Ignore renv files and folders during checks

.Rbuildignore

@@ -1,3 +1,5 @@
+^renv$
+^renv\.lock$
 ^.*\.Rproj$
 ^\.Rproj\.user$
 inst/testpackages/testpkg1/src/testpkg1.so

.gitignore

@@ -7,4 +7,7 @@ vignettes/*.R
 vignettes/*.html
 vignettes/sync.sh
 *.so
-*.o
+*.o
+.Rprofile
+renv
+renv.lock

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: BiocCheck
-Version: 1.25.13
+Version: 1.25.14
 Title: Bioconductor-specific package checks
 Description: Executes Bioconductor-specific package checks.
 Authors@R: c(
@@ -8,7 +8,7 @@ Authors@R: c(
 	role=c("aut", "cre")),
     person("Lori", "Shepherd", role="aut"),
     person("Daniel", "von Twisk", role="ctb"),
-    person("Kevin", "Rue", role="ctb"),
+    person("Kevin", "Rue-Albrecht", role="ctb"),
     person("Marcel", "Ramos", role="ctb"),
     person("Leonardo", "Collado-Torres", role = "ctb"),
     person("Federico", "Marini", role="ctb"))

NEWS

@@ -9,7 +9,7 @@ DEPRECATION ANNOUNCEMENT
 NEW FEATURES
 
     o (1.25.4) Check for single colon typos when using qualified imports pkg::foo()
-    o (1.25.1) Check for warning/notes on too-brief a Description: field 
+    o (1.25.1) Check for warning/notes on too-brief a Description: field
     (@federicomarini, #65)
     o (1.25.8) Validate ORCID IDs (if any) in the DESCRIPTION file
     (@LiNk-NY, #97)
@@ -18,8 +18,8 @@ NEW FEATURES
 
 BUG FIXES
 
-    o (1.25.9) All packages including infrastructure require a vignette 
-    o Usage of donttest and dontrun in manual pages tagged with the keyword 
+    o (1.25.9) All packages including infrastructure require a vignette
+    o Usage of donttest and dontrun in manual pages tagged with the keyword
     'internal' will no longer trigger a NOTE (@grimbough, #59)
     o (1.25.7) Adding the sessionInfo at the end of the vignette (@llrs)
 
@@ -31,6 +31,9 @@ USER SIGNIFICANT CHANGES
     styler over formatR for automatic code re-formatting.
     o (1.25.5) Add warning to new package versions with non-zero x version
     (@mtmorgan, #101)
+    o (1.25.14) Ignore files generated by the renv package during relevant checks.
+    Add a check explicitly raising an ERROR if renv files are detected;
+    with an option to disable the check.
 
 
 CHANGES IN VERSION 1.23

R/BiocCheck.R

@@ -47,6 +47,8 @@ getOptionList <- function()
             help="disable check for if package exists in CRAN"),
         make_option("--no-check-bioc-help", action="store_true",
             help="disable check for registration on Bioconductor mailing list and support site"),
+        make_option("--no-check-renv", action="store_true",
+            help="disable check for renv files"),
         make_option("--build-output-file", type="character",
             help="file containing R CMD build output, for additional analysis",
             metavar="build-output-file"),
@@ -116,6 +118,11 @@ BiocCheck <- function(package=".", ...)
     package_install_dir <- installAndLoad(package)
 
     ## checks
+    if (is.null(dots[["no-check-renv"]])){
+        handleCheck("Checking for renv files")
+        checkForRenvFiles(package_dir)
+    }
+
     if (is.null(dots[["no-check-dependencies"]])){
         handleCheck("Checking Package Dependencies...")
         checkForBadDepends(file.path(package_install_dir, "lib", package_name))
@@ -166,7 +173,7 @@ BiocCheck <- function(package=".", ...)
 
     if (is.null(dots[["no-check-file-size"]])){
         handleCheck("Checking individual file sizes...")
-        checkIndivFileSizes(package_dir)
+        checkIndivFileSizes(package_dir, !is.null(dots[["no-check-renv"]]))
     }
 
     if (is.null(dots[["no-check-bioc-views"]]))

R/checks.R

@@ -20,6 +20,30 @@ checkForVersionNumberMismatch <- function(package, package_dir)
     }
 }
 
+checkForRenvFiles <- function(pkgdir) {
+    removeItems <- character(0)
+    renvDir <- file.path(pkgdir, "renv")
+    if (dir.exists(renvDir)) {
+        removeItems <- c(removeItems, renvDir)
+    }
+    renvFiles <- c(
+        file.path(pkgdir, ".Rprofile"),
+        file.path(pkgdir, "renv.lock")
+    )
+    removeItems <- c(removeItems, renvFiles[file.exists(renvFiles)])
+    if (length(removeItems)){
+        handleError("Detected project library files generated by `renv`. ",
+                    "On your computer, you can use `BiocCheck(`no-check-renv`=TRUE)`. ",
+                    "If this error appears on the Bioconductor Build System, use `git rm --cached` to stop tracking the following directories and files in the Bioconductor repository:")
+        for (i in removeItems)
+            handleMessage(i, indent=8)
+        handleMessage("Then add the following entries to the package `.gitignore` file:")
+        for (i in c(".Rprofile", "renv", "renv.lock"))
+            handleMessage(i, indent=8)
+
+    }
+}
+
 ## Make sure this is run after pkg is installed.
 checkForBadDepends <- function(pkgdir)
 {
@@ -204,13 +228,16 @@ checkPackageSize <- function(pkg, pkgdir, size=5){
     }
 }
 
