Merge pull request #328 from ropensci/cran_resub

Fixes for CRAN resubmission

.github/workflows/style-and-lint.yaml

@@ -50,6 +50,7 @@ jobs:
         if: env.has_changes == 'true'
         run: |
           git add \*.R
+          git add \*.Rmd
           git commit -m 'Style via {styler}'
 
       - uses: r-lib/actions/pr-push@v2

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: rix
-Title: Rix: Reproducible Environments with Nix
+Title: Reproducible Data Science Environments with 'Nix'
 Version: 0.12.0
 Authors@R: c(
     person("Bruno", "Rodrigues", , "bruno@brodrigues.co", role = c("aut", "cre"),
@@ -11,8 +11,13 @@ Authors@R: c(
     person("Jacob", "Wujiciak-Jens", , "jacob@wujciak.de", role = "rev",
            comment = c(ORCID = "0000-0002-7281-3989", "Jacob reviewed the package (v. 0.9.1) for rOpenSci, see <https://github.com/ropensci/software-review/issues/625>"))
   )
-Description: Provides helper functions to create reproducible development
-    environments using the Nix package manager.
+Description: Simplifies the creation of reproducible development environments
+    using the 'Nix' package manager. The included `rix()` function generates a
+    complete description of the development environment as a `default.nix` file,
+    which can then be built using `Nix'. This results in project specific 
+    software environments with pinned versions of R, packages, linked system
+    dependencies, and other tools. Additional helpers make it easy to run R code
+    in 'Nix' software environments for testing and production.
 License: GPL (>= 3)
 URL: https://docs.ropensci.org/rix/
 BugReports: https://github.com/ropensci/rix/issues

R/included-datasets.R

@@ -1,12 +1,13 @@
 #' sysdata
 #'
-#' Nix revisions with old R releases
+#' 'Nix' revisions with old R releases
 #'
 #' @format A data frame with 39 rows and 3 variables:
 #' \describe{
 #'   \item{ version }{ R version }
 #'   \item{ revision }{ Nix revision containing this version of R }
 #'   \item{ date }{ Date when this revision was available }
 #' }
-#' @source Nix Package Version, by Marcelo Lazaroni
+#' @source 'Nix' Package Version, by Marcelo Lazaroni
+#' @noRd
 "available_r"

R/nix_build.R

@@ -1,7 +1,5 @@
 #' Invoke shell command `nix-build` from an R session
 #' @param project_path Path to the folder where the `default.nix` file resides.
-#' The default is `"."`, which is the working directory in the current R
-#' session.
 #' @param message_type Character vector with messaging type, Either `"simple"`
 #' (default), `"quiet"` for no messaging, or `"verbose"`.
 #' @return integer of the process ID (PID) of `nix-build` shell command
@@ -22,7 +20,7 @@
 #' \dontrun{
 #' nix_build()
 #' }
-nix_build <- function(project_path = ".",
+nix_build <- function(project_path = getwd(),
                       message_type = c("simple", "quiet", "verbose")) {
   message_type <- match.arg(message_type,
     choices = c("simple", "quiet", "verbose")

