** help -*** installing help indices -*** copying figures -** building package indices -** installing vignettes -** testing if installed package can be loaded from temporary location -** checking absolute paths in shared objects and dynamic libraries -** testing if installed package can be loaded from final location -** testing if installed package keeps a record of temporary installation path -* DONE (geostan) +# crosshap (plotly) + +# cubble (patchwork) + +# deeptime (ggnewscale) + +# distributional (ggdist) + +# dittoViz (plotly) + +# EGM (missing labels) + +# entropart (default access) + +# epiCleanr (ggdist) + +# esci (ggdist) +# evalITR (unknown) + +``` +#
+# +# * Version: 1.0.0 +# * GitHub: https://github.com/MichaelLLi/evalITR +# * Source code: https://github.com/cran/evalITR +# * Date/Publication: 2023-08-25 23:10:06 UTC +# * Number of recursive dependencies: 167 +# +# Run `revdepcheck::cloud_details(, "evalITR")` for more info +# +#
+# +# ## Newly broken +# +# * checking re-building of vignette outputs ... NOTE +# ``` +# Error(s) in re-building vignettes: +# --- re-building ‘cv_multiple_alg.Rmd’ using rmarkdown +# ``` +# +# ## In both +# +# * checking running R code from vignettes ... ERROR +# ``` +# Errors in running code in vignettes: +# when running code in ‘cv_multiple_alg.Rmd’ +# ... +# intersect, setdiff, setequal, union +# +# +# > load("../data/star.rda") +# Warning in readChar(con, 5L, useBytes = TRUE) : +# cannot open compressed file '../data/star.rda', probable reason 'No such file or directory' +# +# ... +# Execution halted +# +# ‘cv_multiple_alg.Rmd’ using ‘UTF-8’... failed +# ‘cv_single_alg.Rmd’ using ‘UTF-8’... failed +# ‘install.Rmd’ using ‘UTF-8’... OK +# ‘paper_alg1.Rmd’ using ‘UTF-8’... OK +# ‘sample_split.Rmd’ using ‘UTF-8’... failed +# ‘sample_split_caret.Rmd’ using ‘UTF-8’... failed +# ‘user_itr.Rmd’ using ‘UTF-8’... failed +# ‘user_itr_algs.Rmd’ using ‘UTF-8’... failed +# ``` +# +# * checking dependencies in R code ... NOTE +# ``` +# Namespaces in Imports field not imported from: +# ‘forcats’ ‘rqPen’ ‘utils’ +# All declared Imports should be used. +# ``` ``` -# ggedit - -
- -* Version: 0.4.1 -* GitHub: https://github.com/yonicd/ggedit -* Source code: https://github.com/cran/ggedit -* Date/Publication: 2024-03-04 14:40:02 UTC -* Number of recursive dependencies: 95 - -Run `revdepcheck::cloud_details(, "ggedit")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ggedit-Ex.R’ failed - The error most likely occurred in: - - > ### Name: print.ggedit - > ### Title: Print ggedit objects - > ### Aliases: print.ggedit - > - > ### ** Examples - > - > p <- as.gglist(pList[1:2]) - ... - 8. │ └─ggplot2 (local) setup(..., self = self) - 9. │ └─self$facet$compute_layout(data, self$facet_params) - 10. │ └─ggplot2 (local) compute_layout(..., self = self) - 11. │ └─ggplot2:::wrap_layout(id, dims, params$dir) - 12. │ └─ggplot2:::data_frame0(...) - 13. │ └─vctrs::data_frame(..., .name_repair = "minimal") - 14. └─vctrs:::stop_recycle_incompatible_size(...) - 15. └─vctrs:::stop_vctrs(...) - 16. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) - Execution halted - ``` - -# ggfixest - -
- -* Version: 0.1.0 -* GitHub: https://github.com/grantmcdermott/ggfixest -* Source code: https://github.com/cran/ggfixest -* Date/Publication: 2023-12-14 08:00:06 UTC -* Number of recursive dependencies: 78 - -Run `revdepcheck::cloud_details(, "ggfixest")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘tinytest.R’ - Running the tests in ‘tests/tinytest.R’ failed. - Complete output: - > ## Throttle CPU threads if R CMD check (for CRAN) - > - > if (any(grepl("_R_CHECK", names(Sys.getenv()), fixed = TRUE))) { - + # fixest - + if (requireNamespace("fixest", quietly = TRUE)) { - + library(fixest) - + setFixest_nthreads(1) - ... - ----- FAILED[]: test_ggcoefplot.R<66--66> - call| expect_snapshot_plot(p_did_iid_summ, label = "ggcoefplot_did_iid") - diff| 7580 - info| Diff plot saved to: _tinysnapshot_review/ggcoefplot_did_iid.png - ----- FAILED[]: test_ggcoefplot.R<67--67> - call| expect_snapshot_plot(p_did_iid, label = "ggcoefplot_did_iid") - diff| 7580 - info| Diff plot saved to: _tinysnapshot_review/ggcoefplot_did_iid.png - Error: 12 out of 101 tests failed - Execution halted - ``` - -## In both - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘ggiplot.Rmd’ - ... - > iplot(list(TWFE = est_twfe_grp, `Sun & Abraham (2020)` = est_sa20_grp), - + ref.line = -1, main = "Staggered treatment: Split mutli-sample") - The degrees of freedom for the t distribution could not be deduced. Using a Normal distribution instead. - Note that you can provide the argument `df.t` directly. - - When sourcing ‘ggiplot.R’: - Error: in iplot(list(TWFE = est_twfe_grp, `Sun & Abraham (2...: - The 1st element of 'object' raises and error: - Error in nb * sd : non-numeric argument to binary operator - Execution halted - - ‘ggiplot.Rmd’ using ‘UTF-8’... failed - ``` - -# ggfortify - -
- -* Version: 0.4.17 -* GitHub: https://github.com/sinhrks/ggfortify -* Source code: https://github.com/cran/ggfortify -* Date/Publication: 2024-04-17 04:30:04 UTC -* Number of recursive dependencies: 125 - -Run `revdepcheck::cloud_details(, "ggfortify")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘basics.Rmd’ using knitr - - Attaching package: 'zoo' - - The following objects are masked from 'package:base': - - as.Date, as.Date.numeric - ``` - -# ggh4x - -
- -* Version: 0.2.8 -* GitHub: https://github.com/teunbrand/ggh4x -* Source code: https://github.com/cran/ggh4x -* Date/Publication: 2024-01-23 21:00:02 UTC -* Number of recursive dependencies: 77 - -Run `revdepcheck::cloud_details(, "ggh4x")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ggh4x-Ex.R’ failed - The error most likely occurred in: - - > ### Name: facet_nested_wrap - > ### Title: Ribbon of panels with nested strips. - > ### Aliases: facet_nested_wrap - > - > ### ** Examples - > - > # A standard plot - ... - 6. │ └─ggplot2 (local) setup(..., self = self) - 7. │ └─self$facet$compute_layout(data, self$facet_params) - 8. │ └─ggplot2 (local) compute_layout(..., self = self) - 9. │ └─ggplot2:::wrap_layout(id, dims, params$dir) - 10. │ └─ggplot2:::data_frame0(...) - 11. │ └─vctrs::data_frame(..., .name_repair = "minimal") - 12. └─vctrs:::stop_recycle_incompatible_size(...) - 13. └─vctrs:::stop_vctrs(...) - 14. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(ggh4x) - Loading required package: ggplot2 - > - > test_check("ggh4x") - [ FAIL 8 | WARN 0 | SKIP 18 | PASS 723 ] - - ... - 11. │ └─ggplot2:::wrap_layout(id, dims, params$dir) - 12. │ └─ggplot2:::data_frame0(...) - 13. │ └─vctrs::data_frame(..., .name_repair = "minimal") - 14. └─vctrs:::stop_recycle_incompatible_size(...) - 15. └─vctrs:::stop_vctrs(...) - 16. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) - - [ FAIL 8 | WARN 0 | SKIP 18 | PASS 723 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘Facets.Rmd’ using rmarkdown - - Quitting from lines 33-39 [wrap_mimick] (Facets.Rmd) - Error: processing vignette 'Facets.Rmd' failed with diagnostics: - Can't recycle `ROW` (size 0) to size 7. - --- failed re-building ‘Facets.Rmd’ - - --- re-building ‘Miscellaneous.Rmd’ using rmarkdown - ``` - -## In both - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘Facets.Rmd’ - ... - Loading required package: ggplot2 - - > p <- ggplot(mpg, aes(displ, hwy, colour = as.factor(cyl))) + - + geom_point() + labs(x = "Engine displacement", y = "Highway miles per gallon") + .... [TRUNCATED] - - > p + facet_wrap2(vars(class)) - - ... - ℹ Error occurred in the 1st layer. - Caused by error in `setup_params()`: - ! A discrete 'nbinom' distribution cannot be fitted to continuous data. - Execution halted - - ‘Facets.Rmd’ using ‘UTF-8’... failed - ‘Miscellaneous.Rmd’ using ‘UTF-8’... OK - ‘PositionGuides.Rmd’ using ‘UTF-8’... OK - ‘Statistics.Rmd’ using ‘UTF-8’... failed - ‘ggh4x.Rmd’ using ‘UTF-8’... OK - ``` - -# ggheatmap - -
- -* Version: 2.2 -* GitHub: NA -* Source code: https://github.com/cran/ggheatmap -* Date/Publication: 2022-09-10 13:32:55 UTC -* Number of recursive dependencies: 127 - -Run `revdepcheck::cloud_details(, "ggheatmap")` for more info - -
- -## Newly broken - -* checking whether package ‘ggheatmap’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘ggheatmap’ - See ‘/tmp/workdir/ggheatmap/new/ggheatmap.Rcheck/00install.out’ for details. - ``` - -# ggScatRidges - -
- -* Version: 0.1.1 -* GitHub: https://github.com/matbou85/ggScatRidges -* Source code: https://github.com/cran/ggScatRidges -* Date/Publication: 2024-03-25 10:20:05 UTC -* Number of recursive dependencies: 117 - -Run `revdepcheck::cloud_details(, "ggScatRidges")` for more info - -
- -## Newly broken - -* checking whether package ‘ggScatRidges’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘ggScatRidges’ - See ‘/tmp/workdir/ggScatRidges/new/ggScatRidges.Rcheck/00install.out’ for details. - ``` - -# GimmeMyPlot - -
- -* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/GimmeMyPlot -* Date/Publication: 2023-10-18 16:10:02 UTC -* Number of recursive dependencies: 111 - -Run `revdepcheck::cloud_details(, "GimmeMyPlot")` for more info - -
- -## Newly broken - -* checking whether package ‘GimmeMyPlot’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘GimmeMyPlot’ - See ‘/tmp/workdir/GimmeMyPlot/new/GimmeMyPlot.Rcheck/00install.out’ for details. - ``` - -# hilldiv - -
- -* Version: 1.5.1 -* GitHub: https://github.com/anttonalberdi/hilldiv -* Source code: https://github.com/cran/hilldiv -* Date/Publication: 2019-10-01 14:40:02 UTC -* Number of recursive dependencies: 153 - -Run `revdepcheck::cloud_details(, "hilldiv")` for more info - -
- -## Newly broken - -* checking whether package ‘hilldiv’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘hilldiv’ - See ‘/tmp/workdir/hilldiv/new/hilldiv.Rcheck/00install.out’ for details. - ``` - -# hJAM - -
- -* Version: 1.0.0 -* GitHub: https://github.com/lailylajiang/hJAM -* Source code: https://github.com/cran/hJAM -* Date/Publication: 2020-02-20 14:50:05 UTC -* Number of recursive dependencies: 101 -Run `revdepcheck::cloud_details(, "hJAM")` for more info - -
- -## Newly broken - -* checking whether package ‘hJAM’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘hJAM’ - See ‘/tmp/workdir/hJAM/new/hJAM.Rcheck/00install.out’ for details. - ``` - -# iglu - -
- -* Version: 4.0.0 -* GitHub: https://github.com/irinagain/iglu -* Source code: https://github.com/cran/iglu -* Date/Publication: 2024-02-23 17:50:02 UTC -* Number of recursive dependencies: 125 +# eventstudyr (missing labels) + +# EvoPhylo (patchwork) -Run `revdepcheck::cloud_details(, "iglu")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘iglu-Ex.R’ failed - The error most likely occurred in: - - > ### Name: mage_ma_single - > ### Title: Calculates Mean Amplitude of Glycemic Excursions (see "mage") - > ### Aliases: mage_ma_single - > - > ### ** Examples - > - > data(example_data_1_subject) - ... - 12. └─ggplot2 (local) transform_df(..., self = self) - 13. └─base::lapply(df[aesthetics], self$transform) - 14. └─ggplot2 (local) FUN(X[[i]], ...) - 15. └─ggplot2 (local) transform(..., self = self) - 16. └─ggproto_parent(ScaleContinuous, self)$transform(x) - 17. └─ggplot2 (local) transform(..., self = self) - 18. └─transformation$transform(x) - 19. └─cli::cli_abort("{.fun transform_time} works with objects of class {.cls POSIXct} only") - 20. └─rlang::abort(...) - Execution halted - ``` +# expirest (missing labels) -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘MAGE.Rmd’ - ... - - > fig1data <- example_data_1_subject[1:200, ] - - > mage(fig1data, plot = TRUE, show_ma = TRUE, title = "Glucose Trace - Subject 1") - - When sourcing ‘MAGE.R’: - Error: ℹ In index: 1. - Caused by error in `transformation$transform()`: - ! `transform_time()` works with objects of class only - Execution halted - - ‘AGP_and_Episodes.Rmd’ using ‘UTF-8’... OK - ‘MAGE.Rmd’ using ‘UTF-8’... failed - ‘iglu.Rmd’ using ‘UTF-8’... OK - ‘lasagna_plots.Rmd’ using ‘UTF-8’... OK - ‘metrics_list.Rmd’ using ‘UTF-8’... OK - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘AGP_and_Episodes.Rmd’ using rmarkdown - ``` - -# ImFoR - -
- -* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/ImFoR -* Date/Publication: 2023-09-21 18:50:02 UTC -* Number of recursive dependencies: 173 - -Run `revdepcheck::cloud_details(, "ImFoR")` for more info - -
- -## Newly broken - -* checking whether package ‘ImFoR’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘ImFoR’ - See ‘/tmp/workdir/ImFoR/new/ImFoR.Rcheck/00install.out’ for details. - ``` - -# iNEXT.4steps - -
- -* Version: 1.0.0 -* GitHub: https://github.com/KaiHsiangHu/iNEXT.4steps -* Source code: https://github.com/cran/iNEXT.4steps -* Date/Publication: 2024-04-10 20:00:05 UTC -* Number of recursive dependencies: 107 - -Run `revdepcheck::cloud_details(, "iNEXT.4steps")` for more info - -
- -## Newly broken - -* checking whether package ‘iNEXT.4steps’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘iNEXT.4steps’ - See ‘/tmp/workdir/iNEXT.4steps/new/iNEXT.4steps.Rcheck/00install.out’ for details. - ``` - -# insane - -
- -* Version: 1.0.3 -* GitHub: https://github.com/mcanouil/insane -* Source code: https://github.com/cran/insane -* Date/Publication: 2023-11-14 21:50:02 UTC -* Number of recursive dependencies: 127 - -Run `revdepcheck::cloud_details(, "insane")` for more info - -
- -## Newly broken - -* checking whether package ‘insane’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘insane’ - See ‘/tmp/workdir/insane/new/insane.Rcheck/00install.out’ for details. - ``` - -# MarketMatching - -
- -* Version: 1.2.1 -* GitHub: NA -* Source code: https://github.com/cran/MarketMatching -* Date/Publication: 2024-01-31 09:40:02 UTC -* Number of recursive dependencies: 73 - -Run `revdepcheck::cloud_details(, "MarketMatching")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... ERROR - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘MarketMatching-Vignette.Rmd’ using rmarkdown_notangle - - Quitting from lines 114-115 [unnamed-chunk-3] (MarketMatching-Vignette.Rmd) - Error: processing vignette 'MarketMatching-Vignette.Rmd' failed with diagnostics: - `transform_date()` works with objects of class only - --- failed re-building ‘MarketMatching-Vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘MarketMatching-Vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# mc2d - -
- -* Version: 0.2.0 -* GitHub: NA -* Source code: https://github.com/cran/mc2d -* Date/Publication: 2023-07-17 16:00:02 UTC -* Number of recursive dependencies: 84 - -Run `revdepcheck::cloud_details(, "mc2d")` for more info - -
- -## Newly broken - -* checking whether package ‘mc2d’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘mc2d’ - See ‘/tmp/workdir/mc2d/new/mc2d.Rcheck/00install.out’ for details. - ``` - -## In both - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘docmcEnglish.Rnw’ using Sweave - Loading required package: mvtnorm - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘mc2d’ - - Attaching package: ‘mc2d’ - - The following objects are masked from ‘package:base’: - - pmax, pmin - ... - l.179 \RequirePackage{grfext}\relax - ^^M - ! ==> Fatal error occurred, no output PDF file produced! - --- failed re-building ‘mc2dLmEnglish.rnw’ - - SUMMARY: processing the following files failed: - ‘docmcEnglish.Rnw’ ‘mc2dLmEnglish.rnw’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# MetaIntegrator - -
