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

[Jennifer Wokaty]

>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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