R/rix.R

@@ -34,32 +34,31 @@
 #'   for Visual Studio Code. You can also use "radian", an interactive REPL. For
 #'   other editors, use "other". This has been tested with RStudio, VS Code and
 #'   Emacs. If other editors don't work, please open an issue.
-#' @param project_path Character, defaults to the current working directory.
-#'   Where to write `default.nix`, for example "/home/path/to/project". The file
-#'   will thus be written to the file "/home/path/to/project/default.nix". If
-#'   the folder does not exist, it will be created.
+#' @param project_path Character. Where to write `default.nix`, for example
+#'   "/home/path/to/project". The file will thus be written to the file
+#'   "/home/path/to/project/default.nix". If the folder does not exist, it will
+#'   be created.
 #' @param overwrite Logical, defaults to FALSE. If TRUE, overwrite the
 #'   `default.nix` file in the specified path.
 #' @param print Logical, defaults to FALSE. If TRUE, print `default.nix` to
 #'   console.
 #' @param message_type Character. Message type, defaults to `"simple"`, which
-#'   gives minimal but sufficient feedback. Other values are currently
-#'   `"quiet`, which generates the files without message, and `"verbose"`,
-#'   displays all the messages.
+#'   gives minimal but sufficient feedback. Other values are currently `"quiet`,
+#'   which generates the files without message, and `"verbose"`, displays all
+#'   the messages.
 #' @param shell_hook Character of length 1, defaults to `NULL`. Commands added
-#'   to the `shellHook` variable are executed when the Nix shell starts. So by
-#'   default, using `nix-shell default.nix` will start a specific program,
-#'   possibly with flags (separated by space), and/or do shell actions. You can
-#'   for example use `shell_hook = R`, if you want to directly enter the
-#'   declared Nix R session when dropping into the Nix shell.
-#' @details This function will write a `default.nix` and an `.Rprofile` in the
-#'   chosen path. Using the Nix package manager, it is then possible to build a
-#'   reproducible development environment using the `nix-build` command in the
-#'   path. This environment will contain the chosen version of R and packages,
-#'   and will not interfere with any other installed version (via Nix or not) on
-#'   your machine. Every dependency, including both R package dependencies but
-#'   also system dependencies like compilers will get installed as well in that
-#'   environment.
+#' to the `shellHook` variable are executed when the Nix shell starts. So by
+#' default, using `nix-shell default.nix` will start a specific program,
+#' possibly with flags (separated by space), and/or do shell actions. You can
+#' for example use `shell_hook = R`, if you want to directly enter the declared
+#' Nix R session when dropping into the Nix shell. @details This function will
+#' write a `default.nix` and an `.Rprofile` in the chosen path. Using the Nix
+#' package manager, it is then possible to build a reproducible development
+#' environment using the `nix-build` command in the path. This environment will
+#' contain the chosen version of R and packages, and will not interfere with any
+#' other installed version (via Nix or not) on your machine. Every dependency,
+#' including both R package dependencies but also system dependencies like
+#' compilers will get installed as well in that environment.
 #'
 #'   It is possible to use environments built with Nix interactively, either
 #'   from the terminal, or using an interface such as RStudio. If you want to
@@ -75,12 +74,12 @@
 #'   argument to `"other"`. We recommend reading the
 #'   `vignette("e-interactive-use")` for more details.
 #'
-#'   Packages to install from Github or Gitlab must be provided in a list of 3 elements:
-#'   "package_name", "repo_url" and "commit". To install several packages,
-#'   provide a list of lists of these 3 elements, one per package to install. It
-#'   is also possible to install old versions of packages by specifying a
-#'   version. For example, to install the latest version of `{AER}` but an old
-#'   version of `{ggplot2}`, you could write: `r_pkgs = c("AER",
+#'   Packages to install from Github or Gitlab must be provided in a list of 3
+#'   elements: "package_name", "repo_url" and "commit". To install several
+#'   packages, provide a list of lists of these 3 elements, one per package to
+#'   install. It is also possible to install old versions of packages by
+#'   specifying a version. For example, to install the latest version of `{AER}`
+#'   but an old version of `{ggplot2}`, you could write: `r_pkgs = c("AER",
 #'   "ggplot2@2.2.1")`. Note however that doing this could result in dependency
 #'   hell, because an older version of a package might need older versions of
 #'   its dependencies, but other packages might need more recent versions of the
@@ -89,10 +88,10 @@
 #'   the Nix revision closest to that date, by setting `r_ver = "3.1.0"`, which
 #'   was the version of R current at the time. This ensures that Nix builds a
 #'   completely coherent environment. For security purposes, users that wish to
-#'   install packages from Github/Gitlab or from the CRAN archives must provide a
-#'   security hash for each package. `{rix}` automatically precomputes this hash
-#'   for the source directory of R packages from GitHub/Gitlab or from the CRAN
-#'   archives, to make sure the expected trusted sources that match the
+#'   install packages from Github/Gitlab or from the CRAN archives must provide
+#'   a security hash for each package. `{rix}` automatically precomputes this
+#'   hash for the source directory of R packages from GitHub/Gitlab or from the
+#'   CRAN archives, to make sure the expected trusted sources that match the
 #'   precomputed hashes in the `default.nix` are downloaded. If Nix is
 #'   available, then the hash will be computed on the user's machine, however,
 #'   if Nix is not available, then the hash gets computed on a server that we
@@ -157,7 +156,7 @@ rix <- function(r_ver = "latest",
                 local_r_pkgs = NULL,
                 tex_pkgs = NULL,
                 ide = c("other", "code", "radian", "rstudio", "rserver"),
-                project_path = ".",
+                project_path,
                 overwrite = FALSE,
                 print = FALSE,
                 message_type = "simple",