- -* Version: 2.1.3 -* GitHub: NA -* Source code: https://github.com/cran/MetaIntegrator -* Date/Publication: 2020-02-26 13:00:11 UTC -* Number of recursive dependencies: 178 - -Run `revdepcheck::cloud_details(, "MetaIntegrator")` for more info - -
- -## Newly broken - -* checking whether package ‘MetaIntegrator’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘MetaIntegrator’ - See ‘/tmp/workdir/MetaIntegrator/new/MetaIntegrator.Rcheck/00install.out’ for details. - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.8Mb - sub-directories of 1Mb or more: - data 3.9Mb - doc 2.1Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘BiocManager’ ‘DT’ ‘GEOmetadb’ ‘RMySQL’ ‘RSQLite’ ‘gplots’ ‘pheatmap’ - ‘readr’ - All declared Imports should be used. - ``` - -# MF.beta4 - -
- -* Version: 1.0.3 -* GitHub: https://github.com/AnneChao/MF.beta4 -* Source code: https://github.com/cran/MF.beta4 -* Date/Publication: 2024-04-16 16:30:02 UTC -* Number of recursive dependencies: 173 - -Run `revdepcheck::cloud_details(, "MF.beta4")` for more info - -
- -## Newly broken - -* checking whether package ‘MF.beta4’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘MF.beta4’ - See ‘/tmp/workdir/MF.beta4/new/MF.beta4.Rcheck/00install.out’ for details. - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Introduction.Rnw’ using Sweave - Error: processing vignette 'Introduction.Rnw' failed with diagnostics: - Running 'texi2dvi' on 'Introduction.tex' failed. - LaTeX errors: - ! LaTeX Error: File `pdfpages.sty' not found. - - Type X to quit or to proceed, - or enter new name. (Default extension: sty) - ... - l.4 ^^M - - ! ==> Fatal error occurred, no output PDF file produced! - --- failed re-building ‘Introduction.Rnw’ - - SUMMARY: processing the following file failed: - ‘Introduction.Rnw’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# MIMSunit - -
- -* Version: 0.11.2 -* GitHub: https://github.com/mhealthgroup/MIMSunit -* Source code: https://github.com/cran/MIMSunit -* Date/Publication: 2022-06-21 11:00:09 UTC -* Number of recursive dependencies: 114 - -Run `revdepcheck::cloud_details(, "MIMSunit")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘MIMSunit-Ex.R’ failed - The error most likely occurred in: - - > ### Name: illustrate_extrapolation - > ### Title: Plot illustrations about extrapolation in illustration style. - > ### Aliases: illustrate_extrapolation - > - > ### ** Examples - > - > # Use the maxed-out data for the conceptual diagram - ... - 12. └─ggplot2 (local) transform_df(..., self = self) - 13. └─base::lapply(df[aesthetics], self$transform) - 14. └─ggplot2 (local) FUN(X[[i]], ...) - 15. └─ggplot2 (local) transform(..., self = self) - 16. └─ggproto_parent(ScaleContinuous, self)$transform(x) - 17. └─ggplot2 (local) transform(..., self = self) - 18. └─transformation$transform(x) - 19. └─cli::cli_abort("{.fun transform_time} works with objects of class {.cls POSIXct} only") - 20. └─rlang::abort(...) - Execution halted - ``` - -# missingHE - -
- -* Version: 1.5.0 -* GitHub: NA -* Source code: https://github.com/cran/missingHE -* Date/Publication: 2023-03-21 08:50:02 UTC -* Number of recursive dependencies: 151 - -Run `revdepcheck::cloud_details(, "missingHE")` for more info - -
- -## Newly broken - -* checking whether package ‘missingHE’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘missingHE’ - See ‘/tmp/workdir/missingHE/new/missingHE.Rcheck/00install.out’ for details. - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘mcmcr’ - All declared Imports should be used. - ``` - -# MSPRT - -
- -* Version: 3.0 -* GitHub: NA -* Source code: https://github.com/cran/MSPRT -* Date/Publication: 2020-11-13 10:20:05 UTC -* Number of recursive dependencies: 87 - -Run `revdepcheck::cloud_details(, "MSPRT")` for more info - -
- -## Newly broken - -* checking whether package ‘MSPRT’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘MSPRT’ - See ‘/tmp/workdir/MSPRT/new/MSPRT.Rcheck/00install.out’ for details. - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘datasets’ ‘grDevices’ ‘graphics’ ‘iterators’ ‘methods’ - All declared Imports should be used. - ``` - -# nzelect - -
- -* Version: 0.4.0 -* GitHub: NA -* Source code: https://github.com/cran/nzelect -* Date/Publication: 2017-10-02 20:35:23 UTC -* Number of recursive dependencies: 95 - -Run `revdepcheck::cloud_details(, "nzelect")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘nzelect-Ex.R’ failed - The error most likely occurred in: - - > ### Name: polls - > ### Title: New Zealand Opinion Polls - > ### Aliases: polls - > ### Keywords: datasets - > - > ### ** Examples - > - ... - 10. └─ggplot2 (local) FUN(X[[i]], ...) - 11. └─scale$transform_df(df = df) - 12. └─ggplot2 (local) transform_df(..., self = self) - 13. └─base::lapply(df[aesthetics], self$transform) - 14. └─ggplot2 (local) FUN(X[[i]], ...) - 15. └─ggplot2 (local) transform(..., self = self) - 16. └─transformation$transform(x) - 17. └─cli::cli_abort("{.fun transform_date} works with objects of class {.cls Date} only") - 18. └─rlang::abort(...) - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.9Mb - sub-directories of 1Mb or more: - data 5.6Mb - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 6409 marked UTF-8 strings - ``` - -# OenoKPM - -
- -* Version: 2.4.1 -* GitHub: NA -* Source code: https://github.com/cran/OenoKPM -* Date/Publication: 2024-04-08 19:20:10 UTC -* Number of recursive dependencies: 85 - -Run `revdepcheck::cloud_details(, "OenoKPM")` for more info - -
- -## Newly broken - -* checking whether package ‘OenoKPM’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘OenoKPM’ - See ‘/tmp/workdir/OenoKPM/new/OenoKPM.Rcheck/00install.out’ for details. - ``` - -# posologyr - -
- -* Version: 1.2.4 -* GitHub: https://github.com/levenc/posologyr -* Source code: https://github.com/cran/posologyr -* Date/Publication: 2024-02-09 11:50:02 UTC -* Number of recursive dependencies: 98 - -Run `revdepcheck::cloud_details(, "posologyr")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘a_priori_dosing.Rmd’ - ... - 16: source(output, echo = TRUE) - 17: doTryCatch(return(expr), name, parentenv, handler) - 18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) - 19: tryCatchList(expr, classes, parentenv, handlers) - 20: tryCatch({ source(output, echo = TRUE)}, error = function(e) { cat("\n When sourcing ", sQuote(output), ":\n", sep = "") stop(conditionMessage(e), call. = FALSE, domain = NA)}) - 21: tools:::.run_one_vignette("a_priori_dosing.Rmd", "/tmp/workdir/posologyr/new/posologyr.Rcheck/00_pkg_src/posologyr/vignettes", encoding = "UTF-8", pkgdir = "/tmp/workdir/posologyr/new/posologyr.Rcheck/00_pkg_src/posologyr") - An irrecoverable exception occurred. R is aborting now ... - ... - Segmentation fault - - ... incomplete output. Crash? - - ‘a_posteriori_dosing.Rmd’ using ‘UTF-8’... OK - ‘a_priori_dosing.Rmd’ using ‘UTF-8’... failed to complete the test - ‘auc_based_dosing.Rmd’ using ‘UTF-8’... OK - ‘multiple_endpoints.Rmd’ using ‘UTF-8’... OK - ‘patient_data_input.Rmd’ using ‘UTF-8’... OK - ‘posologyr_user_defined_models.Rmd’ using ‘UTF-8’... OK - ``` - -# qicharts - -
- -* Version: 0.5.8 -* GitHub: NA -* Source code: https://github.com/cran/qicharts -* Date/Publication: 2021-04-20 12:20:03 UTC -* Number of recursive dependencies: 56 - -Run `revdepcheck::cloud_details(, "qicharts")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘qicharts-Ex.R’ failed - The error most likely occurred in: - - > ### Name: tcc - > ### Title: Trellis Control Charts - > ### Aliases: tcc - > - > ### ** Examples - > - > # Run chart of 24 random normal variables - ... - 10. └─ggplot2 (local) FUN(X[[i]], ...) - 11. └─scale$transform_df(df = df) - 12. └─ggplot2 (local) transform_df(..., self = self) - 13. └─base::lapply(df[aesthetics], self$transform) - 14. └─ggplot2 (local) FUN(X[[i]], ...) - 15. └─ggplot2 (local) transform(..., self = self) - 16. └─transformation$transform(x) - 17. └─cli::cli_abort("{.fun transform_date} works with objects of class {.cls Date} only") - 18. └─rlang::abort(...) - Execution halted - ``` - -# qicharts2 - -
- -* Version: 0.7.5 -* GitHub: https://github.com/anhoej/qicharts2 -* Source code: https://github.com/cran/qicharts2 -* Date/Publication: 2024-05-09 06:20:03 UTC -* Number of recursive dependencies: 71 - -Run `revdepcheck::cloud_details(, "qicharts2")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘qicharts2.Rmd’ - ... - > qic(month, n, notes = notes, data = cdi, decimals = 0, - + title = "Hospital acquired Clostridium difficile infections", - + ylab = "Count", x .... [TRUNCATED] - - > qic(month, n, data = cdi, decimals = 0, freeze = 24, - + part.labels = c("Baseline", "Intervention"), title = "Hospital acquired Clostridium diff ..." ... [TRUNCATED] - - When sourcing ‘qicharts2.R’: - Error: `transform_time()` works with objects of class only - Execution halted - - ‘qicharts2.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘qicharts2.Rmd’ using rmarkdown - ``` - -# QuadratiK - -
- -* Version: 1.1.0 -* GitHub: https://github.com/giovsaraceno/QuadratiK-package -* Source code: https://github.com/cran/QuadratiK -* Date/Publication: 2024-05-14 13:50:06 UTC -* Number of recursive dependencies: 131 - -Run `revdepcheck::cloud_details(, "QuadratiK")` for more info - -
- -## Newly broken - -* checking whether package ‘QuadratiK’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘QuadratiK’ - See ‘/tmp/workdir/QuadratiK/new/QuadratiK.Rcheck/00install.out’ for details. - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 14.6Mb - sub-directories of 1Mb or more: - libs 12.9Mb - ``` - -# RCTrep - -
- -* Version: 1.2.0 -* GitHub: https://github.com/duolajiang/RCTrep -* Source code: https://github.com/cran/RCTrep -* Date/Publication: 2023-11-02 14:40:02 UTC -* Number of recursive dependencies: 166 - -Run `revdepcheck::cloud_details(, "RCTrep")` for more info - -
- -## Newly broken - -* checking whether package ‘RCTrep’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘RCTrep’ - See ‘/tmp/workdir/RCTrep/new/RCTrep.Rcheck/00install.out’ for details. - ``` +# explainer (plotly) -# scdtb +# ezEDA (missing labels) -
+# ezplot (0-length width) -* Version: 0.1.0 -* GitHub: https://github.com/mightymetrika/scdtb -* Source code: https://github.com/cran/scdtb -* Date/Publication: 2024-04-30 08:50:02 UTC -* Number of recursive dependencies: 97 +# fable.prophet (ggdist) -Run `revdepcheck::cloud_details(, "scdtb")` for more info +# fabletools (ggdist) -
+# factoextra (0-length width) -## Newly broken +# fairmodels (missing labels) -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > # This file is part of the standard setup for testthat. - > # It is recommended that you do not modify it. - > # - > # Where should you do additional test configuration? - > # Learn more about the roles of various files in: - > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview - > # * https://testthat.r-lib.org/articles/special-files.html - ... - Error in `nlme::gls(model = mod_form, data = .df, method = "REML", correlation = nlme::corAR1(form = re_form), - ...)`: false convergence (8) - Backtrace: - ▆ - 1. └─scdtb::mixed_model_analysis(...) at test-mixed_model_analysis.R:114:3 - 2. └─nlme::gls(...) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 45 ] - Error: Test failures - Execution halted - ``` +# fddm (ggforce) -# SCOUTer +# feasts (missing labels) -
+# ffp (ggdist) -* Version: 1.0.0 -* GitHub: NA -* Source code: https://github.com/cran/SCOUTer -* Date/Publication: 2020-06-30 09:30:03 UTC -* Number of recursive dependencies: 99 +# fido (ggdist) -Run `revdepcheck::cloud_details(, "SCOUTer")` for more info +# flipr (unknown) + +``` +#
+# +# * Version: 0.3.3 +# * GitHub: https://github.com/LMJL-Alea/flipr +# * Source code: https://github.com/cran/flipr +# * Date/Publication: 2023-08-23 09:00:02 UTC +# * Number of recursive dependencies: 106 +# +# Run `revdepcheck::cloud_details(, "flipr")` for more info +# +#
+# +# ## Newly broken +# +# * checking re-building of vignette outputs ... NOTE +# ``` +# Error(s) in re-building vignettes: +# --- re-building ‘alternative.Rmd’ using rmarkdown +# --- finished re-building ‘alternative.Rmd’ +# +# --- re-building ‘exactness.Rmd’ using rmarkdown +# +# Quitting from lines 142-177 [unnamed-chunk-1] (exactness.Rmd) +# Error: processing vignette 'exactness.Rmd' failed with diagnostics: +# subscript out of bounds +# --- failed re-building ‘exactness.Rmd’ +# +# --- re-building ‘flipr.Rmd’ using rmarkdown +# ``` +# +# ## In both +# +# * checking running R code from vignettes ... ERROR +# ``` +# Errors in running code in vignettes: +# when running code in ‘exactness.Rmd’ +# ... +# +# > library(flipr) +# +# > load("../R/sysdata.rda") +# Warning in readChar(con, 5L, useBytes = TRUE) : +# cannot open compressed file '../R/sysdata.rda', probable reason 'No such file or directory' +# +# ... +# cannot open compressed file '../R/sysdata.rda', probable reason 'No such file or directory' +# +# When sourcing ‘plausibility.R’: +# Error: cannot open the connection +# Execution halted +# +# ‘alternative.Rmd’ using ‘UTF-8’... OK +# ‘exactness.Rmd’ using ‘UTF-8’... failed +# ‘flipr.Rmd’ using ‘UTF-8’... failed +# ‘plausibility.Rmd’ using ‘UTF-8’... failed +# ``` +# +# * checking installed package size ... NOTE +# ``` +# installed size is 11.0Mb +# sub-directories of 1Mb or more: +# doc 9.1Mb +# libs 1.2Mb +# ``` +``` -
+# foqat (ggnewscale) -## Newly broken +# forestly (patchwork) -* checking whether package ‘SCOUTer’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘SCOUTer’ - See ‘/tmp/workdir/SCOUTer/new/SCOUTer.Rcheck/00install.out’ for details. - ``` - -# sievePH - -
+# frailtyEM (plotly) -* Version: 1.0.4 -* GitHub: https://github.com/mjuraska/sievePH -* Source code: https://github.com/cran/sievePH -* Date/Publication: 2023-02-03 18:40:02 UTC -* Number of recursive dependencies: 82 - -Run `revdepcheck::cloud_details(, "sievePH")` for more info - -
- -## Newly broken - -* checking whether package ‘sievePH’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘sievePH’ - See ‘/tmp/workdir/sievePH/new/sievePH.Rcheck/00install.out’ for details. - ``` +# funcharts (patchwork) -# SouthParkRshiny +# geomtextpath (default access) -
+# GGally (missing labels) -* Version: 1.0.0 -* GitHub: https://github.com/Amalan-ConStat/SouthParkRshiny -* Source code: https://github.com/cran/SouthParkRshiny -* Date/Publication: 2024-03-09 11:10:08 UTC -* Number of recursive dependencies: 118 - -Run `revdepcheck::cloud_details(, "SouthParkRshiny")` for more info - -
- -## Newly broken - -* checking whether package ‘SouthParkRshiny’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘SouthParkRshiny’ - See ‘/tmp/workdir/SouthParkRshiny/new/SouthParkRshiny.Rcheck/00install.out’ for details. - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 8.6Mb - sub-directories of 1Mb or more: - data 8.0Mb - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 1562 marked UTF-8 strings - ``` +# gganimate (gganimate) -# SqueakR +# ggbrain (ggnewscale) -
+# ggbreak (patchwork) -* Version: 1.3.0 -* GitHub: https://github.com/osimon81/SqueakR -* Source code: https://github.com/cran/SqueakR -* Date/Publication: 2022-06-28 09:20:04 UTC -* Number of recursive dependencies: 142 +# ggdark (default access) -Run `revdepcheck::cloud_details(, "SqueakR")` for more info +# ggdist (ggdist) -
