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BUG?: R CMD check with --as-cran *disables* checks for unused imports otherwise performed

2 messages · Henrik Bengtsson, Jeffrey Dick

Original
Henrik Bengtsson
# 
ISSUE:

Using 'R CMD check' with --as-cran,
set_R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_=TRUE, whereas the
default is FALSE, which you get if you don't add --as-cran.
I would expect --as-cran to check more things and more be conservative
than without.  So, is this behavior a mistake?  Could it be a thinko
around the negating "IGNORE", and the behavior is meant to be vice
verse?

Example:

$ R CMD check QDNAseq_1.29.4.tar.gz
...
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
...
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ?future?
  All declared Imports should be used.

whereas, if I run with --as-cran, I don't get that NOTE;

$ R CMD check --as-cran QDNAseq_1.29.4.tar.gz
...
* checking dependencies in R code ... OK


TROUBLESHOOTING:

In src/library/tools/R/check.R [1], the following is set if --as-cran is used:

  Sys.setenv("_R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_" = "TRUE")

whereas, if not set, the default is:

ignore_unused_imports <-
config_val_to_logical(Sys.getenv("_R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_",
"FALSE"))

[1] https://github.com/wch/r-source/blob/b50e3f755674cbb697a4a7395b766647a5cfeea2/src/library/tools/R/check.R#L6335
[2] https://github.com/wch/r-source/blob/b50e3f755674cbb697a4a7395b766647a5cfeea2/src/library/tools/R/QC.R#L5954-L5956

/Henrik
Jeffrey Dick
# 
FWIW, I also encountered this issue and posted on R-pkg-devel about it,
with no resolution at the time (May 2020). See "Dependencies NOTE lost with
--as-cran" (
https://stat.ethz.ch/pipermail/r-package-devel/2020q2/005467.html)

On Wed, Oct 20, 2021 at 11:55 PM Henrik Bengtsson <
henrik.bengtsson at gmail.com> wrote: