merge with old stuff

.github/workflows/build.yml

@@ -0,0 +1,32 @@
+name: Build Docker Image
+
+on:
+  push:
+    branches:
+      - 'v1'
+  workflow_dispatch:
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Login to GHCR (GitHub Packages)
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build and push
+        id: docker_build
+        uses: docker/build-push-action@v5
+        with:
+          push: true
+          tags: |
+            ghcr.io/${{github.repository}}:latest

.github/workflows/recheck.yml

@@ -16,7 +16,7 @@ jobs:
   prepare:
     name: Prepare dependencies
     runs-on: ubuntu-latest
-    container: ghcr.io/r-universe-org/recheck
+    container: ghcr.io/r-devel/recheck
     outputs:
       oldfile: ${{ steps.filenames.outputs.oldfile }}
       newfile: ${{ steps.filenames.outputs.newfile }}
@@ -66,7 +66,7 @@ jobs:
     needs: prepare
     runs-on: ubuntu-latest
     name: Recheck ${{matrix.check == 'oldpkg' && needs.prepare.outputs.oldfile || needs.prepare.outputs.newfile}} (${{matrix.check}})
-    container: ghcr.io/r-universe-org/recheck
+    container: ghcr.io/r-devel/recheck
     timeout-minutes: 600
     strategy:
       matrix:

.gitignore

@@ -0,0 +1,7 @@
+*.o
+*.so
+*.dll
+.Rproj.user
+.Rhistory
+revdeps
+*_recheck

Dockerfile

@@ -0,0 +1,4 @@
+FROM ghcr.io/r-devel/rcheckserver/ubuntu
+
+COPY rechecktools /rechecktools
+RUN R -e 'install.packages("remotes");remotes::install_local("/rechecktools");library(rechecktools)'

rechecktools/.Rbuildignore

@@ -0,0 +1,9 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+^Dockerfile$
+^\.git$
+^\.github$
+^LICENSE.md$
+^action.yml$
+^entrypoint.sh$
+^.*_recheck$

rechecktools/DESCRIPTION

@@ -0,0 +1,13 @@
+Package: rechecktools
+Type: Package
+Title: Reverse Dependency Check Tools
+Version: 0.1.0
+Author: Who wrote it
+Maintainer: The package maintainer <yourself@somewhere.net>
+Description: Runs a reverse dependency check in a similar manner as CRAN incoming.
+License: MIT + file LICENSE
+Encoding: UTF-8
+Imports: 
+    curl
+RoxygenNote: 7.3.1
+Roxygen: list(markdown = TRUE)

rechecktools/LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2024
+COPYRIGHT HOLDER: Jeroen Ooms

rechecktools/LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2024 Jeroen Ooms
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

rechecktools/NAMESPACE

@@ -0,0 +1,4 @@
+# Generated by roxygen2: do not edit by hand
+
+export(install_recheck_deps)
+export(recheck)

rechecktools/R/ci.R

@@ -0,0 +1,24 @@
+#' Wrappers to run in CI
+#'
+#' To call in CI
+#'
+#' @export
+#' @param path path to source package
+#' @param which either be strong or most
+install_recheck_deps <- function(path = '.', which = 'strong'){
+  oldrepos <- enable_all_repos()
+  oldtimeout <- options(timeout = 600)
+  on.exit(options(c(oldrepos, oldtimeout)), add = TRUE)
+  desc <- read.dcf(file.path(path, 'DESCRIPTION'))
+  pkg <- desc[[1, 'Package']]
+  cranrepo <- getOption('repos')['CRAN']
+  cran <- utils::available.packages(repos = cranrepo)
+  packages <- c(pkg, tools::package_dependencies(pkg, db = cran, which = which, reverse = TRUE)[[pkg]])
+  if(grepl("Linux", Sys.info()[['sysname']])){
+    preinstall_linux_binaries(packages)
+  } else {
+    utils::install.packages(packages, dependencies = TRUE)
+    deps <- unique(unlist(unname(tools::package_dependencies(packages, recursive = TRUE))))
+    update.packages(oldPkgs = deps, ask = FALSE)
+  }
+}

rechecktools/R/linux-binaries.R

@@ -0,0 +1,47 @@
+# The goal of this function is to speed up installation of dependencies.
+# This is done in two ways:
+#  - Try to get precompiled binaries when available (mainly on ubuntu)
+#  - Download files in parallel using curl
+# The latter can be removed once fixed in base-R: https://github.com/r-devel/r-svn/pull/155
+preinstall_linux_binaries <- function(tocheck){
+  rver <- getRversion()
+  distro <- system2('lsb_release', '-sc', stdout = TRUE)
+  options(HTTPUserAgent = sprintf("R/%s R (%s); r-universe (%s)", rver, paste(rver, R.version$platform, R.version$arch, R.version$os), distro))
+  bioc <- sprintf("https://bioc.r-universe.dev/bin/linux/%s/4/", distro)
+  cran <- sprintf("https://p3m.dev/cran/__linux__/%s/latest", distro)
+  repos <- c(cran, bioc)
+  db <- utils::available.packages(repos = c(CRAN = cran, BIOC = bioc, official_bioc_repos()))
+  checkdeps <- unique(unlist(unname(tools::package_dependencies(tocheck, db = db, which = 'most'))))
+  alldeps <- tools::package_dependencies(checkdeps, db = db, recursive = TRUE)
+  packages <- unlist(lapply(checkdeps, function(x){
+    c(rev(alldeps[[x]]), x)
+  }))
+  packages <- intersect(unique(packages), row.names(db))
+  packages <- setdiff(packages, loadedNamespaces())
+  versions <- db[packages, 'Version']
+  mirrors <- db[packages, 'Repository']
+  urls <- sprintf("%s/%s_%s.tar.gz", mirrors, packages,  versions)
+  destdir <- tempfile()
+  dir.create(destdir)
+  pwd <- setwd(destdir)
+  on.exit(setwd(pwd), add = TRUE)
+  on.exit(unlink(destdir, recursive = TRUE), add = TRUE)
+  res <- curl::multi_download(urls)
+  res$ok <- res$success & res$status_code == 200
+  failures <- res$destfile[!res$ok]
+  if(length(failures)){
+    warning("Failed downloads for: ", paste(failures, collapse = ', '))
+    unlink(failures)
+    res <- res[res$ok,]
+  }
+  utils::install.packages(res$destfile, repos = NULL, Ncpus = parallel::detectCores())
+}
+
+official_bioc_repos <- function(){
+  version <- utils:::.BioC_version_associated_with_R_version()
+  sprintf(c(
+    BioCsoft = "https://bioconductor.org/packages/%s/bioc",
+    BioCann = "https://bioconductor.org/packages/%s/data/annotation",
+    BioCexp = "https://bioconductor.org/packages/%s/data/experiment"
+  ), version)
+}

