Package and file size checks do not fire when BiocCheck() is given a tarball

[seandavi]

Summary

When BiocCheck() is given a source tarball, all three size checks are silent regardless of
how large the package is:

• checkPackageSize() (the 10 MB tarball ERROR) never fires — on any input, tarball or
  source directory.
• checkIndivFileSizes() and checkDataFileSizes() (the 5 MB WARNINGs) never fire on
  tarball input; they work correctly on source-directory input.

Tested with BiocCheck 1.49.30.

Cause

checkPackageSize() sizes a directory, not the tarball. It reads
.BiocPackage$sourceDir:

checkPackageSize <- function(.BiocPackage, size = 10L) {
    pkg <- .BiocPackage$sourceDir
    ...
    pkgSize <- file.size(pkg)

For tarball input, getPackageDir() untars the archive and sets sourceDir to the unpacked
directory, keeping the tarball path in tarFilename. file.size() on a directory returns the
directory entry size (tens of bytes to a few KB), so pkgSize > maxSize is never true. For
source-directory input sourceDir is likewise a directory, so the check cannot fire there
either.

.findLargeFiles() has no branch that tarball input can reach.
It takes either the
gert::git_ls() branch when isGitClone is TRUE, or the list.files() branch when
isSourceDir is TRUE. A tarball is neither — isSourceDir is set to
!isTar && <is a directory> — so the function falls off the end and returns NULL.

Reproducible example

A minimal Software-type package with one 30 MB file in inst/extdata, built with
R CMD build into a 30,005,481-byte tarball:

bp <- BiocCheck:::.BiocPackage$copy()
bp$initialize("bigpkg_0.99.0.tar.gz")

bp$isTar                                            #> TRUE
bp$packageType                                      #> "Software"
file.size(bp$sourceDir)                             #> 83          <- a directory
file.size(bp$tarFilename)                           #> 30005481    <- the tarball

BiocCheck:::checkPackageSize(bp)                    #> (silent)
BiocCheck:::.findLargeFiles(bp, data_only = FALSE)  #> NULL

A full run confirms it end to end — the two errors and two warnings are unrelated to size:

r <- BiocCheck::BiocCheck("bigpkg_0.99.0.tar.gz")
#> * Checking package size...
#> * Checking individual file sizes...
#> ✖ 2 ERRORS | ⚠ 2 WARNINGS | ℹ 4 NOTES
names(r$error)    #> "checkBiocViews"  "checkVignetteDir"
names(r$warning)  #> "checkDescFieldLength"  "checkBiocDepsDESC"

On the same package as a source directory, the per-file check behaves as documented while the
tarball check still does not:

bp2 <- BiocCheck:::.BiocPackage$copy()
bp2$initialize("bigpkg")

file.size(bp2$sourceDir)                             #> 77
BiocCheck:::checkPackageSize(bp2)                    #> (silent)
BiocCheck:::.findLargeFiles(bp2, data_only = FALSE)  #> .../inst/extdata/blob.bin

Why it matters

Checking a tarball is the documented and common way to run BiocCheck, and it is what automated
pipelines use. In particular, r-universe runs BiocCheck against the built tarball for the
Bioconductor universes
(r-universe-org/actions/bioc-check),
so no size feedback reaches maintainers there at all. The only size limit in force in that
pipeline is r-universe's own 100 MiB per published file — about ten times the Bioconductor
tarball guidance, with no per-file component.

This looks like the same family as #167 (per-file check not firing), which was addressed for
the source-directory path; the tarball path appears to have been left behind, and
checkPackageSize() seems never to have measured the tarball.

Suggested fix

• In checkPackageSize(), size .BiocPackage$tarFilename when isTar is TRUE, and skip (or
  size the unpacked contents) otherwise — the message text, "Package tarball exceeds the
  Bioconductor size requirement", already implies the tarball is what was intended.
• In .findLargeFiles(), allow the tarball case by walking the unpacked sourceDir. The
  gert::git_ls() branch cannot apply there, but the list.files() branch works unchanged.

Happy to open a PR if that would be useful.

Minor, in passing: in the list.files() branch of .findLargeFiles(), the folder list from
list.dirs() contains both "" and its subdirectories, so files under a nested directory are
returned more than once — blob.bin above is reported twice in source-directory mode.

Environment

R version 4.6.1 (2026-06-24)
BiocCheck 1.49.30
BiocManager 1.30.27