+# ggDoubleHeat (ggnewscale) -## Newly broken +# ggeasy (missing labels) -* checking whether package ‘SqueakR’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘SqueakR’ - See ‘/tmp/workdir/SqueakR/new/SqueakR.Rcheck/00install.out’ for details. - ``` +# ggedit (saved to disk) -## In both +# ggESDA (passing NULL aesthetic mapping) -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘SqueakR.Rmd’ - ... - $ experimenters : NULL - $ experimental_data: list() - - > my_new_data <- add_timepoint_data(data_path = "../inst/extdata/Example_Mouse_Data.xlsx", - + t1 = 5, t2 = 25) - Adding call features Excel file to workspace... - - When sourcing ‘SqueakR.R’: - Error: `path` does not exist: ‘../inst/extdata/Example_Mouse_Data.xlsx’ - Execution halted - - ‘SqueakR.Rmd’ using ‘UTF-8’... failed - ``` +# ggfixest (visual differences) -* checking installed package size ... NOTE - ``` - installed size is 8.8Mb - sub-directories of 1Mb or more: - doc 8.2Mb - ``` +# ggforce (ggforce) -# survminer +Note: facet_zoom/facet_col/facet_row -
+# ggformula (docs) -* Version: 0.4.9 -* GitHub: https://github.com/kassambara/survminer -* Source code: https://github.com/cran/survminer -* Date/Publication: 2021-03-09 09:50:03 UTC -* Number of recursive dependencies: 130 +# ggfortify (tests) + +# gggenomes (patchwork) + +# ggh4x (unknown) + +``` +#
+# +# * Version: 0.2.8 +# * GitHub: https://github.com/teunbrand/ggh4x +# * Source code: https://github.com/cran/ggh4x +# * Date/Publication: 2024-01-23 21:00:02 UTC +# * Number of recursive dependencies: 77 +# +# Run `revdepcheck::cloud_details(, "ggh4x")` for more info +# +#
+# +# ## Newly broken +# +# * checking examples ... ERROR +# ``` +# Running examples in ‘ggh4x-Ex.R’ failed +# The error most likely occurred in: +# +# > ### Name: guide_stringlegend +# > ### Title: String legend +# > ### Aliases: guide_stringlegend +# > +# > ### ** Examples +# > +# > p <- ggplot(mpg, aes(displ, hwy)) + +# + geom_point(aes(colour = manufacturer)) +# > +# > # String legend can be set in the `guides()` function +# > p + guides(colour = guide_stringlegend(ncol = 2)) +# Error in (function (layer, df) : +# argument "theme" is missing, with no default +# Calls: ... use_defaults -> eval_from_theme -> %||% -> calc_element +# Execution halted +# ``` +# +# * checking tests ... ERROR +# ``` +# Running ‘testthat.R’ +# Running the tests in ‘tests/testthat.R’ failed. +# Complete output: +# > library(testthat) +# > library(ggh4x) +# Loading required package: ggplot2 +# > +# > test_check("ggh4x") +# [ FAIL 2 | WARN 20 | SKIP 18 | PASS 753 ] +# +# ... +# 25. └─ggplot2 (local) compute_geom_2(..., self = self) +# 26. └─self$geom$use_defaults(...) +# 27. └─ggplot2 (local) use_defaults(..., self = self) +# 28. └─ggplot2:::eval_from_theme(default_aes, theme) +# 29. ├─calc_element("geom", theme) %||% .default_geom_element +# 30. └─ggplot2::calc_element("geom", theme) +# +# [ FAIL 2 | WARN 20 | SKIP 18 | PASS 753 ] +# Error: Test failures +# Execution halted +# ``` +# +# * checking re-building of vignette outputs ... NOTE +# ``` +# Error(s) in re-building vignettes: +# --- re-building ‘Facets.Rmd’ using rmarkdown +# ``` +# +# ## In both +# +# * checking running R code from vignettes ... ERROR +# ``` +# Errors in running code in vignettes: +# when running code in ‘Miscellaneous.Rmd’ +# ... +# +# > ggplot(diamonds, aes(price, carat, colour = clarity)) + +# + geom_point(shape = ".") + scale_colour_brewer(palette = "Dark2", +# + guide = "stri ..." ... [TRUNCATED] +# Warning: The S3 guide system was deprecated in ggplot2 3.5.0. +# ℹ It has been replaced by a ggproto system that can be extended. +# +# ... +# ℹ Error occurred in the 1st layer. +# Caused by error in `setup_params()`: +# ! A discrete 'nbinom' distribution cannot be fitted to continuous data. +# Execution halted +# +# ‘Facets.Rmd’ using ‘UTF-8’... OK +# ‘Miscellaneous.Rmd’ using ‘UTF-8’... failed +# ‘PositionGuides.Rmd’ using ‘UTF-8’... OK +# ‘Statistics.Rmd’ using ‘UTF-8’... failed +# ‘ggh4x.Rmd’ using ‘UTF-8’... OK +# ``` +``` + +# gghighlight (default access) + +# ggHoriPlot (patchwork) + +# ggiraph (additional params) + +# ggiraphExtra (additional params) + +# ggmice (plotly) + +# ggmulti (custom use_defaults) + +# ggnewscale (ggnewscale) + +# ggparallel (unknown) + +``` +#
+# +# * Version: 0.4.0 +# * GitHub: https://github.com/heike/ggparallel +# * Source code: https://github.com/cran/ggparallel +# * Date/Publication: 2024-03-09 22:00:02 UTC +# * Number of recursive dependencies: 51 +# +# Run `revdepcheck::cloud_details(, "ggparallel")` for more info +# +#
+# +# ## Newly broken +# +# * checking tests ... ERROR +# ``` +# Running ‘testthat.R’ +# Running the tests in ‘tests/testthat.R’ failed. +# Complete output: +# > # This file is part of the standard setup for testthat. +# > # It is recommended that you do not modify it. +# > # +# > # Where should you do additional test configuration? +# > # Learn more about the roles of various files in: +# > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview +# > # * https://testthat.r-lib.org/articles/special-files.html +# ... +# 12. └─self$get_layer_key(params, layers[include], data[include], theme) +# 13. └─ggplot2 (local) get_layer_key(...) +# 14. └─base::Map(...) +# 15. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) +# 16. └─ggplot2 (local) ``(layer = dots[[1L]][[1L]], df = dots[[2L]][[1L]]) +# 17. └─layer$compute_geom_2(key, single_params, theme) +# +# [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] +# Error: Test failures +# Execution halted +# ``` +``` -Run `revdepcheck::cloud_details(, "survminer")` for more info +# ggpicrust2 (patchwork) -
+# ggpie (ggnewscale) -## Newly broken +# ggplotlyExtra (plotly) -* checking whether package ‘survminer’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘survminer’ - See ‘/tmp/workdir/survminer/new/survminer.Rcheck/00install.out’ for details. - ``` +# ggpol (default access) -## In both +# ggpubr (update tests) -* checking installed package size ... NOTE - ``` - installed size is 6.3Mb - sub-directories of 1Mb or more: - doc 5.5Mb - ``` +# ggraph (guide theme passing) -# symptomcheckR +# ggredist (unknown) -
+``` +#
+# +# * Version: 0.0.2 +# * GitHub: https://github.com/alarm-redist/ggredist +# * Source code: https://github.com/cran/ggredist +# * Date/Publication: 2022-11-23 11:20:02 UTC +# * Number of recursive dependencies: 67 +# +# Run `revdepcheck::cloud_details(, "ggredist")` for more info +# +#
+# +# ## Newly broken +# +# * checking examples ... ERROR +# ``` +# Running examples in ‘ggredist-Ex.R’ failed +# The error most likely occurred in: +# +# > ### Name: geom_district_text +# > ### Title: Label Map Regions +# > ### Aliases: geom_district_text geom_district_label +# > ### stat_district_coordinates StatDistrictCoordinates GeomDistrictText +# > ### Keywords: datasets +# > +# > ### ** Examples +# ... +# 22. │ └─coord$transform(data, panel_params) +# 23. │ └─ggplot2 (local) transform(..., self = self) +# 24. │ └─ggplot2:::sf_rescale01(...) +# 25. │ └─sf::st_normalize(x, c(x_range[1], y_range[1], x_range[2], y_range[2])) +# 26. └─base::.handleSimpleError(...) +# 27. └─rlang (local) h(simpleError(msg, call)) +# 28. └─handlers[[1L]](cnd) +# 29. └─cli::cli_abort(...) +# 30. └─rlang::abort(...) +# Execution halted +# ``` +``` -* Version: 0.1.3 -* GitHub: https://github.com/ma-kopka/symptomcheckR -* Source code: https://github.com/cran/symptomcheckR -* Date/Publication: 2024-04-16 20:40:06 UTC -* Number of recursive dependencies: 101 +# ggRtsy (missing labels) -Run `revdepcheck::cloud_details(, "symptomcheckR")` for more info +# ggseqplot (length 0 width) -
+# ggside (unknown) -## Newly broken +``` +#
+# +# * Version: 0.3.1 +# * GitHub: https://github.com/jtlandis/ggside +# * Source code: https://github.com/cran/ggside +# * Date/Publication: 2024-03-01 09:12:37 UTC +# * Number of recursive dependencies: 76 +# +# Run `revdepcheck::cloud_details(, "ggside")` for more info +# +#
+# +# ## Newly broken +# +# * checking tests ... ERROR +# ``` +# Running ‘testthat.R’ +# Running the tests in ‘tests/testthat.R’ failed. +# Complete output: +# > library(testthat) +# > library(ggplot2) +# > library(ggside) +# Registered S3 method overwritten by 'ggside': +# method from +# +.gg ggplot2 +# > +# ... +# • ops_meaningful/alpha-0-5-from-function.svg +# • side_layers/boxplot2.svg +# • vdiff_irisScatter/collapsed-histo.svg +# • vdiff_irisScatter/facetgrid-collapsed-density.svg +# • vdiff_irisScatter/facetgrid-histo.svg +# • vdiff_irisScatter/facetgrid-side-density.svg +# • vdiff_irisScatter/stacked-side-density.svg +# • vdiff_irisScatter/yside-histo.svg +# Error: Test failures +# Execution halted +# ``` +# +# * checking for code/documentation mismatches ... WARNING +# ``` +# Codoc mismatches from documentation object 'geom_xsideabline': +# geom_xsidehline +# Code: function(mapping = NULL, data = NULL, position = "identity", +# ..., yintercept, na.rm = FALSE, show.legend = NA) +# Docs: function(mapping = NULL, data = NULL, ..., yintercept, na.rm = +# FALSE, show.legend = NA) +# Argument names in code not in docs: +# position +# Mismatches in argument names (first 3): +# Position: 3 Code: position Docs: ... +# ... +# Docs: function(mapping = NULL, data = NULL, stat = "identity", +# position = "identity", ..., lineend = "butt", linejoin +# = "round", linemitre = 10, arrow = NULL, na.rm = +# FALSE, show.legend = NA, inherit.aes = TRUE) +# Argument names in code not in docs: +# arrow.fill +# Mismatches in argument names: +# Position: 10 Code: arrow.fill Docs: na.rm +# Position: 11 Code: na.rm Docs: show.legend +# Position: 12 Code: show.legend Docs: inherit.aes +# ``` +``` -* checking whether package ‘symptomcheckR’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘symptomcheckR’ - See ‘/tmp/workdir/symptomcheckR/new/symptomcheckR.Rcheck/00install.out’ for details. - ``` +# ggspatial (missing defaults) -# tcgaViz +# ggtern (ggtern) -
+# ggupset (unknown) -* Version: 1.0.2 -* GitHub: NA -* Source code: https://github.com/cran/tcgaViz -* Date/Publication: 2023-04-04 15:40:02 UTC -* Number of recursive dependencies: 139 +``` +#
+# +# * Version: 0.4.0 +# * GitHub: https://github.com/const-ae/ggupset +# * Source code: https://github.com/cran/ggupset +# * Date/Publication: 2024-06-24 10:10:04 UTC +# * Number of recursive dependencies: 46 +# +# Run `revdepcheck::cloud_details(, "ggupset")` for more info +# +#
+# +# ## Newly broken +# +# * checking examples ... ERROR +# ``` +# Running examples in ‘ggupset-Ex.R’ failed +# The error most likely occurred in: +# +# > ### Name: axis_combmatrix +# > ### Title: Convert delimited text labels into a combination matrix axis +# > ### Aliases: axis_combmatrix +# > +# > ### ** Examples +# > +# > library(ggplot2) +# ... +# Datsun 710 Cyl: 4_Gears: 4 +# Hornet 4 Drive Cyl: 6_Gears: 3 +# Hornet Sportabout Cyl: 8_Gears: 3 +# Valiant Cyl: 6_Gears: 3 +# > ggplot(mtcars, aes(x=combined)) + +# + geom_bar() + +# + axis_combmatrix(sep = "_") +# Error in as.unit(e2) : object is not coercible to a unit +# Calls: ... polylineGrob -> is.unit -> unit.c -> Ops.unit -> as.unit +# Execution halted +# ``` +``` -Run `revdepcheck::cloud_details(, "tcgaViz")` for more info +# ggVennDiagram (plotly) -
+# greatR (patchwork) -## Newly broken +# Greymodels (plotly) -* checking whether package ‘tcgaViz’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘tcgaViz’ - See ‘/tmp/workdir/tcgaViz/new/tcgaViz.Rcheck/00install.out’ for details. - ``` +# gtExtras (unknown) -# TestGardener +``` +#
+# +# * Version: 0.5.0 +# * GitHub: https://github.com/jthomasmock/gtExtras +# * Source code: https://github.com/cran/gtExtras +# * Date/Publication: 2023-09-15 22:32:06 UTC +# * Number of recursive dependencies: 105 +# +# Run `revdepcheck::cloud_details(, "gtExtras")` for more info +# +#
+# +# ## Newly broken +# +# * checking tests ... ERROR +# ``` +# Running ‘testthat.R’ +# Running the tests in ‘tests/testthat.R’ failed. +# Complete output: +# > library(testthat) +# > library(gtExtras) +# Loading required package: gt +# +# Attaching package: 'gt' +# +# The following object is masked from 'package:testthat': +# ... +# ══ Failed tests ════════════════════════════════════════════════════════════════ +# ── Failure ('test-gt_plt_bar.R:44:3'): gt_plt_bar svg is created and has specific values ── +# `bar_neg_vals` (`actual`) not equal to c("49.19", "32.79", "16.40", "16.40", "32.79", "49.19") (`expected`). +# +# `actual`: "49.19" "32.79" "16.40" "0.00" "0.00" "0.00" +# `expected`: "49.19" "32.79" "16.40" "16.40" "32.79" "49.19" +# +# [ FAIL 1 | WARN 14 | SKIP 23 | PASS 115 ] +# Error: Test failures +# Execution halted +# ``` +``` -
+# HaploCatcher (patchwork) -* Version: 3.3.3 -* GitHub: NA -* Source code: https://github.com/cran/TestGardener -* Date/Publication: 2024-03-20 13:50:02 UTC -* Number of recursive dependencies: 131 +# healthyR (plotly) -Run `revdepcheck::cloud_details(, "TestGardener")` for more info +# healthyR.ts (plotly) -
+# heatmaply (plotly) -## Newly broken +# hermiter (patchwork) -* checking whether package ‘TestGardener’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘TestGardener’ - See ‘/tmp/workdir/TestGardener/new/TestGardener.Rcheck/00install.out’ for details. - ``` +# hesim (missing labels) -# tidydr +# hidecan (ggnewscale) -
+# HVT (plotly) -* Version: 0.0.5 -* GitHub: https://github.com/YuLab-SMU/tidydr -* Source code: https://github.com/cran/tidydr -* Date/Publication: 2023-03-08 09:20:02 UTC -* Number of recursive dependencies: 71 +# hypsoLoop (namespace conflict) -Run `revdepcheck::cloud_details(, "tidydr")` for more info +# ICvectorfields (ggnewscale) -
+# idopNetwork (patchwork) -## Newly broken +# inferCSN (plotly) -* checking whether package ‘tidydr’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/tidydr/new/tidydr.Rcheck/00install.out’ for details. - ``` +# insurancerating (patchwork) -## Installation +# inTextSummaryTable (default access) -### Devel +# inventorize (unknown) ``` -* installing *source* package ‘tidydr’ ... -** package ‘tidydr’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in get(x, envir = ns, inherits = FALSE) : - object 'len0_null' not found -Error: unable to load R code in package ‘tidydr’ -Execution halted -ERROR: lazy loading failed for package ‘tidydr’ -* removing ‘/tmp/workdir/tidydr/new/tidydr.Rcheck/tidydr’ +#
+# +# * Version: 1.1.1 +# * GitHub: NA +# * Source code: https://github.com/cran/inventorize +# * Date/Publication: 2022-05-31 22:20:09 UTC +# * Number of recursive dependencies: 71 +# +# Run `revdepcheck::cloud_details(, "inventorize")` for more info +# +#