-checkIndivFileSizes <- function(pkgdir)
+checkIndivFileSizes <- function(pkgdir, skip.renv = FALSE)
 {
     pkgType <- getPkgType(pkgdir)
     if (is.na(pkgType) ||  pkgType == "Software") {
         maxSize <- 5*10^6 ## 5MB
         allFiles <- list.files(pkgdir, all.files=TRUE, recursive=TRUE)
         allFilesFullName <- file.path(pkgdir, allFiles)
+        if (skip.renv) {
+            allFilesFullName <- dropRenvFiles(allFilesFullName, pkgdir)
+        }
         sizes <- file.size(allFilesFullName)
         largeFiles <- paste(allFiles[sizes > maxSize], collapse=" ")
         if (any(sizes > maxSize)) {
@@ -1092,9 +1119,8 @@ checkClassEqUsage <- function(pkgdir){
 }
 
 checkSystemCall <- function(pkgdir){
-
     pkgdir <- sprintf("%s%s", pkgdir, .Platform$file.sep)
-    msg_sys <- grepPkgDir(pkgdir, "-rHn '^system(.*'")
+    msg_sys <- grepPkgDir(pkgdir, "-rHn '^system(.*'", skip.renv = TRUE)
 }
 
 
@@ -1642,7 +1668,8 @@ checkBadFiles <- function(package_dir){
                        ".dropbox", ".exrc", ".gdb.history",
                        ".gitattributes", ".gitmodules",
                        ".hgtags",
-                       ".project", ".seed", ".settings", ".tm_properties")
+                       ".project", ".seed", ".settings", ".tm_properties",
+                       "renv", "renv.lock")
 
     fls <- dir(package_dir, ignore.case=TRUE, recursive=TRUE, all.files=TRUE)
     dx <- unlist(lapply(hidden_file_ext,

R/util.R

@@ -441,12 +441,15 @@ makeTempRFile <- function(infile){
     }
 }
 
-grepPkgDir <- function(pkgdir, greparg, full_path=FALSE){
+grepPkgDir <- function(pkgdir, greparg, full_path=FALSE, skip.renv = FALSE){
     args <- sprintf("%s %s*", greparg, pkgdir)
     fnd <- tryCatch(
         system2("grep", args, stdout=TRUE),
         warning=function(w){character()},
         error=function(e){character(0)})
+    if (skip.renv) {
+        fnd <- dropRenvFiles(fnd, pkgdir, .addFS = FALSE)
+    }
     msg_files <- vapply(fnd,
                         FUN=function(x, pkgdir){
                             vl = strsplit(x, split=":")
@@ -715,20 +718,31 @@ doesManPageHaveRunnableExample <- function(rd)
     length(parsed) && !inherits(parsed, "try-error")
 }
 
+dropRenvFiles <- function(files, pkgdir, .addFS = TRUE) {
+  sep <- ifelse(.addFS, .Platform$file.sep, "")
+  renvDir <- sprintf("%s%s%s", pkgdir, sep, "renv")
+  files <- files[!startsWith(files, renvDir)]
+  files <- files[!startsWith(files, "renv/")]
+  files
+}
 
 checkLogicalUseFiles <- function(pkgdir) {
     Rdir <- file.path(pkgdir, "R")
     Rfiles <- dir(pkgdir, recursive=TRUE, pattern = "\\.[rR]$",
                   full.names = TRUE)
+    Rfiles <- dropRenvFiles(Rfiles, pkgdir)
     dx <- startsWith(Rfiles, Rdir)
     RdirFiles <- Rfiles[dx]
     Rother <- Rfiles[!dx]
     manFiles <- dir(pkgdir, recursive=TRUE, pattern = "\\.[Rr][Dd]$",
         full.names = TRUE)
+    manFiles <- dropRenvFiles(manFiles, pkgdir)
     RNWFiles <- dir(pkgdir, recursive=TRUE, pattern = "\\.[Rr][Nn][wW]$",
         full.names = TRUE)
+    RNWFiles <- dropRenvFiles(RNWFiles, pkgdir)
     RMDFiles <- dir(pkgdir, recursive=TRUE, pattern = "\\.[Rr][Mm][Dd]$",
         full.names = TRUE)
+    RMDFiles <- dropRenvFiles(RMDFiles, pkgdir)
 
     allFiles <- c(Rother, RMDFiles, RNWFiles, manFiles)
     fileNames1 <- character()

vignettes/BiocCheck.Rmd

@@ -725,6 +725,9 @@ occur when trying to use helper functions like packageVersion() or packageDate()
 instead of using meta$Version or meta$Date. See [R documentation](https://cran.r-project.org/doc/manuals/r-release/R-exts.html#CITATION-files) for more
 information.
 
+## Compatibility with the `r BiocStyle::CRANpkg("renv")` package
+
+Files in the `renv` sub-directory are ignored, as those can crash `BiocCheck`.
 
 # Expanding `BiocCheck`
 
@@ -735,4 +738,4 @@ Please adhere to the Pull Request template when submitting your contributions.
 
 ```{r sessionInfo}
 sessionInfo()
-```
+```