Merge pull request #63 from ThinkR-open/att-rebase-0.3

Att rebase 0.3

.github/workflows/R-CMD-check-HTML5.yaml

@@ -0,0 +1,42 @@
+# 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
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check-HTML5
+
+jobs:
+  R-CMD-check:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+      _R_CHECK_RD_VALIDATE_RD2HTML_: TRUE
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install pdflatex
+        run: sudo apt-get install texlive-latex-base texlive-fonts-recommended texlive-fonts-extra texlive-latex-extra
+
+      - name: Install tidy
+        run: sudo apt install tidy
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'devel'
+          http-user-agent: 'release'
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          args: '"--as-cran"'
+          build_args: 'character()'
+          error-on: '"note"'

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: attachment
 Title: Deal with Dependencies
-Version: 0.2.5.9000
+Version: 0.3.0
 Authors@R:
     c(person(given = "Sébastien",
              family = "Rochette",
@@ -15,18 +15,17 @@ Authors@R:
              "previous maintainer")),
      person(given = "ThinkR",
              role = c("cph", "fnd")))
-Description: Tools to help manage dependencies during package
-    development.  This can retrieve all dependencies that are used in R
-    files in the "R" directory, in Rmd files in "vignettes" directory and
+Description: Manage dependencies during package
+    development. This can retrieve all dependencies that are used in ".R"
+    files in the "R/" directory, in ".Rmd" files in "vignettes/" directory and
     in 'roxygen2' documentation of functions. There is a function to
-    update the Description file of your package and a function to create a
-    file with the R commands to install all dependencies of your package.
-    All functions to retrieve dependencies of R scripts and Rmd files can
+    update the "DESCRIPTION" file of your package with 'CRAN' packages or any other remote package.
+    All functions to retrieve dependencies of ".R" scripts and ".Rmd" or ".qmd" files can
     be used independently of a package development.
 License: GPL-3
 URL: https://thinkr-open.github.io/attachment/,
-    https://github.com/Thinkr-open/attachment
-BugReports: https://github.com/Thinkr-open/attachment/issues
+    https://github.com/ThinkR-open/attachment
+BugReports: https://github.com/ThinkR-open/attachment/issues
 VignetteBuilder:
     knitr
 Encoding: UTF-8

NAMESPACE

@@ -4,6 +4,8 @@ export("%>%")
 export(att_amend_desc)
 export(att_from_description)
 export(att_from_namespace)
+export(att_from_qmd)
+export(att_from_qmds)
 export(att_from_rmd)
 export(att_from_rmds)
 export(att_from_rscript)

NEWS.md

@@ -1,12 +1,12 @@
-# attachment (development version)
+# attachment 0.3.0
 
 ## New features
 
-- `set_remotes_to_desc()` now detects github, gitlab, git, local installations (@MurielleDelmotte)
+- `find_remotes()` and `set_remotes_to_desc()` now detects github, gitlab, git, bitbucket, local installations to add to the "Remotes:" part of the DESCRIPTION file (@MurielleDelmotte)
+- Quarto documents can be parsed with `att_from_qmds()` as an alias of `att_from_rmds()`.
 
 ## Minor changes
 
-- Quarto documents can be parsed with `att_from_rmds()`.
 - Documentation for bookdown and quarto dependencies extraction updated
 
 ## Bug fixes 

R/att_from_rmds.R

@@ -114,3 +114,12 @@ att_from_rmds <- function(path = "vignettes",
     res
   }
 }
+
+#' @rdname att_from_rmds
+#' @export
+att_from_qmds <- att_from_rmds
+
+#' @rdname att_from_rmd
+#' @export
+att_from_qmd <- att_from_rmd
+

R/attachment-deprecated.R

@@ -1,7 +1,13 @@
 #' Deprecated functions
 #'
-#' @name attachment-deprecated
+#' @description
+#' List of functions deprecated. They will be removed in a future release.
+#'
 #'
+#' @name attachment-deprecated
+#' @keywords internal
+#' @return List of functions used for deprecation side effects.
+#' Output depends on the deprecated function.
 #' @section Details:
 #' \tabular{rl}{
 #'    `att_to_description` \tab is now called `att_amend_desc`