R/rix_init.R

@@ -62,8 +62,7 @@
 #' it and set the `rprofile_action` to `"append"`.
 #'
 #' @param project_path Character with the folder path to the isolated nix-R
-#'   project. Defaults to `"."`, which is the current working directory path. If
-#'   the folder does not exist yet, it will be created.
+#'   project. If the folder does not exist yet, it will be created.
 #' @param rprofile_action Character. Action to take with `.Rprofile` file
 #'   destined for `project_path` folder. Possible values include
 #'   `"create_missing"`, which only writes `.Rprofile` if it does not yet exist
@@ -94,7 +93,7 @@
 #'   message_type = c("simple")
 #' )
 #' }
-rix_init <- function(project_path = ".",
+rix_init <- function(project_path,
                      rprofile_action = c(
                        "create_missing", "create_backup",
                        "overwrite", "append"

cran-comments.md

@@ -1,3 +1,57 @@
+## 23-09-2024 Resubmission
+
+### R CMD check results
+
+0 errors | 0 warnings | 1 note
+
+Note is because it's a new release.
+
+#### Comments from CRAN maintainers from submission of the 20-09-2024:
+
+- The Title field starts with the package name. Please omit it.
+
+Done.
+
+- Please always write package names, software names and API (application
+programming interface) names in single quotes in title and description.
+e.g: --> 'Nix'
+Please note that package names are case sensitive.
+
+Done.
+
+- The Description field is intended to be a (one paragraph) description of
+what the package does and why it may be useful. Please add more details
+about the package functionality and implemented methods in your
+Description text.
+
+Done.
+
+- If there are references describing the methods in your package, please
+add these in the description field of your DESCRIPTION file in the form
+authors (year) <doi:...>
+authors (year, ISBN:...)
+or if those are not available: <https:...>
+with no space after 'doi:', 'https:' and angle brackets for
+auto-linking. (If you want to add a title as well please put it in
+quotes: "Title")
+
+We added a reference to a paper describing Nix.
+
+- Please ensure that your functions do not write by default or in your
+examples/vignettes/tests in the user's home filespace (including the
+package directory and getwd()). This is not allowed by CRAN policies.
+Please omit any default path in writing functions. In your
+examples/vignettes/tests you can write to tempdir().
+-> R/rix.R; R/rix_init.R
+
+There was a vignette writing to `"."` instead of `tempdir()`, this has
+been fixed with https://github.com/ropensci/rix/pull/328/commits/0f92911d6959b6f87cc4013744f2ede3c49d19d5
+
+Regarding functions `rix()` and `rix_init()`: we don't set `project_path` to
+`"."` by default anymore.
+
+* This is a new release.
+
 ## R CMD check results
 
 0 errors | 0 warnings | 1 note

vignettes/z-advanced-topic-running-r-or-shell-code-in-nix-from-r.Rmd

@@ -231,8 +231,7 @@ from. Accordingly, we define the R 4.2.0 environment in a
 *`env`*`_1_2_R-4-2-0`using Nix via `rix::rix()`. The latter environment will be
 the target environment where `df_as_vector()` will be evaluated in.
 
-
-```{r parsermd-chunk-11}
+```{r, eval = F}
 library("rix")
 path_env_1_2 <- file.path(".", "_env_1_2_R-4-2-0")
 
@@ -246,6 +245,23 @@ rix(
 list.files(path_env_1_2)
 ```
 
+```{r, include = F}
+library("rix")
+
+path_env_1_2 <- file.path(tempdir(), "_env_1_2_R-4-2-0")
+
+rix(
+  r_ver = "4.2.0",
+  overwrite = TRUE,
+  project_path = path_env_1_2,
+  shell_hook = "R"
+)
+```
+
+```{r, echo = F}
+list.files(path_env_1_2)
+```
+
 Now, initiate a new R session as development environment using `nix-shell`. Open
 a new terminal at the current working directory of your R session. The provided
 expression `default.nix`. defines R 4.1.3 in a "subfolder per subshell"
@@ -327,8 +343,7 @@ compile!).
 Let's build a subshell with the latest version of R, but an older version
 of `{stringr}`:
 
-
-```{r parsermd-chunk-18}
+```{r, eval = F}
 library("rix")
 
 path_env_stringr <- file.path(".", "_env_stringr_1.4.1")
@@ -343,8 +358,21 @@ rix(
 list.files(path = path_env_stringr, all.files = TRUE)
 ```
 
-```{r, include = FALSE}
-unlink(path_env_stringr, recursive = TRUE, force = TRUE)
+```{r, include = F}
+library("rix")
+
+path_env_stringr <- file.path(tempdir(), "_env_stringr_1.4.1")
+
+rix(
+  r_ver = "4.3.1",
+  r_pkgs = "stringr@1.4.1",
+  overwrite = TRUE,
+  project_path = path_env_stringr
+)
+```
+
+```{r, echo = F}
+list.files(path = path_env_stringr, all.files = TRUE)
 ```
 
 We can now run the code in the subshell