+# +# ## Newly broken +# +# * checking whether package ‘inventorize’ can be installed ... ERROR +# ``` +# Installation failed. +# See ‘/tmp/workdir/inventorize/new/inventorize.Rcheck/00install.out’ for details. +# ``` +# +# ## Installation +# +# ### Devel +# +# ``` +# * installing *source* package ‘inventorize’ ... +# ** package ‘inventorize’ successfully unpacked and MD5 sums checked +# ** using staged installation +# ** R +# ** byte-compile and prepare package for lazy loading +# Error in pm[[2]] : subscript out of bounds +# Error: unable to load R code in package ‘inventorize’ +# Execution halted +# ERROR: lazy loading failed for package ‘inventorize’ +# * removing ‘/tmp/workdir/inventorize/new/inventorize.Rcheck/inventorize’ +# +# +# ``` +# ### CRAN +# +# ``` +# * installing *source* package ‘inventorize’ ... +# ** package ‘inventorize’ successfully unpacked and MD5 sums checked +# ** using staged installation +# ** R +# ** byte-compile and prepare package for lazy loading +# Warning in qgamma(service_level, alpha, beta) : NaNs produced +# Warning in qgamma(service_level, alpha, beta) : NaNs produced +# ** help +# *** installing help indices +# ** building package indices +# ** testing if installed package can be loaded from temporary location +# ** testing if installed package can be loaded from final location +# ** testing if installed package keeps a record of temporary installation path +# * DONE (inventorize) +# +# +# ``` +``` +# karel (gganimate) + +# kDGLM (plotly) + +# latentcor (plotly) + +# lcars (device issue) + +# lemon (resolve theme) + +# lfproQC (plotly) + +# LMoFit (saved to disk) + +# manydata (plot slots) + +# MARVEL (ggnewscale) + +# MBNMAdose (cannot reproduce) + +# MBNMAtime (ggdist) + +# MetaNet (ggnewscale) +# metR (fixed in dev) +# migraph (missing labels) + +# MiMIR (plotly) + +# miRetrieve (plotly) + +# misspi (plotly) + +# mizer (cannot reproduce) + +# mlr3spatiotempcv (patchwork) + +# mlr3viz (patchwork) + +# modeltime.resample (plotly) + +# move (false positive) + +# mtb (missing labels) + +# neatmaps (plotly) + +# NetFACS (false positive) + +# NeuralSens (ggnewscale) + +# NHSRplotthedots (missing labels) + +# NIMAA (plotly) + +# OBIC (patchwork) + +# OmicNavigator (plotly) + +# oncomsm (patchwork) + +# pafr (missing labels) + +# patchwork (patchwork) + +# pathviewr (missing labels) + +# pcutils (patchwork) + +# pdxTrees (gganimate) + +# personalized (plotly) + +# phylepic (ggnewscale) + +# Plasmidprofiler (plotly) + +# platetools (faulty tests) + +# plotDK (missing labels) + +# plotly (plotly) + +# pmartR (unknown) + +``` +#
+# +# * Version: 2.4.5 +# * GitHub: https://github.com/pmartR/pmartR +# * Source code: https://github.com/cran/pmartR +# * Date/Publication: 2024-05-21 15:50:02 UTC +# * Number of recursive dependencies: 149 +# +# Run `revdepcheck::cloud_details(, "pmartR")` for more info +# +#
+# +# ## Newly broken +# +# * checking tests ... ERROR +# ``` +# Running ‘testthat.R’ +# Running the tests in ‘tests/testthat.R’ failed. +# Complete output: +# > library(testthat) +# > library(pmartR) +# > +# > test_check("pmartR") +# [ FAIL 1 | WARN 1 | SKIP 11 | PASS 2375 ] +# +# ══ Skipped tests (11) ══════════════════════════════════════════════════════════ +# ... +# • plots/plot-spansres-color-high-color-low.svg +# • plots/plot-spansres.svg +# • plots/plot-statres-anova-volcano.svg +# • plots/plot-statres-anova.svg +# • plots/plot-statres-combined-volcano.svg +# • plots/plot-statres-combined.svg +# • plots/plot-statres-gtest.svg +# • plots/plot-totalcountfilt.svg +# Error: Test failures +# Execution halted +# ``` +# +# ## In both +# +# * checking installed package size ... NOTE +# ``` +# installed size is 10.4Mb +# sub-directories of 1Mb or more: +# R 1.5Mb +# help 1.5Mb +# libs 6.3Mb +# ``` ``` -### CRAN + +# pmxTools (ggdist) + +# posterior (ggdist) + +# PPQplan (plotly) + +# ppseq (plotly) + +# precrec (patchwork) + +# priorsense (ggdist) + +# ProAE (ggnewscale) + +# probably (missing labels) + +# processmapR (plotly) + +# psborrow (missing labels) + +# r2dii.plot (missing labels) + +# Radviz (accessing defaults) + +# rassta (plotly) + +# REddyProc (false positive) + +# redist (patchwork) + +# reReg (length 0 width) + +# reservr (patchwork) + +# rKOMICS (unknown) ``` -* installing *source* package ‘tidydr’ ... -** package ‘tidydr’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -** help -*** installing help indices -** building package indices -** installing vignettes -** testing if installed package can be loaded from temporary location -** testing if installed package can be loaded from final location -** testing if installed package keeps a record of temporary installation path -* DONE (tidydr) +#
+# +# * Version: 1.3 +# * GitHub: NA +# * Source code: https://github.com/cran/rKOMICS +# * Date/Publication: 2023-06-29 22:40:03 UTC +# * Number of recursive dependencies: 128 +# +# Run `revdepcheck::cloud_details(, "rKOMICS")` for more info +# +#
+# +# ## Newly broken +# +# * checking examples ... ERROR +# ``` +# Running examples in ‘rKOMICS-Ex.R’ failed +# The error most likely occurred in: +# +# > ### Name: msc.pca +# > ### Title: Prinicple Component Analysis based on MSC +# > ### Aliases: msc.pca +# > +# > ### ** Examples +# > +# > data(matrices) +# ... +# 11. │ └─base::withCallingHandlers(...) +# 12. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) +# 13. └─l$compute_geom_2(d, theme = plot$theme) +# 14. └─ggplot2 (local) compute_geom_2(..., self = self) +# 15. └─self$geom$use_defaults(...) +# 16. └─ggplot2 (local) use_defaults(..., self = self) +# 17. └─ggplot2:::check_aesthetics(new_params, nrow(data)) +# 18. └─cli::cli_abort(...) +# 19. └─rlang::abort(...) +# Execution halted +# ``` +# +# ## In both +# +# * checking installed package size ... NOTE +# ``` +# installed size is 24.8Mb +# sub-directories of 1Mb or more: +# extdata 24.0Mb +# ``` +# +# * checking re-building of vignette outputs ... NOTE +# ``` +# Error(s) in re-building vignettes: +# --- re-building ‘example.Rnw’ using Sweave +# Loading required package: viridisLite +# Warning: Removed 95 rows containing non-finite outside the scale range +# (`stat_boxplot()`). +# Warning: Removed 89 rows containing non-finite outside the scale range +# (`stat_boxplot()`). +# Warning: Removed 149 rows containing non-finite outside the scale range +# (`stat_boxplot()`). +# Warning: Removed 286 rows containing non-finite outside the scale range +# ... +# l.5 \usepackage +# {xcolor}^^M +# ! ==> Fatal error occurred, no output PDF file produced! +# --- failed re-building ‘example.Rnw’ +# +# SUMMARY: processing the following file failed: +# ‘example.Rnw’ +# +# Error: Vignette re-building failed. +# Execution halted +# ``` +``` + +# RKorAPClient (missing labels) + +# RNAseqQC (patchwork) + +# roahd (plotly) + +# romic (plotly) + +# roptions (plotly) + +# santaR (plot slots) + +# scdtb (missing labels) + +# scoringutils (ggdist) + +# scUtils (missing labels) + +# SCVA (plotly) + +# SDMtune (missing labels) + +# SeaVal (plotly) + +# sgsR (missing labels) + +# SHAPforxgboost (ggforce) +# SHELF (unknown) ``` -# tis - -
- -* Version: 1.39 -* GitHub: NA -* Source code: https://github.com/cran/tis -* Date/Publication: 2021-09-28 19:50:02 UTC -* Number of recursive dependencies: 15 +#
+# +# * Version: 1.10.0 +# * GitHub: https://github.com/OakleyJ/SHELF +# * Source code: https://github.com/cran/SHELF +# * Date/Publication: 2024-05-07 14:20:03 UTC +# * Number of recursive dependencies: 126 +# +# Run `revdepcheck::cloud_details(, "SHELF")` for more info +# +#
+# +# ## Newly broken +# +# * checking re-building of vignette outputs ... NOTE +# ``` +# Error(s) in re-building vignettes: +# --- re-building ‘Dirichlet-elicitation.Rmd’ using rmarkdown +# ``` +``` + +# shinipsum (plot slots) + +# SimNPH (missing labels) + +# smallsets (patchwork) + +# spbal (empty sf) + +# spinifex (plotly) + +# sport (missing labels) + +# SqueakR (false positive) + +# statgenGWAS (device issue) + +# surveyexplorer (ggupset) + +# Sysrecon (patchwork) + +# tabledown (plotly) + +# TCIU (plotly) + +# tensorEVD (ggnewscale) + +# thematic (thematic) + +# tidybayes (ggdist) + +# tidycat (ggforce) + +# tidyCDISC (plotly) + +# tidydr (uses internals) + +# tidysdm (patchwork) + +# tidytreatment (ggdist) -Run `revdepcheck::cloud_details(, "tis")` for more info - -
+# timetk (plotly) -## Newly broken +# tinyarray (patchwork) -* checking examples ... ERROR - ``` - Running examples in ‘tis-Ex.R’ failed - The error most likely occurred in: - - > ### Name: fortify.tis - > ### Title: Fortify a tis object - > ### Aliases: fortify.tis - > - > ### ** Examples - > - > if(require("ggplot2") && require("reshape")) { - ... - 10. └─ggplot2 (local) FUN(X[[i]], ...) - 11. └─scale$transform_df(df = df) - 12. └─ggplot2 (local) transform_df(..., self = self) - 13. └─base::lapply(df[aesthetics], self$transform) - 14. └─ggplot2 (local) FUN(X[[i]], ...) - 15. └─ggplot2 (local) transform(..., self = self) - 16. └─transformation$transform(x) - 17. └─cli::cli_abort("{.fun transform_date} works with objects of class {.cls Date} only") - 18. └─rlang::abort(...) - Execution halted - ``` +# tornado (length 0 width) -## In both +# TOSTER (ggdist) -* checking package dependencies ... NOTE - ``` - Package which this enhances but not available for checking: ‘zoo’ - ``` +# TreatmentPatterns (plotly) -# UniprotR +# trelliscopejs (plotly) -
+# tricolore (ggtern) -* Version: 2.4.0 -* GitHub: https://github.com/Proteomicslab57357/UniprotR -* Source code: https://github.com/cran/UniprotR -* Date/Publication: 2024-03-05 15:10:02 UTC -* Number of recursive dependencies: 192 +# triptych (patchwork) -Run `revdepcheck::cloud_details(, "UniprotR")` for more info +# tsnet (ggdist) -
+# umiAnalyzer (plotly) -## Newly broken +# valr (missing labels) -* checking whether package ‘UniprotR’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘UniprotR’ - See ‘/tmp/workdir/UniprotR/new/UniprotR.Rcheck/00install.out’ for details. - ``` +# vivaldi (plotly) -# VALERIE +# vivid (ggnewscale) -
+# vvshiny (plotly) -* Version: 1.1.0 -* GitHub: NA -* Source code: https://github.com/cran/VALERIE -* Date/Publication: 2020-07-10 10:20:13 UTC -* Number of recursive dependencies: 133 +# wilson (plotly) -Run `revdepcheck::cloud_details(, "VALERIE")` for more info +# xaringanthemer (default access) -
- -## Newly broken - -* checking whether package ‘VALERIE’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘VALERIE’ - See ‘/tmp/workdir/VALERIE/new/VALERIE.Rcheck/00install.out’ for details. - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 9.6Mb - sub-directories of 1Mb or more: - extdata 8.7Mb - ``` - -# vannstats - -
- -* Version: 1.3.4.14 -* GitHub: NA -* Source code: https://github.com/cran/vannstats -* Date/Publication: 2023-04-15 04:30:02 UTC -* Number of recursive dependencies: 101 - -Run `revdepcheck::cloud_details(, "vannstats")` for more info - -
- -## Newly broken - -* checking whether package ‘vannstats’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘vannstats’ - See ‘/tmp/workdir/vannstats/new/vannstats.Rcheck/00install.out’ for details. - ``` - -# vici - -
- -* Version: 0.7.3 -* GitHub: https://github.com/sistm/vici -* Source code: https://github.com/cran/vici -* Date/Publication: 2024-02-02 16:20:02 UTC -* Number of recursive dependencies: 113 - -Run `revdepcheck::cloud_details(, "vici")` for more info - -
- -## Newly broken - -* checking whether package ‘vici’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘vici’ - See ‘/tmp/workdir/vici/new/vici.Rcheck/00install.out’ for details. - ``` - -# Wats - -
- -* Version: 1.0.1 -* GitHub: https://github.com/OuhscBbmc/Wats -* Source code: https://github.com/cran/Wats -* Date/Publication: 2023-03-10 22:50:05 UTC -* Number of recursive dependencies: 122 - -Run `revdepcheck::cloud_details(, "Wats")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘Wats-Ex.R’ failed - The error most likely occurred in: - - > ### Name: cartesian_periodic - > ### Title: Linear Plot with Periodic Elements - > ### Aliases: cartesian_periodic - > ### Keywords: Cartesian - > - > ### ** Examples - > - ... - 10. └─ggplot2 (local) FUN(X[[i]], ...) - 11. └─scale$transform_df(df = df) - 12. └─ggplot2 (local) transform_df(..., self = self) - 13. └─base::lapply(df[aesthetics], self$transform) - 14. └─ggplot2 (local) FUN(X[[i]], ...) - 15. └─ggplot2 (local) transform(..., self = self) - 16. └─transformation$transform(x) - 17. └─cli::cli_abort("{.fun transform_date} works with objects of class {.cls Date} only") - 18. └─rlang::abort(...) - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘mbr-figures.Rmd’ - ... - + dv_name = "birth_rate", center_function = stats::median, - + spread_function = h_sprea .... [TRUNCATED] - - > cartesian_rolling(ds_linear = portfolio_cartesian$ds_linear, - + x_name = "date", y_name = "birth_rate", stage_id_name = "stage_id", - + chang .... [TRUNCATED] - - When sourcing ‘mbr-figures.R’: - Error: `transform_date()` works with objects of class only - Execution halted - - ‘mbr-figures.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘mbr-figures.Rmd’ using rmarkdown - - Quitting from lines 135-165 [fig-2-individual-basic] (mbr-figures.Rmd) - Error: processing vignette 'mbr-figures.Rmd' failed with diagnostics: - `transform_date()` works with objects of class only - --- failed re-building ‘mbr-figures.Rmd’ - - SUMMARY: processing the following file failed: - ‘mbr-figures.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# xaringanthemer - -
- -* Version: 0.4.2 -* GitHub: https://github.com/gadenbuie/xaringanthemer -* Source code: https://github.com/cran/xaringanthemer -* Date/Publication: 2022-08-20 18:40:02 UTC -* Number of recursive dependencies: 75 - -Run `revdepcheck::cloud_details(, "xaringanthemer")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(xaringanthemer) - > - > test_check("xaringanthemer") - [ FAIL 1 | WARN 18 | SKIP 1 | PASS 308 ] - - ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ - ... - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure ('test-ggplot2.R:267:3'): theme_xaringan_restore_defaults() restores defaults ── - res$after_restore$line_colour (`actual`) not equal to res$original$colour (`expected`). - - `actual`: "#0088ff" - `expected`: "black" - - [ FAIL 1 | WARN 18 | SKIP 1 | PASS 308 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘xaringanthemer.Rmd’ - ... - Warning in file(con, "r") : - cannot open file './../man/fragments/_quick-intro.Rmd': No such file or directory - - Quitting from lines 43-43 [unnamed-chunk-2] (xaringanthemer.Rmd) - - When tangling ‘xaringanthemer.Rmd’: - Error: cannot open the connection - Execution halted - - ‘ggplot2-themes.Rmd’ using ‘UTF-8’... OK - ‘template-variables.Rmd’ using ‘UTF-8’... OK - ‘xaringanthemer.Rmd’ using ‘UTF-8’... failed - ``` +# yamlet (missing labels) diff --git a/tests/testthat/_snaps/coord-cartesian/clip-on-by-default-only-inside-visible.svg b/tests/testthat/_snaps/coord-cartesian/clip-on-by-default-only-inside-visible.svg index 6f424b0c4a..8532b083e3 100644 --- a/tests/testthat/_snaps/coord-cartesian/clip-on-by-default-only-inside-visible.svg +++ b/tests/testthat/_snaps/coord-cartesian/clip-on-by-default-only-inside-visible.svg @@ -27,14 +27,14 @@ -inside -inside -inside -inside -outside -outside -outside -outside +inside +inside +inside +inside +outside +outside +outside +outside clip on by default, only 'inside' visible diff --git a/tests/testthat/_snaps/coord-cartesian/clip-turned-off-both-inside-and-outside-visible.svg b/tests/testthat/_snaps/coord-cartesian/clip-turned-off-both-inside-and-outside-visible.svg index 89932b9196..b2120e5e14 100644 --- a/tests/testthat/_snaps/coord-cartesian/clip-turned-off-both-inside-and-outside-visible.svg +++ b/tests/testthat/_snaps/coord-cartesian/clip-turned-off-both-inside-and-outside-visible.svg @@ -20,14 +20,14 @@ -inside -inside -inside -inside -outside -outside -outside -outside +inside +inside +inside +inside +outside +outside +outside +outside clip turned off, both 'inside' and 'outside' visible diff --git a/tests/testthat/_snaps/coord-polar/bottom-half-circle-with-rotated-text.svg b/tests/testthat/_snaps/coord-polar/bottom-half-circle-with-rotated-text.svg index 30c4b0fc24..caa297b3f5 100644 --- a/tests/testthat/_snaps/coord-polar/bottom-half-circle-with-rotated-text.svg +++ b/tests/testthat/_snaps/coord-polar/bottom-half-circle-with-rotated-text.svg @@ -40,18 +40,18 @@ -cat -strawberry -cake -coffee -window -fluid -cat -strawberry -cake -coffee -window -fluid +cat +strawberry +cake +coffee +window +fluid +cat +strawberry +cake +coffee +window +fluid 1 2 3 diff --git a/tests/testthat/_snaps/facet-/facet-wrap-with-omitted-inner-axis-labels.svg b/tests/testthat/_snaps/facet-/facet-wrap-with-omitted-inner-axis-labels.svg index 66caee5c07..7c936b4768 100644 --- a/tests/testthat/_snaps/facet-/facet-wrap-with-omitted-inner-axis-labels.svg +++ b/tests/testthat/_snaps/facet-/facet-wrap-with-omitted-inner-axis-labels.svg @@ -108,83 +108,110 @@ - - + + - + + +6 - - + + - - -6 + 1 - - + + - + 8 - -0 - - + + - + + +0 - - + + - + 4 + + + + + + + + + 0 - - + + - + 4 + + + + + + + + + 1 - - + + - + 6 + + + + + + + + + 0 diff --git a/tests/testthat/_snaps/facet-labels/outside-justified-labels.svg b/tests/testthat/_snaps/facet-labels/outside-justified-labels.svg new file mode 100644 index 0000000000..9b04f0b614 --- /dev/null +++ b/tests/testthat/_snaps/facet-labels/outside-justified-labels.svg @@ -0,0 +1,144 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +C + + + + + + + + + + +D + + + + + + + + + + +A + + + + + + + + + + +B + + + +X +X +X +X +X + +X + +X +X +X +X +X + +X +YYYYY + +Y + + +YYYYY + +Y +x +y +outside-justified labels + + diff --git a/tests/testthat/_snaps/facet-layout.md b/tests/testthat/_snaps/facet-layout.md index 142bde22fe..1ab4474443 100644 --- a/tests/testthat/_snaps/facet-layout.md +++ b/tests/testthat/_snaps/facet-layout.md @@ -22,6 +22,10 @@ `nrow` must be a whole number or `NULL`, not the number 1.5. +--- + + Cannot use `space = "free_x"` with custom `nrow` or `ncol`. + --- Need 3 panels, but together `nrow` and `ncol` only provide 1. diff --git a/tests/testthat/_snaps/facet-layout/axes-are-positioned-correctly-in-non-table-layout.svg b/tests/testthat/_snaps/facet-layout/axes-are-positioned-correctly-in-non-table-layout.svg index c3f247ebe5..7d546bcc7e 100644 --- a/tests/testthat/_snaps/facet-layout/axes-are-positioned-correctly-in-non-table-layout.svg +++ b/tests/testthat/_snaps/facet-layout/axes-are-positioned-correctly-in-non-table-layout.svg @@ -93,24 +93,6 @@ - - - - - - - - - - - - - - - - - - @@ -349,15 +331,6 @@ - - - - - - - - - @@ -380,15 +353,6 @@ - - - - - - - - - diff --git a/tests/testthat/_snaps/geom-sf/labels-for-north-carolina.svg b/tests/testthat/_snaps/geom-sf/labels-for-north-carolina.svg index cf5ffdbbf2..f11f41251b 100644 --- a/tests/testthat/_snaps/geom-sf/labels-for-north-carolina.svg +++ b/tests/testthat/_snaps/geom-sf/labels-for-north-carolina.svg @@ -27,8 +27,8 @@ - -ashe + +ashe diff --git a/tests/testthat/_snaps/geom-sf/texts-for-north-carolina.svg b/tests/testthat/_snaps/geom-sf/texts-for-north-carolina.svg index 96ffe43109..ec2184a425 100644 --- a/tests/testthat/_snaps/geom-sf/texts-for-north-carolina.svg +++ b/tests/testthat/_snaps/geom-sf/texts-for-north-carolina.svg @@ -27,7 +27,7 @@ -ashe +ashe diff --git a/tests/testthat/_snaps/scale-hue.md b/tests/testthat/_snaps/scale-hue.md index bccf63c43a..8221bba045 100644 --- a/tests/testthat/_snaps/scale-hue.md +++ b/tests/testthat/_snaps/scale-hue.md @@ -1,4 +1,4 @@ # scale_hue() checks the type input - `type` must be a character vector or a list of character vectors. + `type` must be a character vector or list of character vectors, not an integer vector. diff --git a/tests/testthat/_snaps/theme/theme-bw-large.svg b/tests/testthat/_snaps/theme/theme-bw-large.svg index 148d1a93ca..cbffb819ac 100644 --- a/tests/testthat/_snaps/theme/theme-bw-large.svg +++ b/tests/testthat/_snaps/theme/theme-bw-large.svg @@ -45,9 +45,9 @@ - - - + + + @@ -87,9 +87,9 @@ z - + - + a b theme_bw_large diff --git a/tests/testthat/_snaps/theme/theme-classic-large.svg b/tests/testthat/_snaps/theme/theme-classic-large.svg index 96767cc14f..7105d5474b 100644 --- a/tests/testthat/_snaps/theme/theme-classic-large.svg +++ b/tests/testthat/_snaps/theme/theme-classic-large.svg @@ -27,9 +27,9 @@ - - - + + + @@ -43,36 +43,36 @@ 1 - - - - - - -1.0 -1.5 -2.0 -2.5 -3.0 - -1.0 -1.5 -2.0 -2.5 -3.0 - - - - - + + + + + + +1.0 +1.5 +2.0 +2.5 +3.0 + +1.0 +1.5 +2.0 +2.5 +3.0 + + + + + x y z - + - + a b theme_classic_large diff --git a/tests/testthat/_snaps/theme/theme-classic.svg b/tests/testthat/_snaps/theme/theme-classic.svg index 8588be9819..45ef7ef076 100644 --- a/tests/testthat/_snaps/theme/theme-classic.svg +++ b/tests/testthat/_snaps/theme/theme-classic.svg @@ -43,28 +43,28 @@ 1 - - - - - - -1.0 -1.5 -2.0 -2.5 -3.0 - -1.0 -1.5 -2.0 -2.5 -3.0 - - - - - + + + + + + +1.0 +1.5 +2.0 +2.5 +3.0 + +1.0 +1.5 +2.0 +2.5 +3.0 + + + + + x y diff --git a/tests/testthat/_snaps/theme/theme-dark-large.svg b/tests/testthat/_snaps/theme/theme-dark-large.svg index 9bad950947..f6f9c1058f 100644 --- a/tests/testthat/_snaps/theme/theme-dark-large.svg +++ b/tests/testthat/_snaps/theme/theme-dark-large.svg @@ -45,9 +45,9 @@ - - - + + + @@ -86,9 +86,9 @@ z - + - + a b theme_dark_large diff --git a/tests/testthat/_snaps/theme/theme-gray-large.svg b/tests/testthat/_snaps/theme/theme-gray-large.svg index a827864db6..4348638185 100644 --- a/tests/testthat/_snaps/theme/theme-gray-large.svg +++ b/tests/testthat/_snaps/theme/theme-gray-large.svg @@ -45,9 +45,9 @@ - - - + + + @@ -86,9 +86,9 @@ z - + - + a b theme_gray_large diff --git a/tests/testthat/_snaps/theme/theme-light-large.svg b/tests/testthat/_snaps/theme/theme-light-large.svg index 727f55ae02..29fc210917 100644 --- a/tests/testthat/_snaps/theme/theme-light-large.svg +++ b/tests/testthat/_snaps/theme/theme-light-large.svg @@ -45,9 +45,9 @@ - - - + + + @@ -87,9 +87,9 @@ z - + - + a b theme_light_large diff --git a/tests/testthat/_snaps/theme/theme-linedraw-large.svg b/tests/testthat/_snaps/theme/theme-linedraw-large.svg index 66998cd898..e2aadff6e7 100644 --- a/tests/testthat/_snaps/theme/theme-linedraw-large.svg +++ b/tests/testthat/_snaps/theme/theme-linedraw-large.svg @@ -45,9 +45,9 @@ - - - + + + @@ -87,9 +87,9 @@ z - + - + a b theme_linedraw_large diff --git a/tests/testthat/_snaps/theme/theme-minimal-large.svg b/tests/testthat/_snaps/theme/theme-minimal-large.svg index 4673e9cc60..8ec3b18625 100644 --- a/tests/testthat/_snaps/theme/theme-minimal-large.svg +++ b/tests/testthat/_snaps/theme/theme-minimal-large.svg @@ -43,9 +43,9 @@ - - - + + + @@ -71,8 +71,8 @@ x y z - - + + a b theme_minimal_large diff --git a/tests/testthat/_snaps/utilities-break.md b/tests/testthat/_snaps/utilities-break.md new file mode 100644 index 0000000000..31563a6cd7 --- /dev/null +++ b/tests/testthat/_snaps/utilities-break.md @@ -0,0 +1,4 @@ +# cut_interval throws the correct error message + + Specify exactly one of `n` and `length`. + diff --git a/tests/testthat/test-aes-calculated.R b/tests/testthat/test-aes-calculated.R index 62d25697d3..b453af02f5 100644 --- a/tests/testthat/test-aes-calculated.R +++ b/tests/testthat/test-aes-calculated.R @@ -6,7 +6,7 @@ test_that("names surrounded by .. is calculated", { expect_equal(is_calculated_aes(aes(..x.., ..x, x..)), c(TRUE, FALSE, FALSE)) # even when nested - expect_equal(is_calculated_aes(aes(f(..x..))), TRUE) + expect_true(is_calculated_aes(aes(f(..x..)))) }) test_that("call to stat() is calculated", { diff --git a/tests/testthat/test-aes-grouping.R b/tests/testthat/test-aes-grouping.R index bea15e2630..d5536cc417 100644 --- a/tests/testthat/test-aes-grouping.R +++ b/tests/testthat/test-aes-grouping.R @@ -26,7 +26,7 @@ test_that("no error for aes(groupS)", { g <- add_group(df2) expect_equal(nrow(g), nrow(df2)) - expect_equal(names(g), c("x", "y", "groupS", "group")) + expect_named(g, c("x", "y", "groupS", "group")) }) test_that("label is not used as a grouping var", { diff --git a/tests/testthat/test-coord-.R b/tests/testthat/test-coord-.R index b372478981..76a174454c 100644 --- a/tests/testthat/test-coord-.R +++ b/tests/testthat/test-coord-.R @@ -37,8 +37,7 @@ test_that("guide names are not removed by `train_panel_guides()`", { layout$setup_panel_guides(guides_list(NULL), plot$layers) # Line showing change in outcome - expect_equal(names(layout$panel_params[[1]]$guides$aesthetics), - c("x", "y", "x.sec", "y.sec")) + expect_named(layout$panel_params[[1]]$guides$aesthetics, c("x", "y", "x.sec", "y.sec")) }) test_that("check coord limits errors only on bad inputs", { diff --git a/tests/testthat/test-coord-polar.R b/tests/testthat/test-coord-polar.R index a663a43d98..da49368108 100644 --- a/tests/testthat/test-coord-polar.R +++ b/tests/testthat/test-coord-polar.R @@ -1,7 +1,7 @@ test_that("polar distance is calculated correctly", { dat <- data_frame( theta = c(0, 2*pi, 2, 6, 6, 1, 1, 0), - r = c(0, 0, 0.5, 0.5, 1, 1, 0.75, .5)) + r = c(0, 0, 0.5, 0.5, 1, 1, 0.75, 0.5)) scales <- list( x = scale_x_continuous(limits = c(0, 2*pi)), @@ -158,6 +158,9 @@ test_that("bounding box calculations are sensible", { # Visual tests ------------------------------------------------------------ +#TODO: Once {vdiffr} supports non-rectangular clipping paths, we should add a +# test for `coord_radial(clip = "on")`'s ability to clip to the sector + test_that("polar coordinates draw correctly", { theme <- theme_test() + theme( @@ -176,7 +179,7 @@ test_that("polar coordinates draw correctly", { dat <- data_frame( theta = c(0, 2*pi, 2, 6, 6, 1, 1, 0), - r = c(0, 0, 0.5, 0.5, 1, 1, 0.75, .5), + r = c(0, 0, 0.5, 0.5, 1, 1, 0.75, 0.5), g = 1:8 ) expect_doppelganger("Rays, circular arcs, and spiral arcs", diff --git a/tests/testthat/test-coord-train.R b/tests/testthat/test-coord-train.R index b326fc6fe1..9d42ec3c79 100644 --- a/tests/testthat/test-coord-train.R +++ b/tests/testthat/test-coord-train.R @@ -5,7 +5,7 @@ test_that("NA's don't appear in breaks", { ns <- names(trained)[grepl("(\\.major)|(\\.minor)$", names(trained))] for (n in ns) { - if (!is.null(trained[n]) && any(is.na(trained[n]))) + if (!is.null(trained[n]) && anyNA(trained[n])) return(TRUE) } @@ -19,8 +19,8 @@ test_that("NA's don't appear in breaks", { # This is a test to make sure the later tests will be useful! # It's possible that changes to the way that breaks are calculated will # make it so that scale_break_positions will no longer give NA for range 1, 12 - expect_true(any(is.na(scale_x$break_positions()))) - expect_true(any(is.na(scale_y$break_positions()))) + expect_true(anyNA(scale_x$break_positions())) + expect_true(anyNA(scale_y$break_positions())) # Check the various types of coords to make sure they don't have NA breaks expect_false(any_NA_major_minor(coord_polar()$setup_panel_params(scale_x, scale_y))) diff --git a/tests/testthat/test-coord_sf.R b/tests/testthat/test-coord_sf.R index c668b3ec79..12a667be5b 100644 --- a/tests/testthat/test-coord_sf.R +++ b/tests/testthat/test-coord_sf.R @@ -309,8 +309,8 @@ test_that("sf_transform_xy() works", { # transform back out2 <- sf_transform_xy(out, 4326, 3347) expect_identical(data$city, out2$city) - expect_true(all(abs(out2$x - data$x) < .01)) - expect_true(all(abs(out2$y - data$y) < .01)) + expect_true(all(abs(out2$x - data$x) < 0.01)) + expect_true(all(abs(out2$y - data$y) < 0.01)) }) diff --git a/tests/testthat/test-empty-data.R b/tests/testthat/test-empty-data.R index 3d7c27c52d..bdcc02003c 100644 --- a/tests/testthat/test-empty-data.R +++ b/tests/testthat/test-empty-data.R @@ -88,13 +88,13 @@ test_that("empty layers still generate one grob per panel", { geom_point() + facet_wrap(~y) - expect_equal(length(get_layer_grob(d)), 3) + expect_length(get_layer_grob(d), 3) }) test_that("missing layers generate one grob per panel", { df <- data_frame(x = 1:4, y = rep(1:2, 2), g = rep(1:2, 2)) base <- ggplot(df, aes(x, y)) + geom_point(shape = NA, na.rm = TRUE) - expect_equal(length(get_layer_grob(base)), 1) - expect_equal(length(get_layer_grob(base + facet_wrap(~ g))), 2) + expect_length(get_layer_grob(base), 1) + expect_length(get_layer_grob(base + facet_wrap(~ g)), 2) }) diff --git a/tests/testthat/test-facet-labels.R b/tests/testthat/test-facet-labels.R index 6d086e0b7b..c8613bc978 100644 --- a/tests/testthat/test-facet-labels.R +++ b/tests/testthat/test-facet-labels.R @@ -157,3 +157,30 @@ test_that("parsed labels are rendered correctly", { facet_wrap(~ f, labeller = label_parsed) ) }) + +test_that("outside-justified labels are justified across panels", { + + df <- data.frame( + x = c("X\nX\nX\nX\nX", "X"), + y = c("YYYYY", "Y"), + f1 = c("A", "B"), + f2 = c("C", "D") + ) + + # By default, axis labels are inside-justified so it doesn't matter whether + # justification occurs across panels. This changes for outside-justification. + # See #5820 + + p <- ggplot(df, aes(x, y)) + + geom_point() + + facet_grid(f1 ~ f2, scales = "free") + + guides(x.sec = "axis", y.sec = "axis") + + theme( + axis.text.y.left = element_text(hjust = 0), + axis.text.y.right = element_text(hjust = 1), + axis.text.x.top = element_text(vjust = 1), + axis.text.x.bottom = element_text(vjust = 0) + ) + + expect_doppelganger("outside-justified labels", p) +}) diff --git a/tests/testthat/test-facet-layout.R b/tests/testthat/test-facet-layout.R index 70a4ed30e8..a008a0c80d 100644 --- a/tests/testthat/test-facet-layout.R +++ b/tests/testthat/test-facet-layout.R @@ -172,6 +172,25 @@ test_that("grid: drop = FALSE preserves unused levels", { expect_equal(as.character(grid_ab$b), as.character(rep(4:1, 4))) }) +test_that("wrap: space = 'free_x/y' sets panel sizes", { + + df <- data.frame(x = 1:3) + p <- ggplot(df, aes(x, x)) + + geom_point() + + scale_x_continuous(limits = c(0, NA), expand = c(0, 0)) + + scale_y_continuous(limits = c(0, NA), expand = c(0, 0)) + + # Test free_x + gt <- ggplotGrob(p + facet_wrap(~x, scales = "free_x", space = "free_x")) + test <- gt$widths[panel_cols(gt)$l] + expect_equal(as.numeric(test), 1:3) + + # Test free_y + gt <- ggplotGrob(p + facet_wrap(~x, scales = "free_y", space = "free_y")) + test <- gt$heights[panel_rows(gt)$t] + expect_equal(as.numeric(test), 1:3) +}) + # Missing behaviour ---------------------------------------------------------- a3 <- data_frame( @@ -207,6 +226,8 @@ test_that("facet_wrap throws errors at bad layout specs", { expect_snapshot_error(facet_wrap(~test, nrow = -1)) expect_snapshot_error(facet_wrap(~test, nrow = 1.5)) + expect_snapshot_warning(facet_wrap(~test, nrow = 2, space = "free_x")) + p <- ggplot(mtcars) + geom_point(aes(mpg, disp)) + facet_wrap(~gear, ncol = 1, nrow = 1) @@ -232,6 +253,23 @@ test_that("facet_grid throws errors at bad layout specs", { expect_snapshot_error(ggplotGrob(p)) }) +test_that("facet_grid can respect coord aspect with free scales/space", { + df <- expand.grid(x = letters[1:6], y = LETTERS[1:3]) + p <- ggplot(df, aes(x, y)) + + geom_tile() + + facet_grid( + rows = vars(y == "C"), + cols = vars(x %in% c("e", "f")), + scales = "free", space = "free" + ) + + coord_fixed(3, expand = FALSE) + gt <- ggplotGrob(p) + width <- gt$widths[panel_cols(gt)$l] + height <- gt$heights[panel_rows(gt)$t] + expect_equal(as.numeric(width), c(4, 2)) + expect_equal(as.numeric(height), c(6, 3)) +}) + test_that("facet_wrap and facet_grid throws errors when using reserved words", { mtcars2 <- mtcars mtcars2$PANEL <- mtcars2$cyl diff --git a/tests/testthat/test-facet-strips.R b/tests/testthat/test-facet-strips.R index c2f131191e..d13f8d500c 100644 --- a/tests/testthat/test-facet-strips.R +++ b/tests/testthat/test-facet-strips.R @@ -143,16 +143,16 @@ test_that("padding is only added if axis is present", { strip.switch.pad.grid = unit(10, "mm") ) pg <- ggplotGrob(p) - expect_equal(length(pg$heights), 19) - expect_equal(length(pg$widths), 18) + expect_length(pg$heights, 19) + expect_length(pg$widths, 