[Bioc-devel] New BioC 3.21 settings for R 4.5.0

[Kristian Ullrich]

Dear Jennifer,

I do understand the reasoning behind the _R_CHECK_EXCESSIVE_IMPORTS_=20. However, the threshold needs to be discussed in my opinion.

Given that a lot of bioconductor packages e.g. rely on the Biostrings and GenomicRanges package (rank 9 and 10 / 2289), the Biostrings package itself has currently 24 dependencies, which as a consequence would mean that all packages relying on Biostrings will automatically be classified as excessive import packages.

To be honest, I would then no longer understand the meaningfulness of such a “note flag” if one Bioconductor package uses a TOP10 package as an import and should therefore be considered vulnerable?

Have you checked in Bioc 3.20, how many packages from the 2289 packages would fall under this "vulnerable" category?

Best regards and thank you in anticipation

Kristian
-- 
Dr. Kristian Ullrich, Dipl.-Bio.
Max Planck Institute
For Evolutionary Biology

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ullrich using evolbio.mpg.de

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> On 11. Nov 2024, at 19:08, Jennifer Wokaty <Jennifer.Wokaty using sph.cuny.edu> wrote:
> 
> From 11/13, we will add new settings to Bioconductor 3.21 to prepare for R 4.5.0.
> From Kurt Hornik:
> 
>  For the upcoming R 4.5.0 release, we would like to make two changes
>  which remove API legacy convenience features which keep causing
>  problems.
> 
>  Specifically:
> 
>  One, defining STRICT_R_HEADERS to 1 which removes
> 
>  - the legacy definition of PI (use POSIX's M_PI, available in R fer ever).
>  - the RS.h declarations for Calloc, Realloc, Free (use R_ forms i
>    available since R 3.4.0).
> 
>  The aim is to clean the namespace: in particular having a definition
>  for Free has conflicted with some packages' C++ code.
> 
>  Two, compiling C++ code with R_NO_REMAP defined.  See chapter "The R
>  API: entry points for C code" in "Writing R Extensions" for more
>  information.
> 
>  We could like to switch to using STRICT_R_HEADERS and R_NO_REMAP by
>  default later this year.
> 
>  For now, one can get these defined via setting env vars
> 
>    _R_USE_STRICT_R_HEADERS_=true
>    _R_CXX_USE_NO_REMAP_=true
> 
>  (using a recent enough version of R-devel, of course).
> 
> ...
> 
>  Fixing errors from _R_USE_STRICT_R_HEADERS_=true typically is very
>  simple: one needs to change Calloc/Realloc/Free to the corresponding R_
>  forms, which can be done via variants of
> 
>    perl -pi -e 's/Calloc\(/R_Calloc\(/g' *
> 
>  in the package src directory.  (Similarly for replacing PI by M_PI.)
> 
>  Fixing errors from _R_CXX_USE_NO_REMAP_=true can similarly use e.g.
> 
>    perl -pi -e 's/allocList\(/Rf_allocList\(/g' *
> 
>  but it is more effort as one does not know in advance what to replace
>  (well, everything in the API which is no longer remapped, of course) and
>  one only gets the errors for the first compilation unit one at a time.
> 
> We will also add _R_CHECK_EXCESSIVE_IMPORTS_=20 following CRAN's standard: https://cran.r-project.org/doc/manuals/r-release/R-ints.html#index-_005fR_005fCHECK_005fEXCESSIVE_005fIMPORTS_005f.
> 
> 
> Jennifer Wokaty (they/them)
> 
> Waldron Lab at CUNY SPH
> Bioconductor Core Team
> 
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> 
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