Merge branch 'master' into todoRename

Author: badasahog

.ci/linters/rd/backtick_linter.R

@@ -0,0 +1,22 @@
+# ensure no markdown-style backticks wind up in Rd where \code is intended
+options_documentation_linter = function(rd_file) {
+  rd = tools::parse_Rd(rd_file)
+
+  error_if_backtick = function(rd_obj) {
+    if (!is.recursive(rd_obj)) {
+      if (any(grepl("`", rd_obj, fixed=TRUE))) {
+        stop(sprintf(
+          "Rd is not markdown -- backticks (`) don't render as code! Use \\code{...}.\nObserved in string '%s' in file %s",
+          trimws(rd_obj), rd_file
+        ))
+      }
+      return(invisible())
+    }
+    tags = vapply(rd_obj, \(x) attr(x, "Rd_tag") %||% "", FUN.VALUE="")
+     # backtick is valid inside R code (e.g. \examples, \code, \preformatted)
+    rd_obj = rd_obj[!tags %in% c("RCODE", "VERB")]
+    lapply(rd_obj, error_if_backtick)
+  }
+
+  invisible(error_if_backtick(rd))
+}

.ci/linters/rd/options_doc_check.R …inters/rd/options_documentation_linter.R.ci/linters/rd/options_doc_check.R renamed to .ci/linters/rd/options_documentation_linter.R .ci/linters/rd/options_doc_check.R renamed to .ci/linters/rd/options_documentation_linter.R

@@ -562,9 +562,9 @@ ls -1 *.tar.gz | grep -E 'Chicago|dada2|flowWorkspace|LymphoSeq' | TZ='UTC' para
 #  3) dllVersion() at the end of init.c
 # DO NOT push to GitHub's master branch. Prevents even a slim possibility of user getting premature version. 
 # Even release numbers must have been obtained from CRAN and only CRAN. There were too many support problems in the past before this procedure was brought in.
-du -k inst/tests                # 1.5MB before
+du -k inst/tests                # 1.5MiB before
 bzip2 inst/tests/*.Rraw         # compress *.Rraw just for release to CRAN; do not commit compressed *.Rraw to git
-du -k inst/tests                # 0.75MB after
+du -k inst/tests                # 0.75MiB after
 R CMD build .
 export GITHUB_PAT="f1c.. github personal access token ..7ad"
 Rdevel -q -e "packageVersion('xml2')"   # ensure installed

.dev/CRAN_Release.cmd

@@ -67,7 +67,7 @@ options(repos = BiocManager::repositories())
 
 options(warn=1)  # warning at the time so we can more easily see what's going on package by package when we scroll through output
 cat("options()$timeout==", options()$timeout," set by R_DEFAULT_INTERNET_TIMEOUT in .dev/.bash_aliases revdepsh\n",sep="")
-# R's default is 60. Before Dec 2020, we used 300 but that wasn't enough to download Bioc package BSgenome.Hsapiens.UCSC.hg19 (677GB) which is
+# R's default is 60. Before Dec 2020, we used 300 but that wasn't enough to download Bioc package BSgenome.Hsapiens.UCSC.hg19 (677MiB) which is
 # suggested by CRAN package CNVScope which imports data.table. From Dec 2020 we use 3600.
 
 if (is.null(utils::old.packages(.libPaths()[2]))) {

.dev/revdep.R

@@ -151,7 +151,7 @@ test-lin-rel-cran:
     _R_CHECK_CRAN_INCOMING_: "TRUE"           ## stricter --as-cran checks should run in dev pipelines continuously (not sure what they are though)
     _R_CHECK_CRAN_INCOMING_REMOTE_: "FALSE"   ## Other than no URL checking (takes many minutes) or 'Days since last update 0' NOTEs needed, #3284
     _R_CHECK_CRAN_INCOMING_TARBALL_THRESHOLD_: "7500000" ## bytes
-    _R_CHECK_PKG_SIZES_THRESHOLD_: "10"        ## MB 'checking installed package size' NOTE increased due to po
+    _R_CHECK_PKG_SIZES_THRESHOLD_: "10"        ## MiB 'checking installed package size' NOTE increased due to po
   script:
     - *install-deps
     - echo 'CFLAGS=-g -O2 -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2' > ~/.R/Makevars