Merge pull request #7 from fcampelo/Update_2024Sep

Update 2024 sep

.github/workflows/R-CMD-check.yaml

@@ -1,16 +1,18 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+#
+# NOTE: This workflow is overkill for most R packages and
+# check-standard.yaml is likely a better choice.
+# usethis::use_github_action("check-standard") will install it.
 on:
   push:
-    branches:
-      - main
-      - master
+    branches: [main, master, Update_2024Sep]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master, Update_2024Sep]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -22,66 +24,39 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macos-latest,   r: 'release'}
+
           - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          # use 4.0 or 4.1 to check with rtools40's older compiler
+          - {os: windows-latest, r: 'oldrel-3'}
+
+          - {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'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-          _R_CHECK_FORCE_SUGGESTS_: false
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: CALANGO
 Type: Package
 Title: Comparative Analysis with Annotation-Based Genomic Components
-Version: 1.0.16
-Date: 2023-04-26
+Version: 1.0.20
+Date: 2024-09-03
 Language: en-US
 Authors@R: c(person("Francisco", "Lobo",
     email   = "franciscolobo@gmail.com",
@@ -35,7 +35,6 @@ Imports: assertthat (>= 0.2.1),
          rmarkdown (>= 2.1.0),
          nlme (>= 3.1.0),
          BiocManager (>= 1.30.10),
-         taxize (>= 0.9.92),
          dendextend (>= 1.15.2),
          heatmaply (>= 1.1.0),
          ggplot2 (>= 2.3.2),
@@ -49,7 +48,7 @@ Suggests: AnnotationDbi,
           KEGGREST,
           GO.db
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 URL: https://labpackages.github.io/CALANGO/
 BugReports: https://github.com/fcampelo/CALANGO/issues/
 VignetteBuilder: knitr

NEWS.md

@@ -3,6 +3,9 @@
 - Regular maintenance update:  
     - Minor bug fix that resulted in occasional errors on Windows machines  
     - Minor updates to documentation
+    - Minor tweak to dependencies
+    - Fixed problem that resulted in `retrieve_calanguize_genomes()` wiping out 
+    the target folder
 
 # CALANGO 1.0.14
 

R/GenerateTree.R

@@ -1,7 +1,11 @@
+# Function removed since it's not being used anywhere else in the package
+# by: F. Campelo, 3 Sept 2024
+
+
 # Function to generate and plot a taxonomic tree
-GenerateTree <- function(taxonIds, db = "ncbi") {
-  taxize_class <- taxize::classification(taxonIds, db = db)
-  taxize_tree  <- taxize::class2tree(taxize_class, check = TRUE)
-  # taxize::plot.classtree(taxize_tree)
-  invisible(taxize_tree)
-}
+# GenerateTree <- function(taxonIds, db = "ncbi") {
+#   taxize_class <- taxize::classification(taxonIds, db = db)
+#   taxize_tree  <- class2tree(taxize_class, check = TRUE)
+#   # taxize::plot.classtree(taxize_tree)
+#   invisible(taxize_tree)
+# }

R/retrieve_calanguize_genomes.R

@@ -17,6 +17,9 @@
 #' documentation of \code{utils::download.file()}.
 #' @param unzip The unzip method to be used. See the documentation of
 #' \code{utils::unzip()} for details.
+#' @param overwrite If TRUE, overwrite existing files in target the folder 
+#' (the equivalent of unzip -o), otherwise ignore such files (the equivalent of 
+#' unzip -n).
 #'
 #' @export
 #'
@@ -29,18 +32,16 @@
 
 retrieve_calanguize_genomes <- function(target.dir,
                                 method = "auto",
-                                unzip  = getOption("unzip")){
+                                unzip  = getOption("unzip"),
+                                overwrite = TRUE){
 
   # ================== Sanity checks ==================
   assertthat::assert_that(is.character(target.dir),
                           length(url) == 1)
 
   if(!dir.exists(target.dir)){
     dir.create(target.dir, recursive = TRUE)
-  } else {
-    filelist <- dir(target.dir, full.names = TRUE)
-    unlink(filelist, recursive = TRUE, force = TRUE)
-  }
+  } 
 
   url <- "https://github.com/fcampelo/CALANGO/raw/master/inst/extdata/calanguize_genomes.zip"
 
@@ -53,8 +54,9 @@ retrieve_calanguize_genomes <- function(target.dir,
 
   utils::unzip(paste0(target.dir, "/tmpdata.zip"),
                unzip = unzip,
-               exdir = target.dir)
-  unlink(paste0(target.dir, "/__MACOSX"), recursive = TRUE, force = TRUE)
+               exdir = target.dir, 
+               overwrite = overwrite)
+  #unlink(paste0(target.dir, "/__MACOSX"), recursive = TRUE, force = TRUE)
 
   file.remove(paste0(target.dir, "/tmpdata.zip"))