R/set_remotes.R

@@ -3,7 +3,9 @@
 #' @param pkg Character. Packages to test for potential non-CRAN installation
 #'
 #' @return
-#' List of non-CRAN packages and code to add in Remotes field in DESCRIPTION
+#' List of all non-CRAN packages and code to add in Remotes field in DESCRIPTION.
+#' NULL otherwise.
+#' @importFrom utils packageDescription
 #' @export
 #'
 #' @examples
@@ -15,10 +17,16 @@
 #' path = file.path(dummypackage, "DESCRIPTION")) %>%
 #' find_remotes()
 #' \dontrun{
-#' # For your current directory
+#' # For the current package directory
 #' att_from_description() %>% find_remotes()
-#' # Find from all installed packages
-#' head(find_remotes(installed.packages()[,1]))
+#' }
+#'
+#' \donttest{
+#' # For a specific package name
+#' find_remotes("attachment")
+#'
+#' # Find remotes from all installed packages
+#' find_remotes(list.dirs(.libPaths(), full.names = FALSE, recursive = FALSE))
 #' }
 find_remotes <- function(pkg) {
 
@@ -27,6 +35,19 @@ find_remotes <- function(pkg) {
   }) %>%
     setNames(pkg)
 
+  # Keep only thos that are packages
+  w.notpkg <- which(unlist(lapply(pkgdesc, function(x) all(is.na(x)))))
+  if (length(w.notpkg) != 0) {
+      message(glue::glue_collapse(names(pkgdesc)[w.notpkg], sep = ", ", last = " & "),
+              ifelse(length(w.notpkg) == 1,
+                     " does not seem to be a package. It is removed from exploration.",
+                     " do not seem to be packages. They are removed from exploration."
+              )
+      )
+    pkgdesc <- pkgdesc[-w.notpkg]
+    if (length(pkgdesc) == 0) {return(NULL)}
+  }
+
   extract_pkg_info(pkgdesc)
 }
 
@@ -112,6 +133,7 @@ internal_remotes_to_desc <- function(remotes, path.d = "DESCRIPTION",
 
   w.unique <- !duplicated(names(new_remotes))
   new_remotes <- unlist(new_remotes)[w.unique]
+  new_remotes <- new_remotes[sort(names(new_remotes))]
 
   if (length(new_remotes) != 0) {
     desc$set_remotes(new_remotes)
@@ -146,22 +168,24 @@ extract_pkg_info <- function(pkgdesc) {
     guess_repo <- lapply(pkg_not_cran, function(x) {
       desc <- pkgdesc[[x]]
       if (!is.null(desc$RemoteType) && desc$RemoteType == "github") {
-        tolower(paste(desc$RemoteUsername, desc$RemoteRepo, sep = "/"))
+        paste(desc$RemoteUsername, desc$RemoteRepo, sep = "/")
       } else if (!is.null(desc$RemoteType) && desc$RemoteType %in% c("gitlab", "bitbucket")) {
-        tolower(paste0(desc$RemoteType, "::",
-                       paste(desc$RemoteUsername, desc$RemoteRepo, sep = "/")))
+        paste0(desc$RemoteType, "::",
+                       paste(desc$RemoteUsername, desc$RemoteRepo, sep = "/"))
       } else if (desc$RemoteType == "local" && !is.null(desc$RemoteUrl)  && is.null(desc$RemoteHost)) {
-        tolower(paste0(desc$RemoteType, "::", desc$RemoteUrl))
-      } else if (!is.null(desc$RemoteType) && !(desc$RemoteType %in% c("github","gitlab","bitbucket","local")) &&  grepl(".git",x = desc$RemoteUrl) ){
-        tolower(paste0("git::",desc$RemoteUrl))
+        paste0(desc$RemoteType, "::", desc$RemoteUrl)
+      } else if (!is.null(desc$RemoteType) &&
+                 !(desc$RemoteType %in% c("github","gitlab","bitbucket","local")) &&
+                 grepl("git",x = desc$RemoteType) ){
+        paste0("git::",desc$RemoteUrl)
       } else if (is.null(desc$RemoteType) && isTRUE(grepl("bioconductor",x = desc$URL))) {
         biocversion <-  desc$git_branch %>%
           gsub(pattern = "RELEASE_", replacement = "") %>%
           gsub(pattern = "_", replacement = ".")
-        tolower(paste0("bioc::",biocversion,"/",desc$Package))
-      } else if (!is.null(desc$RemoteType) && is.null(desc$RemoteHost)) {
-        c("Maybe ?" = tolower(paste0(desc$RemoteType, "::", desc$RemoteHost, ":",
-                                     paste(desc$RemoteUsername, desc$RemoteRepo, sep = "/"))))
+        paste0("bioc::",biocversion,"/",desc$Package)
+      } else if (!is.null(desc$RemoteType) && !is.null(desc$RemoteHost)) {
+        c("Maybe ?" = paste0(desc$RemoteType, "::", desc$RemoteHost, ":",
+                                     paste(desc$RemoteUsername, desc$RemoteRepo, sep = "/")))
       } else {
         c("local maybe ?" = NA)
       }