rechecktools/R/recheck.R

@@ -0,0 +1,90 @@
+#' Reverse Dependency Check
+#'
+#' Run a reverse dependency check similar to CRAN.
+#'
+#' @export
+#' @rdname recheck
+#' @param sourcepkg path or URL to a source package tarball
+#' @param which passed to `tools::package_dependencies`; set to "most" to
+#' also check reverse suggests.
+#' @param preinstall_dependencies start by installing dependencies for all
+#' packages to be checked.
+recheck <- function(sourcepkg, which = "strong", preinstall_dependencies = TRUE){
+  # Some temporary settings
+  oldrepos <- enable_all_repos()
+  oldtimeout <- options(timeout = 600)
+  on.exit(options(c(oldrepos, oldtimeout)), add = TRUE)
+
+  # Get the tarball
+  if(grepl('^https:', sourcepkg)){
+    curl::curl_download(sourcepkg, basename(sourcepkg))
+    sourcepkg <- basename(sourcepkg)
+  }
+  if(!grepl("_", sourcepkg)){
+    dl <- utils::download.packages(sourcepkg, '.')
+    sourcepkg <- basename(dl[,2])
+  }
+  pkg <- sub("_.*", "", basename(sourcepkg))
+  checkdir <- dirname(sourcepkg)
+  cranrepo <- getOption('repos')['CRAN'] #
+  cran <- utils::available.packages(repos = cranrepo)
+  packages <- c(pkg, tools::package_dependencies(pkg, db = cran, which = which, reverse = TRUE)[[pkg]])
+  if(preinstall_dependencies){
+    group_output("Preparing dependencies", {
+      if(grepl("Linux", Sys.info()[['sysname']])){
+        preinstall_linux_binaries(packages)
+      } else {
+        utils::install.packages(packages, dependencies = TRUE)
+        deps <- unique(unlist(unname(tools::package_dependencies(packages, recursive = TRUE))))
+        update.packages(oldPkgs = deps, ask = FALSE)
+      }
+    })
+  }
+  check_args <- character()
+  if(nchar(Sys.which('pdflatex')) == 0){
+    message("No pdflatex found, skipping pdf checks")
+    check_args <- c(check_args, '--no-manual --no-build-vignettes')
+  }
+  group_output("Running checks", {
+    Sys.setenv('_R_CHECK_FORCE_SUGGESTS_' = 'false')
+    if(.Platform$OS.type == 'windows') Sys.setenv(TAR = 'internal')
+    tools::check_packages_in_dir(checkdir, basename(sourcepkg),
+                                 reverse = list(repos = cranrepo, which = which),
+                                 Ncpus = parallel::detectCores(),
+                                 check_args = check_args)
+  })
+  group_output("Check results details", {
+    details <- tools::check_packages_in_dir_details(checkdir)
+    write.csv(details, file.path(checkdir, 'check-details.csv'))
+    writeLines(paste(format(details), collapse = "\n\n"), file.path(checkdir, 'check-details.txt'))
+    print(details)
+  })
+  tools::summarize_check_packages_in_dir_results(checkdir)
+}
+
+enable_all_repos <- function(){
+  old <- options(repos = c(CRAN = 'https://cloud.r-project.org'))
+  utils::setRepositories(ind = 1:4) #adds bioc
+  my_universe <- Sys.getenv('MY_UNIVERSE')
+  if(nchar(my_universe)){
+    options(repos = c(my_universe = my_universe, getOption('repos')))
+  }
+  return(old)
+}
+
+group_output<- function(title, expr){
+  if(Sys.getenv('CI') != ""){
+    cat("::group::", title, "\n", sep = "")
+    on.exit(cat("::endgroup::\n"))
+  }
+  cat("===========", title, "===========\n")
+  eval(expr)
+}
+
+test_recheck <- function(pkg, which = 'strong'){
+  checkdir <- paste(pkg, 'recheck', sep = '_')
+  unlink(checkdir, recursive = TRUE)
+  dir.create(checkdir)
+  utils::download.packages(pkg, checkdir, repos = 'https://cloud.r-project.org')
+  recheck(list.files(checkdir, pattern = 'tar.gz$', full.names = TRUE), which = which)
+}

rechecktools/recheck.Rproj

@@ -0,0 +1,20 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source