18) pg <- ggplotGrob( p + scale_x_continuous(position = "top") + scale_y_continuous(position = "right") ) - expect_equal(length(pg$heights), 20) + expect_length(pg$heights, 20) expect_equal(as.character(pg$heights[9]), "1cm") - expect_equal(length(pg$widths), 19) + expect_length(pg$widths, 19) expect_equal(as.character(pg$widths[13]), "1cm") # Also add padding with negative ticks and no text (#5251) @@ -160,7 +160,7 @@ test_that("padding is only added if axis is present", { p + scale_x_continuous(labels = NULL, position = "top") + theme(axis.ticks.length.x.top = unit(-2, "mm")) ) - expect_equal(length(pg$heights), 20) + expect_length(pg$heights, 20) expect_equal(as.character(pg$heights[9]), "1cm") # Inverse should be true when strips are switched @@ -172,17 +172,17 @@ test_that("padding is only added if axis is present", { ) pg <- ggplotGrob(p) - expect_equal(length(pg$heights), 20) + expect_length(pg$heights, 20) expect_equal(as.character(pg$heights[13]), "1cm") - expect_equal(length(pg$widths), 19) + expect_length(pg$widths, 19) expect_equal(as.character(pg$widths[7]), "1cm") pg <- ggplotGrob( p + scale_x_continuous(position = "top") + scale_y_continuous(position = "right") ) - expect_equal(length(pg$heights), 19) - expect_equal(length(pg$widths), 18) + expect_length(pg$heights, 19) + expect_length(pg$widths, 18) }) test_that("y strip labels are rotated when strips are switched", { diff --git a/tests/testthat/test-fortify.R b/tests/testthat/test-fortify.R index 03980c19c1..3a48c76ba0 100644 --- a/tests/testthat/test-fortify.R +++ b/tests/testthat/test-fortify.R @@ -11,7 +11,7 @@ test_that("spatial polygons have correct ordering", { y - dely,y - dely,y + dely,y + dely,y - dely), ncol = 2)) } - make_hole <- function(x = 0, y = 0, height = .5, width = .5){ + make_hole <- function(x = 0, y = 0, height = 0.5, width = 0.5){ p <- make_square(x = x, y = y, height = height, width = width) p@hole <- TRUE p diff --git a/tests/testthat/test-geom-.R b/tests/testthat/test-geom-.R index 61063d5d95..6766178f22 100644 --- a/tests/testthat/test-geom-.R +++ b/tests/testthat/test-geom-.R @@ -6,20 +6,43 @@ test_that("aesthetic checking in geom throws correct errors", { expect_snapshot_error(check_aesthetics(aes, 4)) }) +test_that("get_geom_defaults can use various sources", { + + test <- get_geom_defaults(geom_point) + expect_equal(test$colour, "black") + + test <- get_geom_defaults(geom_point(colour = "red")) + expect_equal(test$colour, "red") + + test <- get_geom_defaults("point") + expect_equal(test$colour, "black") + + test <- get_geom_defaults(GeomPoint, theme(geom = element_geom("red"))) + expect_equal(test$colour, "red") +}) + test_that("geom defaults can be set and reset", { l <- geom_point() - test <- l$geom$use_defaults(data_frame0()) + orig <- l$geom$default_aes$colour + test <- get_geom_defaults(l) expect_equal(test$colour, "black") inv <- update_geom_defaults("point", list(colour = "red")) - test <- l$geom$use_defaults(data_frame0()) + test <- get_geom_defaults(l) expect_equal(test$colour, "red") - expect_equal(inv$colour, "black") + expect_equal(inv$colour, orig) inv <- update_geom_defaults("point", NULL) - test <- l$geom$use_defaults(data_frame0()) + test <- get_geom_defaults(l) expect_equal(test$colour, "black") expect_equal(inv$colour, "red") + + inv <- update_geom_defaults("line", list(colour = "blue")) + reset <- reset_geom_defaults() + + expect_equal(reset$geom_line$colour, "blue") + expect_equal(reset$geom_point$colour, GeomPoint$default_aes$colour) + expect_equal(GeomLine$default_aes$colour, inv$colour) }) test_that("updating geom aesthetic defaults preserves class and order", { diff --git a/tests/testthat/test-geom-dotplot.R b/tests/testthat/test-geom-dotplot.R index 3cf61d4216..648c52f926 100644 --- a/tests/testthat/test-geom-dotplot.R +++ b/tests/testthat/test-geom-dotplot.R @@ -17,7 +17,7 @@ test_that("dodging works", { ndodge <- 3 # The amount of space allocated within each dodge group - dwidth <- .9 / ndodge + dwidth <- 0.9 / ndodge # This should be the x position for each before dodging xbase <- ceiling(df$group / ndodge) @@ -36,20 +36,20 @@ test_that("dodging works", { test_that("binning works", { bp <- ggplot(dat, aes(y)) + - geom_dotplot(binwidth = .4, method = "histodot") + geom_dotplot(binwidth = 0.4, method = "histodot") x <- get_layer_data(bp)$x # Need ugly hack to make sure mod function doesn't give values like -3.99999 # due to floating point error - expect_true(all(abs((x - min(x) + 1e-7) %% .4) < 1e-6)) + expect_true(all(abs((x - min(x) + 1e-7) %% 0.4) < 1e-6)) bp <- ggplot(dat, aes(x = y)) + - geom_dotplot(binwidth = .4, method = "dotdensity") + geom_dotplot(binwidth = 0.4, method = "dotdensity") x <- get_layer_data(bp)$x # This one doesn't ensure that dotdensity works, but it does check that it's not # doing fixed bin sizes - expect_false(all(abs((x - min(x) + 1e-7) %% .4) < 1e-6)) + expect_false(all(abs((x - min(x) + 1e-7) %% 0.4) < 1e-6)) }) test_that("NA's result in warning from stat_bindot", { @@ -58,7 +58,7 @@ test_that("NA's result in warning from stat_bindot", { dat$x[c(2,10)] <- NA # Need to assign it to a var here so that it doesn't automatically print - expect_snapshot_warning(ggplot_build(ggplot(dat, aes(x)) + geom_dotplot(binwidth = .2))) + expect_snapshot_warning(ggplot_build(ggplot(dat, aes(x)) + geom_dotplot(binwidth = 0.2))) }) test_that("when binning on y-axis, limits depend on the panel", { @@ -92,99 +92,99 @@ test_that("geom_dotplot draws correctly", { # Basic dotplot with binning along x axis expect_doppelganger("basic dotplot with dot-density binning, binwidth = .4", - ggplot(dat, aes(x)) + geom_dotplot(binwidth = .4) + ggplot(dat, aes(x)) + geom_dotplot(binwidth = 0.4) ) expect_doppelganger("histodot binning (equal bin spacing)", - ggplot(dat, aes(x)) + geom_dotplot(binwidth = .4, method = "histodot") + ggplot(dat, aes(x)) + geom_dotplot(binwidth = 0.4, method = "histodot") ) expect_doppelganger("dots stacked closer: stackratio=.5, fill=white", - ggplot(dat, aes(x)) + geom_dotplot(binwidth = .4, stackratio = .5, fill = "white") + ggplot(dat, aes(x)) + geom_dotplot(binwidth = 0.4, stackratio = 0.5, fill = "white") ) expect_doppelganger("larger dots: dotsize=1.5, fill=white", - ggplot(dat, aes(x)) + geom_dotplot(binwidth = .4, dotsize = 1.4, fill = "white") + ggplot(dat, aes(x)) + geom_dotplot(binwidth = 0.4, dotsize = 1.4, fill = "white") ) # Stacking methods expect_doppelganger("stack up", - ggplot(dat, aes(x)) + geom_dotplot(binwidth = .4, stackdir = "up") + ggplot(dat, aes(x)) + geom_dotplot(binwidth = 0.4, stackdir = "up") ) expect_doppelganger("stack down", - ggplot(dat, aes(x)) + geom_dotplot(binwidth = .4, stackdir = "down") + ggplot(dat, aes(x)) + geom_dotplot(binwidth = 0.4, stackdir = "down") ) expect_doppelganger("stack center", - ggplot(dat, aes(x)) + geom_dotplot(binwidth = .4, stackdir = "center") + ggplot(dat, aes(x)) + geom_dotplot(binwidth = 0.4, stackdir = "center") ) expect_doppelganger("stack centerwhole", - ggplot(dat, aes(x)) + geom_dotplot(binwidth = .4, stackdir = "centerwhole") + ggplot(dat, aes(x)) + geom_dotplot(binwidth = 0.4, stackdir = "centerwhole") ) # Stacking methods with coord_flip expect_doppelganger("stack up with coord_flip", - ggplot(dat, aes(x)) + geom_dotplot(binwidth = .4, stackdir = "up") + coord_flip() + ggplot(dat, aes(x)) + geom_dotplot(binwidth = 0.4, stackdir = "up") + coord_flip() ) expect_doppelganger("stack down with coord_flip", - ggplot(dat, aes(x)) + geom_dotplot(binwidth = .4, stackdir = "down") + coord_flip() + ggplot(dat, aes(x)) + geom_dotplot(binwidth = 0.4, stackdir = "down") + coord_flip() ) expect_doppelganger("stack center with coord_flip", - ggplot(dat, aes(x)) + geom_dotplot(binwidth = .4, stackdir = "center") + coord_flip() + ggplot(dat, aes(x)) + geom_dotplot(binwidth = 0.4, stackdir = "center") + coord_flip() ) expect_doppelganger("stack centerwhole with coord_flip", - ggplot(dat, aes(x)) + geom_dotplot(binwidth = .4, stackdir = "centerwhole") + coord_flip() + ggplot(dat, aes(x)) + geom_dotplot(binwidth = 0.4, stackdir = "centerwhole") + coord_flip() ) # Binning along x, with groups expect_doppelganger("multiple groups, bins not aligned", - ggplot(dat, aes(x, fill = g)) + geom_dotplot(binwidth = .4, alpha = .4) + ggplot(dat, aes(x, fill = g)) + geom_dotplot(binwidth = 0.4, alpha = 0.4) ) expect_doppelganger("multiple groups, bins aligned", - ggplot(dat, aes(x, fill = g)) + geom_dotplot(binwidth = .4, alpha = .4, binpositions = "all") + ggplot(dat, aes(x, fill = g)) + geom_dotplot(binwidth = 0.4, alpha = 0.4, binpositions = "all") ) # Binning along y axis expect_doppelganger("bin along y, stack center", - ggplot(dat, aes(0, x)) + geom_dotplot(binwidth = .4, binaxis = "y", stackdir = "center") + ggplot(dat, aes(0, x)) + geom_dotplot(binwidth = 0.4, binaxis = "y", stackdir = "center") ) expect_doppelganger("bin along y, stack centerwhole", - ggplot(dat, aes(0, x)) + geom_dotplot(binwidth = .4, binaxis = "y", stackdir = "centerwhole") + ggplot(dat, aes(0, x)) + geom_dotplot(binwidth = 0.4, binaxis = "y", stackdir = "centerwhole") ) expect_doppelganger("bin along y, stack centerwhole, histodot", - ggplot(dat, aes(0, x)) + geom_dotplot(binwidth = .4, binaxis = "y", stackdir = "centerwhole", method = "histodot") + ggplot(dat, aes(0, x)) + geom_dotplot(binwidth = 0.4, binaxis = "y", stackdir = "centerwhole", method = "histodot") ) # Binning along y, with multiple grouping factors dat2 <- data_frame(x = rep(factor(LETTERS[1:3]), 30), y = rnorm(90), g = rep(factor(LETTERS[1:2]), 45)) expect_doppelganger("bin x, three y groups, stack centerwhole", - ggplot(dat2, aes(y, x)) + geom_dotplot(binwidth = .25, binaxis = "x", stackdir = "centerwhole") + ggplot(dat2, aes(y, x)) + geom_dotplot(binwidth = 0.25, binaxis = "x", stackdir = "centerwhole") ) expect_doppelganger("bin y, three x groups, stack centerwhole", - ggplot(dat2, aes(x, y)) + geom_dotplot(binwidth = .25, binaxis = "y", stackdir = "centerwhole") + ggplot(dat2, aes(x, y)) + geom_dotplot(binwidth = 0.25, binaxis = "y", stackdir = "centerwhole") ) expect_doppelganger("bin y, three x groups, bins aligned across groups", - ggplot(dat2, aes(x, y)) + geom_dotplot(binwidth = .25, binaxis = "y", stackdir = "center", binpositions = "all") + ggplot(dat2, aes(x, y)) + geom_dotplot(binwidth = 0.25, binaxis = "y", stackdir = "center", binpositions = "all") ) expect_doppelganger("bin y, three x groups, bins aligned, coord_flip", - ggplot(dat2, aes(x, y)) + geom_dotplot(binwidth = .25, binaxis = "y", stackdir = "center", binpositions = "all") + + ggplot(dat2, aes(x, y)) + geom_dotplot(binwidth = 0.25, binaxis = "y", stackdir = "center", binpositions = "all") + coord_flip() ) expect_doppelganger("bin y, dodged", - ggplot(dat2, aes("foo", y, fill = x)) + scale_y_continuous(breaks = seq(-4, 4, .4)) + - geom_dotplot(binwidth = .25, position = "dodge", binaxis = "y", stackdir = "center") + ggplot(dat2, aes("foo", y, fill = x)) + scale_y_continuous(breaks = seq(-4, 4, 0.4)) + + geom_dotplot(binwidth = 0.25, position = "dodge", binaxis = "y", stackdir = "center") ) expect_doppelganger("bin y, dodged, coord_flip", - ggplot(dat2, aes("foo", y, fill = x)) + scale_y_continuous(breaks = seq(-4, 4, .4)) + - geom_dotplot(binwidth = .25, position = "dodge", binaxis = "y", stackdir = "center") + + ggplot(dat2, aes("foo", y, fill = x)) + scale_y_continuous(breaks = seq(-4, 4, 0.4)) + + geom_dotplot(binwidth = 0.25, position = "dodge", binaxis = "y", stackdir = "center") + coord_flip() ) expect_doppelganger("bin y, three x groups, fill and dodge", - ggplot(dat2, aes(x, y, fill = g)) + scale_y_continuous(breaks = seq(-4 ,4, .4)) + - geom_dotplot(binwidth = .2, position = "dodge", binaxis = "y", stackdir = "center") + ggplot(dat2, aes(x, y, fill = g)) + scale_y_continuous(breaks = seq(-4 ,4, 0.4)) + + geom_dotplot(binwidth = 0.2, position = "dodge", binaxis = "y", stackdir = "center") ) expect_doppelganger("bin y, continous x-axis, grouping by x", - ggplot(dat2, aes(as.numeric(x), y, group = x)) + geom_dotplot(binwidth = .2, binaxis = "y", stackdir = "center") + ggplot(dat2, aes(as.numeric(x), y, group = x)) + geom_dotplot(binwidth = 0.2, binaxis = "y", stackdir = "center") ) expect_doppelganger("bin y, continous x-axis, single x group", - ggplot(dat2, aes(as.numeric(x), y)) + geom_dotplot(binwidth = .2, binaxis = "y", stackdir = "center") + ggplot(dat2, aes(as.numeric(x), y)) + geom_dotplot(binwidth = 0.2, binaxis = "y", stackdir = "center") ) # border width and size @@ -198,31 +198,31 @@ test_that("geom_dotplot draws correctly", { stroke = rep(c(1, 2), length.out = nrow(dat)) ) ) + - geom_dotplot(binwidth = .4, fill = "red", col = "blue") + + geom_dotplot(binwidth = 0.4, fill = "red", col = "blue") + continuous_scale("stroke", palette = function(x) scales::rescale(x, to = c(1, 6))) + guides(linetype = guide_legend(order = 1)) ) # Stacking groups expect_doppelganger("3 stackgroups, dot-density with aligned bins", - ggplot(dat2, aes(y, fill = x)) + geom_dotplot(binwidth = .25, stackgroups = TRUE, binpositions = "all", alpha = 0.5) + ggplot(dat2, aes(y, fill = x)) + geom_dotplot(binwidth = 0.25, stackgroups = TRUE, binpositions = "all", alpha = 0.5) ) expect_doppelganger("3 stackgroups, histodot", - ggplot(dat2, aes(y, fill = x)) + geom_dotplot(binwidth = .25, stackgroups = TRUE, method = "histodot", alpha = 0.5) + ggplot(dat2, aes(y, fill = x)) + geom_dotplot(binwidth = 0.25, stackgroups = TRUE, method = "histodot", alpha = 0.5) ) expect_doppelganger("3 stackgroups, bin y, histodot", - ggplot(dat2, aes(1, y, fill = x)) + geom_dotplot(binaxis = "y", binwidth = .25, stackgroups = TRUE, method = "histodot", alpha = 0.5) + ggplot(dat2, aes(1, y, fill = x)) + geom_dotplot(binaxis = "y", binwidth = 0.25, stackgroups = TRUE, method = "histodot", alpha = 0.5) ) # This one is currently broken but it would be a really rare case, and it # probably requires a really ugly hack to fix expect_doppelganger("bin y, dodging, 3 stackgroups, histodot", ggplot(dat2, aes(x, y, fill = g)) + - geom_dotplot(binaxis = "y", binwidth = .25, stackgroups = TRUE, method = "histodot", + geom_dotplot(binaxis = "y", binwidth = 0.25, stackgroups = TRUE, method = "histodot", alpha = 0.5, stackdir = "centerwhole") ) expect_doppelganger("facets, 3 groups, histodot, stackgroups", - ggplot(dat2, aes(y, fill = g)) + geom_dotplot(binwidth = .25, stackgroups = TRUE, method = "histodot", alpha = 0.5) + + ggplot(dat2, aes(y, fill = g)) + geom_dotplot(binwidth = 0.25, stackgroups = TRUE, method = "histodot", alpha = 0.5) + facet_grid(x ~ .) ) @@ -231,10 +231,10 @@ test_that("geom_dotplot draws correctly", { dat2$x[c(1, 10)] <- NA expect_warning(expect_doppelganger("2 NA values, dot-density binning, binwidth = .4", - ggplot(dat2, aes(x)) + geom_dotplot(binwidth = .4) + ggplot(dat2, aes(x)) + geom_dotplot(binwidth = 0.4) )) expect_warning(expect_doppelganger("2 NA values, bin along y, stack center", - ggplot(dat2, aes(0, x)) + geom_dotplot(binwidth = .4, binaxis = "y", stackdir = "center") + ggplot(dat2, aes(0, x)) + geom_dotplot(binwidth = 0.4, binaxis = "y", stackdir = "center") )) }) diff --git a/tests/testthat/test-geom-path.R b/tests/testthat/test-geom-path.R index 6cf55aece9..3255a2f4cb 100644 --- a/tests/testthat/test-geom-path.R +++ b/tests/testthat/test-geom-path.R @@ -1,8 +1,8 @@ test_that("keep_mid_true drops leading/trailing