dev/dev_history.R

@@ -60,6 +60,7 @@ usethis::use_appveyor()
 usethis::use_github_action_check_standard()
 usethis::use_github_action("pkgdown")
 usethis::use_github_action("test-coverage")
+usethis::use_github_action(url = "https://github.com/DavisVaughan/extrachecks-html5/blob/main/R-CMD-check-HTML5.yaml")
 
 usethis::use_vignette("use_renv")
 usethis::use_build_ignore("_pkgdown.yml")
@@ -79,7 +80,8 @@ usethis::use_roxygen_md()
 roxygen2md::roxygen2md()
 roxygen2::roxygenise()
 attachment::att_amend_desc(
-  pkg_ignore = c("remotes", "i", "usethis", "rstudioapi", "renv"), #i
+  pkg_ignore = c("remotes", "i", "usethis", "rstudioapi", "renv",
+                 "gitlab", "git", "local", "find.rscript", "bioc"), #i
   extra.suggests = c("testthat", "rstudioapi", "renv", "lifecycle"), #"pkgdown", "covr",
   dir.t = "",
   normalize = FALSE)
@@ -108,6 +110,9 @@ devtools::test()
 devtools::load_all()
 testthat::test_file(here::here("tests/testthat/test-amend-description.R"))
 
+# Test for dependencies
+tools:::.check_packages_used_in_tests(dir = ".", testdir = "tests/testthat")
+
 # Checks for CRAN release ----
 # Check package as CRAN
 rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"))
@@ -128,19 +133,22 @@ urlchecker::url_update()
 
 # check on other distributions
 # _rhub
-devtools::check_rhub()
+# devtools::check_rhub()
 rhub::local_check_linux_images()
 rhub::local_check_linux(image = "rhub/debian-gcc-release")
 rhub::local_check_linux(image = "rhub/debian-clang-devel")
 
+rhub::platforms()
 rhub::check(platform = "windows-x86_64-devel", show_status = FALSE)
+rhub::check(platform = "windows-x86_64-oldrel", show_status = FALSE)
 rhub::check_on_solaris(show_status = FALSE)
-aa <- rhub::check_for_cran(show_status = FALSE)
-aa
+rhub::check_for_cran(show_status = FALSE)
+
 
 # _win devel
 devtools::check_win_devel()
 devtools::check_win_release()
+devtools::check_win_oldrelease()
 devtools::check_mac_release()
 
 # Check reverse dependencies
@@ -157,6 +165,7 @@ id <- rstudioapi::terminalExecute("Rscript -e 'revdepcheck::revdep_check(num_wor
 rstudioapi::terminalKill(id)
 # See outputs
 revdep_details(revdep = "fusen")
+revdep_details(revdep = "golem")
 revdep_summary()
 # table of results by package
 revdep_report() # in revdep/

inst/dummypackage/tests/testthat/test-addition.R

@@ -0,0 +1,3 @@
+test_that("Add works", {
+  expect_equal(1 + 1, 2)
+})