Run BiocCheck

Author: jeroen

DESCRIPTION

@@ -9,6 +9,7 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Imports:
+    BiocCheck,
     cffr,
     commonmark,
     curl,
@@ -28,5 +29,6 @@ Imports:
     unix,
     yaml,
     xml2
-RoxygenNote: 7.3.2.9000
+RoxygenNote: 7.3.3
 Additional_repositories: https://rcppcore.r-universe.dev
+Remotes: Bioconductor/BiocCheck

NAMESPACE

@@ -4,6 +4,7 @@ export(annotated_error)
 export(backfill_bioc_downloads)
 export(backfill_indexurls)
 export(backfill_search_results)
+export(bioc_check)
 export(commit_info_base64)
 export(find_logo)
 export(find_readme_url)

R/bioccheck.R

@@ -0,0 +1,12 @@
+#' @export
+bioc_check <- function(sourcepkg, install = FALSE){
+  options(BiocManager.check_repositories = FALSE)
+  if(Sys.getenv("UNIVERSE_NAME") == 'bioc-release'){
+    Sys.setenv(R_BIOC_VERSION = as.character(BiocManager:::.version_bioc("release")))
+  } else {
+    Sys.setenv(R_BIOC_VERSION = as.character(BiocManager:::.version_bioc("devel")))
+  }
+
+  library(BiocCheck)
+  BiocCheck(sourcepkg, install = install, 'no-check-R-ver' = TRUE)
+}

entrypoint.sh

@@ -273,6 +273,13 @@ Rscript -e "buildtools::render_html_manual('$PACKAGE', 'outputs/$PACKAGE/extra')
 Rscript -e "buildtools::generate_metadata_files('$PACKAGE', '$REPO', '$SUBDIR', 'outputs/$PACKAGE', '$PKGDIR', '$URL', '$BRANCH')"
 echo "::endgroup::"
 
+# Run BiocCheck for Bioconductor repos only
+if [ "${UNIVERSE_NAME:0:4}" == "bioc" ]; then
+echo "::group::BiocCheck('$SOURCEPKG')"
+Rscript -e "buildtools::bioc_check('$SOURCEPKG', 'install.log')"
+echo "::endgroup::"
+fi
+
 # if outputs has any files, add them to tarball
 echo "::group::Adding extra files to tarball"
 gunzip "$SOURCEPKG"