FALSE", { - expect_equal(keep_mid_true(c(F, F)), c(F, F)) - expect_equal(keep_mid_true(c(F, T, F, T, F)), c(F, T, T, T, F)) - expect_equal(keep_mid_true(c(T, T, F, T, F)), c(T, T, T, T, F)) - expect_equal(keep_mid_true(c(F, T, F, T, T)), c(F, T, T, T, T)) + expect_equal(keep_mid_true(c(FALSE, FALSE)), c(FALSE, FALSE)) + expect_equal(keep_mid_true(c(FALSE, TRUE, FALSE, TRUE, FALSE)), c(FALSE, TRUE, TRUE, TRUE, FALSE)) + expect_equal(keep_mid_true(c(TRUE, TRUE, FALSE, TRUE, FALSE)), c(TRUE, TRUE, TRUE, TRUE, FALSE)) + expect_equal(keep_mid_true(c(FALSE, TRUE, FALSE, TRUE, TRUE)), c(FALSE, TRUE, TRUE, TRUE, TRUE)) }) test_that("geom_path() throws meaningful error on bad combination of varying aesthetics", { diff --git a/tests/testthat/test-geom-quantile.R b/tests/testthat/test-geom-quantile.R index 742e2850ed..7b6feecb9b 100644 --- a/tests/testthat/test-geom-quantile.R +++ b/tests/testthat/test-geom-quantile.R @@ -8,7 +8,7 @@ test_that("geom_quantile matches quantile regression", { set.seed(6531) x <- rnorm(10) - df <- tibble::tibble( + df <- data_frame0( x = x, y = x^2 + 0.5 * rnorm(10) ) diff --git a/tests/testthat/test-geom-rug.R b/tests/testthat/test-geom-rug.R index 28aa17efcb..7539a494a6 100644 --- a/tests/testthat/test-geom-rug.R +++ b/tests/testthat/test-geom-rug.R @@ -1,4 +1,4 @@ -n = 10 +n <- 10 df <- data_frame(x = 1:n, y = (1:n)^3) p <- ggplot(df, aes(x, y)) + geom_point() + geom_rug(sides = 'l') @@ -7,16 +7,16 @@ test_that("coord_flip flips the rugs", { b <- get_layer_grob(p + coord_flip(), 2) # Rugs along y-axis, all x coordinates are the same - expect_equal(length(a[[1]]$children[[1]]$x0), 1) - expect_equal(length(a[[1]]$children[[1]]$x1), 1) - expect_equal(length(a[[1]]$children[[1]]$y0), n) - expect_equal(length(a[[1]]$children[[1]]$y1), n) + expect_length(a[[1]]$children[[1]]$x0, 1) + expect_length(a[[1]]$children[[1]]$x1, 1) + expect_length(a[[1]]$children[[1]]$y0, n) + expect_length(a[[1]]$children[[1]]$y1, n) # Rugs along x-axis, all y coordinates are the same - expect_equal(length(b[[1]]$children[[1]]$x0), n) - expect_equal(length(b[[1]]$children[[1]]$x1), n) - expect_equal(length(b[[1]]$children[[1]]$y0), 1) - expect_equal(length(b[[1]]$children[[1]]$y1), 1) + expect_length(b[[1]]$children[[1]]$x0, n) + expect_length(b[[1]]$children[[1]]$x1, n) + expect_length(b[[1]]$children[[1]]$y0, 1) + expect_length(b[[1]]$children[[1]]$y1, 1) }) test_that("Rug length needs unit object", { diff --git a/tests/testthat/test-geom-sf.R b/tests/testthat/test-geom-sf.R index fac4c8b87a..e52a13e917 100644 --- a/tests/testthat/test-geom-sf.R +++ b/tests/testthat/test-geom-sf.R @@ -30,23 +30,23 @@ test_that("geom_sf() determines the legend type automatically", { } # test the automatic choice - expect_identical(fun_geom_sf(mp, TRUE)$plot$layers[[1]]$show.legend, TRUE) + expect_true(fun_geom_sf(mp, TRUE)$plot$layers[[1]]$show.legend) expect_identical(fun_geom_sf(mp, TRUE)$plot$layers[[1]]$computed_geom_params$legend, "point") - expect_identical(fun_geom_sf(mls, TRUE)$plot$layers[[1]]$show.legend, TRUE) + expect_true(fun_geom_sf(mls, TRUE)$plot$layers[[1]]$show.legend) expect_identical(fun_geom_sf(mls, TRUE)$plot$layers[[1]]$computed_geom_params$legend, "line") - expect_identical(fun_geom_sf(mpol, TRUE)$plot$layers[[1]]$show.legend, TRUE) + expect_true(fun_geom_sf(mpol, TRUE)$plot$layers[[1]]$show.legend) expect_identical(fun_geom_sf(mpol, TRUE)$plot$layers[[1]]$computed_geom_params$legend, "other") # test that automatic choice can be overridden manually - expect_identical(fun_geom_sf(mp, "point")$plot$layers[[1]]$show.legend, TRUE) + expect_true(fun_geom_sf(mp, "point")$plot$layers[[1]]$show.legend) expect_identical(fun_geom_sf(mp, "point")$plot$layers[[1]]$computed_geom_params$legend, "point") - expect_identical(fun_geom_sf(mls, "point")$plot$layers[[1]]$show.legend, TRUE) + expect_true(fun_geom_sf(mls, "point")$plot$layers[[1]]$show.legend) expect_identical(fun_geom_sf(mls, "point")$plot$layers[[1]]$computed_geom_params$legend, "point") - expect_identical(fun_geom_sf(mpol, "point")$plot$layers[[1]]$show.legend, TRUE) + expect_true(fun_geom_sf(mpol, "point")$plot$layers[[1]]$show.legend) expect_identical(fun_geom_sf(mpol, "point")$plot$layers[[1]]$computed_geom_params$legend, "point") }) diff --git a/tests/testthat/test-geom-smooth.R b/tests/testthat/test-geom-smooth.R index 5f8282c176..42c82108c7 100644 --- a/tests/testthat/test-geom-smooth.R +++ b/tests/testthat/test-geom-smooth.R @@ -57,6 +57,8 @@ test_that("default smoothing methods for small and large data sets work", { y = x^2 + 0.5 * rnorm(1001) ) + skip_if_not_installed("mgcv") + m <- mgcv::gam(y ~ s(x, bs = "cs"), data = df, method = "REML") range <- range(df$x, na.rm = TRUE) xseq <- seq(range[1], range[2], length.out = 80) @@ -96,6 +98,18 @@ test_that("geom_smooth() works when one group fails", { expect_gte(nrow(ld), 2) }) +test_that("a fallback message is thrown when `method = 'gam'` and {mgcv} is absent", { + p <- ggplot(mpg, aes(displ, hwy)) + + geom_smooth(method = "gam", formula = y ~ x) + + with_mocked_bindings( + expect_message( + ggplot_build(p), regexp = "Falling back to `method = \"lm\"`" + ), + is_installed = function(...) FALSE + ) +}) + # Visual tests ------------------------------------------------------------ test_that("geom_smooth() works with alternative stats", { diff --git a/tests/testthat/test-geom-tile.R b/tests/testthat/test-geom-tile.R index 581963a4b2..9034e3c9f7 100644 --- a/tests/testthat/test-geom-tile.R +++ b/tests/testthat/test-geom-tile.R @@ -17,11 +17,10 @@ test_that("accepts width and height aesthetics", { geom_tile(fill = NA, colour = "black", linewidth = 1) out <- get_layer_data(p) - boundary <- as.data.frame(tibble::tribble( - ~xmin, ~xmax, ~ymin, ~ymax, - -1, 1, -1, 1, - -2, 2, -2, 2 - )) + boundary <- data_frame0( + xmin = c(-1, -2), xmax = c(1, 2), + ymin = c(-1, -2), ymax = c(1, 2) + ) expect_equal(out[c("xmin", "xmax", "ymin", "ymax")], boundary) }) diff --git a/tests/testthat/test-geom-violin.R b/tests/testthat/test-geom-violin.R index eabbc5c95c..7d73c04e94 100644 --- a/tests/testthat/test-geom-violin.R +++ b/tests/testthat/test-geom-violin.R @@ -43,7 +43,7 @@ test_that("quantiles do not fail on zero-range data", { p <- ggplot(zero.range.data) + geom_violin(aes(1, y), draw_quantiles = 0.5) # This should return without error and have length one - expect_equal(length(get_layer_grob(p)), 1) + expect_length(get_layer_grob(p), 1) }) test_that("quantiles fails outside 0-1 bound", { @@ -81,7 +81,7 @@ test_that("quantiles do not issue warning", { test_that("geom_violin draws correctly", { set.seed(111) dat <- data_frame(x = rep(factor(LETTERS[1:3]), 30), y = rnorm(90)) - dat <- dat[dat$x != "C" | c(T, F),] # Keep half the C's + dat <- dat[dat$x != "C" | c(TRUE, FALSE),] # Keep half the C's expect_doppelganger("basic", ggplot(dat, aes(x = x, y = y)) + geom_violin() @@ -90,13 +90,13 @@ test_that("geom_violin draws correctly", { ggplot(dat, aes(x = x, y = y)) + geom_violin(scale = "count"), ) expect_doppelganger("narrower (width=.5)", - ggplot(dat, aes(x = x, y = y)) + geom_violin(width = .5) + ggplot(dat, aes(x = x, y = y)) + geom_violin(width = 0.5) ) expect_doppelganger("with tails and points", ggplot(dat, aes(x = x, y = y)) + geom_violin(trim = FALSE) + geom_point(shape = 21) ) expect_doppelganger("with smaller bandwidth and points", - ggplot(dat, aes(x = x, y = y)) + geom_violin(adjust = .3) + geom_point(shape = 21) + ggplot(dat, aes(x = x, y = y)) + geom_violin(adjust = 0.3) + geom_point(shape = 21) ) expect_doppelganger("dodging", ggplot(dat, aes(x = "foo", y = y, fill = x)) + geom_violin() @@ -126,6 +126,6 @@ test_that("geom_violin draws correctly", { ) expect_doppelganger("grouping on x and fill, dodge width = 0.5", ggplot(dat2, aes(x = x, y = y, fill = g)) + - geom_violin(position = position_dodge(width = .5)) + geom_violin(position = position_dodge(width = 0.5)) ) }) diff --git a/tests/testthat/test-guides.R b/tests/testthat/test-guides.R index a2e4af3e4f..23df1f75e2 100644 --- a/tests/testthat/test-guides.R +++ b/tests/testthat/test-guides.R @@ -44,7 +44,7 @@ test_that("colourbar trains without labels", { sc <- scale_colour_continuous(limits = c(0, 4), labels = NULL) out <- g$train(scale = sc) - expect_equal(names(out$key), c("colour", ".value")) + expect_named(out$key, c("colour", ".value")) }) test_that("Colorbar respects show.legend in layer", { @@ -222,7 +222,7 @@ test_that("guide merging for guide_legend() works as expected", { }) test_that("size = NA doesn't throw rendering errors", { - df = data.frame( + df <- data.frame( x = c(1, 2), group = c("a","b") ) @@ -912,7 +912,7 @@ test_that("guides are positioned correctly", { p2 <- p2 + theme(legend.position = "inside") # Placement of legend inside expect_doppelganger("legend inside plot, centered", - p2 + theme(legend.position.inside = c(.5, .5)) + p2 + theme(legend.position.inside = c(0.5, 0.5)) ) expect_doppelganger("legend inside plot, bottom left", p2 + theme(legend.justification = c(0,0), legend.position.inside = c(0,0)) @@ -921,7 +921,7 @@ test_that("guides are positioned correctly", { p2 + theme(legend.justification = c(1,1), legend.position.inside = c(1,1)) ) expect_doppelganger("legend inside plot, bottom left of legend at center", - p2 + theme(legend.justification = c(0,0), legend.position.inside = c(.5,.5)) + p2 + theme(legend.justification = c(0,0), legend.position.inside = c(0.5,0.5)) ) }) diff --git a/tests/testthat/test-labels.R b/tests/testthat/test-labels.R index f0d5c4e974..60f5165c1b 100644 --- a/tests/testthat/test-labels.R +++ b/tests/testthat/test-labels.R @@ -74,6 +74,21 @@ test_that("Labels can be extracted from attributes", { expect_equal(labels$y, "disp") }) +test_that("Labels from static aesthetics are ignored (#6003)", { + + df <- data.frame(x = 1, y = 1, f = 1) + + p <- ggplot(df, aes(x, y, colour = f)) + geom_point() + labels <- ggplot_build(p)$plot$labels + + expect_equal(labels$colour, "f") + + p <- ggplot(df, aes(x, y, colour = f)) + geom_point(colour = "blue") + labels <- ggplot_build(p)$plot$labels + + expect_null(labels$colour) +}) + test_that("alt text is returned", { p <- ggplot(mtcars, aes(mpg, disp)) + geom_point() diff --git a/tests/testthat/test-layer.R b/tests/testthat/test-layer.R index 0a89af1da8..51f0cd9eee 100644 --- a/tests/testthat/test-layer.R +++ b/tests/testthat/test-layer.R @@ -25,6 +25,13 @@ test_that("unknown aesthetics create warning", { expect_warning(geom_point(aes(blah = "red")), "unknown aesthetics") }) +test_that("empty aesthetics create warning", { + expect_warning( + geom_point(fill = NULL, shape = character()), + "Ignoring empty aesthetics" + ) +}) + test_that("invalid aesthetics throws errors", { # We want to test error and ignore the scale search message suppressMessages({ @@ -80,7 +87,7 @@ test_that("if an aes is mapped to a function that returns NULL, it is removed", df <- data_frame(x = 1:10) null <- function(...) NULL p <- cdata(ggplot(df, aes(x, null()))) - expect_identical(names(p[[1]]), c("x", "PANEL", "group")) + expect_named(p[[1]], c("x", "PANEL", "group")) }) test_that("layers are stateless except for the computed params", { @@ -138,6 +145,22 @@ test_that("layer warns for constant aesthetics", { expect_snapshot_warning(ggplot_build(p)) }) +test_that("layer names can be resolved", { + + p <- ggplot() + geom_point() + geom_point() + expect_equal(names(p$layers), c("geom_point", "geom_point...2")) + + p <- ggplot() + geom_point(name = "foo") + geom_point(name = "bar") + expect_equal(names(p$layers), c("foo", "bar")) + + l <- geom_point(name = "foobar") + expect_error( + p + l + l, + "names are duplicated" + ) +}) + + # Data extraction --------------------------------------------------------- test_that("AsIs data passes unmodified", { diff --git a/tests/testthat/test-scale-discrete.R b/tests/testthat/test-scale-discrete.R index 084511571f..9e8eeaf717 100644 --- a/tests/testthat/test-scale-discrete.R +++ b/tests/testthat/test-scale-discrete.R @@ -1,10 +1,9 @@ # Missing values ---------------------------------------------------------- -df <- tibble::tibble( +df <- data_frame0( x1 = c("a", "b", NA), - x2 = factor(x1), - x3 = addNA(x2), - + x2 = factor(c("a", "b", NA)), + x3 = factor(c("a", "b", NA), levels = c("a", "b", NA), exclude = NULL), y = 1:3 ) diff --git a/tests/testthat/test-scale-hue.R b/tests/testthat/test-scale-hue.R index 12568590a8..6f0b0c5234 100644 --- a/tests/testthat/test-scale-hue.R +++ b/tests/testthat/test-scale-hue.R @@ -1,6 +1,5 @@ test_that("scale_hue() checks the type input", { - pal <- pal_qualitative(type = 1:4) - expect_snapshot_error(pal(4)) + expect_snapshot_error(pal_qualitative(type = 1:4)) pal <- pal_qualitative(type = colors()) expect_silent(pal(4)) pal <- pal_qualitative(type = list(colors()[1:10], colors()[11:30])) diff --git a/tests/testthat/test-scale-type.R b/tests/testthat/test-scale-type.R index 4be2fe9ebf..3ca1f06637 100644 --- a/tests/testthat/test-scale-type.R +++ b/tests/testthat/test-scale-type.R @@ -1,9 +1,9 @@ test_that("no scale for NULL aesthetic", { - expect_equal(find_scale("colour", NULL), NULL) + expect_null(find_scale("colour", NULL)) }) test_that("no scale for Inf aesthetic", { - expect_equal(find_scale("colour", Inf), NULL) + expect_null(find_scale("colour", Inf)) }) test_that("message + continuous for unknown type", { diff --git a/tests/testthat/test-scales-breaks-labels.R b/tests/testthat/test-scales-breaks-labels.R index d24e0ab638..c3a314cacc 100644 --- a/tests/testthat/test-scales-breaks-labels.R +++ b/tests/testthat/test-scales-breaks-labels.R @@ -47,9 +47,9 @@ test_that("out-of-range breaks are dropped", { # Limits are specified, and all breaks are out of range sc <- scale_x_continuous(breaks = c(1,5), labels = letters[c(1,5)], limits = c(2, 4)) bi <- sc$break_info() - expect_equal(length(bi$labels), 0) - expect_equal(length(bi$major), 0) - expect_equal(length(bi$major_source), 0) + expect_length(bi$labels, 0) + expect_length(bi$major, 0) + expect_length(bi$major_source, 0) # limits aren't specified, automatic labels # limits are set by the data @@ -72,36 +72,36 @@ test_that("out-of-range breaks are dropped", { sc <- scale_x_continuous(breaks = c(1,5), labels = letters[c(1,5)]) sc$train_df(data_frame(x = 2:4)) bi <- sc$break_info() - expect_equal(length(bi$labels), 0) - expect_equal(length(bi$major), 0) - expect_equal(length(bi$major_source), 0) + expect_length(bi$labels, 0) + expect_length(bi$major, 0) + expect_length(bi$major_source, 0) }) test_that("no minor breaks when only one break", { sc1 <- scale_x_discrete(limits = "a") sc2 <- scale_x_continuous(limits = 1) - expect_equal(length(sc1$get_breaks_minor()), 0) - expect_equal(length(sc2$get_breaks_minor()), 0) + expect_length(sc1$get_breaks_minor(), 0) + expect_length(sc2$get_breaks_minor(), 0) }) init_scale <- function(...) { sc <- scale_x_discrete(...) sc$train(factor(1:100)) - expect_equal(length(sc$get_limits()), 100) + expect_length(sc$get_limits(), 100) sc } test_that("discrete labels match breaks", { sc <- init_scale(breaks = 0:5 * 10) - expect_equal(length(sc$get_breaks()), 5) - expect_equal(length(sc$get_labels()), 5) + expect_length(sc$get_breaks(), 5) + expect_length(sc$get_labels(), 5) expect_equal(sc$get_labels(), sc$get_breaks(), ignore_attr = TRUE) sc <- init_scale(breaks = 0:5 * 10, labels = letters[1:6]) - expect_equal(length(sc$get_breaks()), 5) - expect_equal(length(sc$get_labels()), 5) + expect_length(sc$get_breaks(), 5) + expect_length(sc$get_labels(), 5) expect_equal(sc$get_labels(), letters[2:6]) sc <- init_scale(breaks = 0:5 * 10, labels = @@ -110,8 +110,8 @@ test_that("discrete labels match breaks", { pick_5 <- function(x) sample(x, 5) sc <- init_scale(breaks = pick_5) - expect_equal(length(sc$get_breaks()), 5) - expect_equal(length(sc$get_labels()), 5) + expect_length(sc$get_breaks(), 5) + expect_length(sc$get_labels(), 5) }) test_that("scale breaks work with numeric log transformation", { @@ -141,30 +141,30 @@ test_that("passing continuous limits to a discrete scale generates a warning", { }) test_that("suppressing breaks, minor_breask, and labels works", { - expect_equal(scale_x_continuous(breaks = NULL, limits = c(1, 3))$get_breaks(), NULL) - expect_equal(scale_x_discrete(breaks = NULL, limits = c("one", "three"))$get_breaks(), NULL) - expect_equal(scale_x_continuous(minor_breaks = NULL, limits = c(1, 3))$get_breaks_minor(), NULL) + expect_null(scale_x_continuous(breaks = NULL, limits = c(1, 3))$get_breaks()) + expect_null(scale_x_discrete(breaks = NULL, limits = c("one", "three"))$get_breaks()) + expect_null(scale_x_continuous(minor_breaks = NULL, limits = c(1, 3))$get_breaks_minor()) - expect_equal(scale_x_continuous(labels = NULL, limits = c(1, 3))$get_labels(), NULL) - expect_equal(scale_x_discrete(labels = NULL, limits = c("one", "three"))$get_labels(), NULL) + expect_null(scale_x_continuous(labels = NULL, limits = c(1, 3))$get_labels()) + expect_null(scale_x_discrete(labels = NULL, limits = c("one", "three"))$get_labels()) # date, datetime lims <- as.Date(c("2000/1/1", "2000/2/1")) - expect_equal(scale_x_date(breaks = NULL, limits = lims)$get_breaks(), NULL) + expect_null(scale_x_date(breaks = NULL, limits = lims)$get_breaks()) # NA is defunct, should throw error expect_error(scale_x_date(breaks = NA, limits = lims)$get_breaks()) - expect_equal(scale_x_date(labels = NULL, limits = lims)$get_labels(), NULL) + expect_null(scale_x_date(labels = NULL, limits = lims)$get_labels()) expect_error(scale_x_date(labels = NA, limits = lims)$get_labels()) - expect_equal(scale_x_date(minor_breaks = NULL, limits = lims)$get_breaks_minor(), NULL) + expect_null(scale_x_date(minor_breaks = NULL, limits = lims)$get_breaks_minor()) expect_error(scale_x_date(minor_breaks = NA, limits = lims)$get_breaks_minor()) # date, datetime lims <- as.POSIXct(c("2000/1/1 0:0:0", "2010/1/1 0:0:0")) - expect_equal(scale_x_datetime(breaks = NULL, limits = lims)$get_breaks(), NULL) + expect_null(scale_x_datetime(breaks = NULL, limits = lims)$get_breaks()) expect_error(scale_x_datetime(breaks = NA, limits = lims)$get_breaks()) - expect_equal(scale_x_datetime(labels = NULL, limits = lims)$get_labels(), NULL) + expect_null(scale_x_datetime(labels = NULL, limits = lims)$get_labels()) expect_error(scale_x_datetime(labels = NA, limits = lims)$get_labels()) - expect_equal(scale_x_datetime(minor_breaks = NULL, limits = lims)$get_breaks_minor(), NULL) + expect_null(scale_x_datetime(minor_breaks = NULL, limits = lims)$get_breaks_minor()) expect_error(scale_x_datetime(minor_breaks = NA, limits = lims)$get_breaks_minor()) }) diff --git a/tests/testthat/test-scales.R b/tests/testthat/test-scales.R index 4e104f9024..0ba2989e39 100644 --- a/tests/testthat/test-scales.R +++ b/tests/testthat/test-scales.R @@ -2,10 +2,10 @@ test_that("building a plot does not affect its scales", { dat <- data_frame(x = rnorm(20), y = rnorm(20)) p <- ggplot(dat, aes(x, y)) + geom_point() - expect_equal(length(p$scales$scales), 0) + expect_length(p$scales$scales, 0) ggplot_build(p) - expect_equal(length(p$scales$scales), 0) + expect_length(p$scales$scales, 0) }) test_that("ranges update only for variables listed in aesthetics", { diff --git a/tests/testthat/test-sec-axis.R b/tests/testthat/test-sec-axis.R index 2b8fde0d94..7530c4a70c 100644 --- a/tests/testthat/test-sec-axis.R +++ b/tests/testthat/test-sec-axis.R @@ -171,7 +171,7 @@ test_that("sec axis works with tidy eval", { g } - t <- tibble(x = letters, y = seq(10, 260, 10), z = 1:26) + t <- data_frame0(x = letters, y = seq(10, 260, 10), z = 1:26) p <- f(t, x, y, z) @@ -242,7 +242,7 @@ test_that("sec_axis() respects custom transformations", { expect_doppelganger( "sec_axis, custom transform", ggplot(dat, aes(x = x, y = y)) + - geom_line(linewidth = 1, na.rm = T) + + geom_line(linewidth = 1, na.rm = TRUE) + scale_y_continuous( transform = magnify_trans_log(interval_low = 0.5, interval_high = 1, reducer = 0.5, reducer2 = 8), breaks = @@ -364,21 +364,21 @@ test_that("sec_axis() works for power transformations (monotonicity test doesn't scale_y_continuous(sec.axis = sec_axis(transform = ~ .^0.5)) scale <- get_panel_scales(p)$y breaks <- scale$break_info() - expect_equal(breaks$major, sqrt(breaks$sec.major), tolerance = .005) + expect_equal(breaks$major, sqrt(breaks$sec.major), tolerance = 0.005) p <- ggplot(foo, aes(x, y)) + geom_point() + scale_x_sqrt(sec.axis = dup_axis()) scale <- get_panel_scales(p)$x breaks <- scale$break_info() - expect_equal(breaks$major, breaks$sec.major, tolerance = .001) + expect_equal(breaks$major, breaks$sec.major, tolerance = 0.001) p <- ggplot(foo, aes(x, y)) + geom_point() + scale_x_sqrt(sec.axis = sec_axis(~ . * 100)) scale <- get_panel_scales(p)$x breaks <- scale$break_info() - expect_equal(breaks$major, breaks$sec.major, tolerance = .001) + expect_equal(breaks$major, breaks$sec.major, tolerance = 0.001) }) test_that("discrete scales can have secondary axes", { @@ -400,3 +400,22 @@ test_that("discrete scales can have secondary axes", { expect_equal(y$.value, c(1.5, 2.5), ignore_attr = TRUE) expect_equal(y$.label, c("grault", "garply")) }) + +test_that("n.breaks is respected by secondary axes (#4483)", { + + b <- ggplot_build( + ggplot(data.frame(x = c(0, 10)), aes(x, x)) + + scale_y_continuous( + n.breaks = 11, + sec.axis = sec_axis(~.x*100) + ) + ) + + # We get scale breaks via guide data + prim <- get_guide_data(b, "y") + sec <- get_guide_data(b, "y.sec") + + expect_equal(prim$.value, sec$.value) # .value is in primary scale + expect_equal(prim$.label, as.character(seq(0, 10, length.out = 11))) + expect_equal(sec$.label, as.character(seq(0, 1000, length.out = 11))) +}) diff --git a/tests/testthat/test-stat-align.R b/tests/testthat/test-stat-align.R index 4c418037b3..457992e747 100644 --- a/tests/testthat/test-stat-align.R +++ b/tests/testthat/test-stat-align.R @@ -1,44 +1,29 @@ test_that("standard alignment works", { - df <- tibble::tribble( - ~g, ~x, ~y, - "a", 1, 2, - "a", 3, 5, - "a", 5, 1, - "b", 2, 3, - "b", 4, 6, - "b", 6, 7 + df <- data_frame0( + g = rep(c("a", "b"), each = 3L), + x = c(1, 3, 5, 2, 4, 6), + y = c(2, 5, 1, 3, 6, 7) ) p <- ggplot(df, aes(x, y, fill = g)) + geom_area(color = "black") expect_doppelganger("align two areas", p) }) test_that("alignment with cliffs works", { - df <- tibble::tribble( - ~g, ~x, ~y, - "a", 1, 2, - "a", 3, 5, - "a", 5, 1, - "b", 2, 3, - "b", 4, 3, - "b", 4, 6, - "b", 6, 7 + df <- data_frame0( + g = rep(c("a", "b"), 3:4), + x = c(1, 3, 5, 2, 4, 4, 6), + y = c(2, 5, 1, 3, 3, 6, 7) ) - p <- ggplot(df, aes(x, y, fill = g)) + geom_area(color = "black") expect_doppelganger("align two areas with cliff", p) }) test_that("alignment with negative and positive values works", { - df <- tibble::tribble( - ~g, ~x, ~y, - "a", 1, 1, - "a", 2, 4, - "a", 3, -4, - "a", 8, 0, - "b", 2, 4, - "b", 6, -4 + df <- data_frame0( + g = rep(c("a", "b"), c(4L, 2L)), + x = c(1, 2, 3, 8, 2, 6), + y = c(1, 4, -4, 0, 4, -4) ) - p <- ggplot(df, aes(x, y, fill = g)) + geom_area(color = "black") expect_doppelganger("align two areas with pos/neg y", p) }) diff --git a/tests/testthat/test-stat-density.R b/tests/testthat/test-stat-density.R index 5f2ec3adb8..0894fc2944 100644 --- a/tests/testthat/test-stat-density.R +++ b/tests/testthat/test-stat-density.R @@ -123,7 +123,7 @@ test_that("compute_density returns useful df and throws warning when <2 values", expect_warning(dens <- compute_density(1, NULL, from = 0, to = 0)) expect_equal(nrow(dens), 1) - expect_equal(names(dens), c("x", "density", "scaled", "ndensity", "count", "wdensity", "n")) + expect_named(dens, c("x", "density", "scaled", "ndensity", "count", "wdensity", "n")) expect_type(dens$x, "double") }) diff --git a/tests/testthat/test-stat-function.R b/tests/testthat/test-stat-function.R index 4025dcca96..483578d97f 100644 --- a/tests/testthat/test-stat-function.R +++ b/tests/testthat/test-stat-function.R @@ -18,8 +18,8 @@ test_that("uses scale limits, not data limits", { expect_equal(ret$y[c(1, 101)], ret_log$y[c(1, 101)]) expect_equal(range(ret$x), c(0.1, 100)) expect_equal(range(ret_log$x), c(-1, 2)) - expect_false(any(is.na(ret$y))) - expect_false(any(is.na(ret_log$y))) + expect_false(anyNA(ret$y)) + expect_false(anyNA(ret_log$y)) }) test_that("works in plots without any data", { diff --git a/tests/testthat/test-stat-ydensity.R b/tests/testthat/test-stat-ydensity.R index d9f39b4708..3b70fc7673 100644 --- a/tests/testthat/test-stat-ydensity.R +++ b/tests/testthat/test-stat-ydensity.R @@ -17,13 +17,13 @@ test_that("`drop = FALSE` preserves groups with 1 observations", { ld <- get_layer_data(p + geom_violin(drop = TRUE)), "Groups with fewer than two datapoints have been dropped" ) - expect_equal(length(unique(ld$x)), 3) + expect_length(unique(ld$x), 3) expect_warning( ld <- get_layer_data(p + geom_violin(drop = FALSE)), "Cannot compute density for groups with fewer than two datapoints" ) - expect_equal(length(unique(ld$x)), 4) + expect_length(unique(ld$x), 4) }) test_that("mapped_discrete class is preserved", { diff --git a/tests/testthat/test-stats.R b/tests/testthat/test-stats.R index b1acda601e..25c30e2fb1 100644 --- a/tests/testthat/test-stats.R +++ b/tests/testthat/test-stats.R @@ -3,12 +3,12 @@ test_that("plot succeeds even if some computation fails", { p1 <- ggplot(df, aes(x, y)) + geom_point() b1 <- ggplot_build(p1) - expect_equal(length(b1$data), 1) + expect_length(b1$data, 1) p2 <- p1 + stat_summary(fun = function(x) stop("Failed computation")) expect_warning(b2 <- ggplot_build(p2), "Computation failed") - expect_equal(length(b2$data), 2) + expect_length(b2$data, 2) }) test_that("error message is thrown when aesthetics are missing", { @@ -47,7 +47,7 @@ test_that("erroneously dropped aesthetics are found and issue a warning", { # colour is dropped because group a's colour is not constant (GeomBar$default_aes$colour is NA) expect_true(all(is.na(b2$data[[1]]$colour))) # fill is dropped because group b's fill is not constant - expect_true(all(b2$data[[1]]$fill == GeomBar$default_aes$fill)) + expect_true(all(b2$data[[1]]$fill == "#595959FF")) # case 2-1) dropped partially with NA diff --git a/tests/testthat/test-theme.R b/tests/testthat/test-theme.R index a9568cfd72..9c10202504 100644 --- a/tests/testthat/test-theme.R +++ b/tests/testthat/test-theme.R @@ -240,14 +240,12 @@ test_that("complete and non-complete themes interact correctly with ggplot objec expect_identical(pt, tt) p <- ggplot_build(base + theme(text = element_text(colour = 'red', face = 'italic'))) - expect_false(attr(p$plot$theme, "complete")) expect_equal(p$plot$theme$text$colour, "red") expect_equal(p$plot$theme$text$face, "italic") p <- ggplot_build(base + theme(text = element_text(colour = 'red')) + theme(text = element_text(face = 'italic'))) - expect_false(attr(p$plot$theme, "complete")) expect_equal(p$plot$theme$text$colour, "red") expect_equal(p$plot$theme$text$face, "italic") }) @@ -412,7 +410,7 @@ test_that("current theme can be updated with new elements", { ) # theme calculation for nonexisting element returns NULL - expect_identical(calc_element("abcde", plot_theme(b1)), NULL) + expect_null(calc_element("abcde", plot_theme(b1))) # element tree gets merged properly register_theme_elements( @@ -730,12 +728,12 @@ test_that("axes ticks can have independent lengths", { scale_x_continuous(sec.axis = dup_axis()) + scale_y_continuous(sec.axis = dup_axis()) + theme( - axis.ticks.length.x.top = unit(-.5, "cm"), - axis.ticks.length.x.bottom = unit(-.25, "cm"), - axis.ticks.length.y.left = unit(.25, "cm"), - axis.ticks.length.y.right = unit(.5, "cm"), - axis.text.x.bottom = element_text(margin = margin(t = .25, unit = "cm")), - axis.text.x.top = element_text(margin = margin(b = .25, unit = "cm")) + axis.ticks.length.x.top = unit(-0.5, "cm"), + axis.ticks.length.x.bottom = unit(-0.25, "cm"), + axis.ticks.length.y.left = unit(0.25, "cm"), + axis.ticks.length.y.right = unit(0.5, "cm"), + axis.text.x.bottom = element_text(margin = margin(t = 0.25, unit = "cm")), + axis.text.x.top = element_text(margin = margin(b = 0.25, unit = "cm")) ) expect_doppelganger("ticks_length", plot) }) diff --git a/tests/testthat/test-utilities-break.R b/tests/testthat/test-utilities-break.R new file mode 100644 index 0000000000..23bc143a45 --- /dev/null +++ b/tests/testthat/test-utilities-break.R @@ -0,0 +1,3 @@ +test_that("cut_interval throws the correct error message", { + expect_snapshot_error(cut_interval(x = 1:10, width = 10)) +}) diff --git a/tests/testthat/test-utilities.R b/tests/testthat/test-utilities.R index 4537b03210..08e948ca82 100644 --- a/tests/testthat/test-utilities.R +++ b/tests/testthat/test-utilities.R @@ -2,14 +2,14 @@ test_that("finite_cases.data.frame", { finite_cases <- function(x) cases(x, is_finite) # All finite -------------------------------------------------------------- - expect_identical(finite_cases(data_frame(x = 4)), TRUE) # 1x1 - expect_identical(finite_cases(data_frame(x = 4, y = 11)), TRUE) # 1x2 + expect_true(finite_cases(data_frame(x = 4))) # 1x1 + expect_true(finite_cases(data_frame(x = 4, y = 11))) # 1x2 expect_identical(finite_cases(data_frame(x = 4:5)), c(TRUE, TRUE)) # 2x1 expect_identical(finite_cases(data_frame(x = 4:5, y = 11:12)), c(TRUE, TRUE)) # 2x2 # Has one NA -------------------------------------------------------------- - expect_identical(finite_cases(data_frame(x = NA)), FALSE) # 1x1 - expect_identical(finite_cases(data_frame(x = 4, y = NA)), FALSE) # 1x2 + expect_false(finite_cases(data_frame(x = NA))) # 1x1 + expect_false(finite_cases(data_frame(x = 4, y = NA))) # 1x2 expect_identical(finite_cases(data_frame(x = c(4, NA))), c(TRUE, FALSE)) # 2x1 expect_identical(finite_cases(data_frame(x = c(4, NA), y = c(11, NA))), c(TRUE, FALSE)) # 2x2 expect_identical(finite_cases(data_frame(x = c(4, NA), y = c(NA, 12))), c(FALSE, FALSE)) # 2x2 @@ -17,7 +17,7 @@ test_that("finite_cases.data.frame", { # Testing NaN and Inf, using miscellaneous data shapes -------------------- expect_identical(finite_cases(data_frame(x = c(4, NaN))), c(TRUE, FALSE)) - expect_identical(finite_cases(data_frame(x = Inf)), FALSE) + expect_false(finite_cases(data_frame(x = Inf))) expect_identical(finite_cases(data_frame(x = c(4, 5), y = c(-Inf, 12))), c(FALSE, TRUE)) }) @@ -87,7 +87,7 @@ test_that("parse_safe works with multi expressions", { }) test_that("x and y aesthetics have the same length", { - expect_equal(length(ggplot_global$x_aes), length(ggplot_global$y_aes)) + expect_length(ggplot_global$x_aes, length(ggplot_global$y_aes)) }) test_that("check_required_aesthetics() errors on missing", { @@ -189,8 +189,8 @@ test_that("expose/ignore_data() can round-trip a data.frame", { # data.frame with ignored columns df <- data_frame0(a = 1:3, b = I(4:6), c = LETTERS[1:3], d = I(LETTERS[4:6])) test <- .ignore_data(df)[[1]] - expect_equal(names(test), c("a", "c", ".ignored")) - expect_equal(names(test$.ignored), c("b", "d")) + expect_named(test, c("a", "c", ".ignored")) + expect_named(test$.ignored, c("b", "d")) test <- .expose_data(test)[[1]] expect_equal(test, df[, c("a", "c", "b", "d")])