search

Bioconductor / Biostrings

Efficient manipulation of biological strings
https://bioconductor.org/packages/Biostrings
54 stars 16 forks source link

Package installation fails in latest R 4.2.0-nightly #64

Closed mtiberti closed 2 years ago

mtiberti commented 2 years ago

Hi, I am trying to set up my environment for the development of a R package in Bioconductor, using the latest (15/03) nightly build and installing dependencies using Bioconductor devel. It looks like the package fails to compile under these conditions:

> BiocManager::install('Biostrings', version="devel")
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://mirrors.dotsrc.org/cran

Bioconductor version 3.15 (BiocManager 1.30.16), R Under development (unstable)
  (2022-03-14 r81896)
Installing package(s) 'Biostrings'
trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/Biostrings_2.63.1.tar.gz'
Content type 'application/x-gzip' length 12645826 bytes (12.1 MB)
==================================================
downloaded 12.1 MB

* installing *source* package ‘Biostrings’ ...
** using staged installation
** libs
gcc -I"/data/user/teo/builds/R-4.2.0-devel/lib/R/include" -DNDEBUG  -I'/data/user/teo/builds/R-4.2.0-devel/lib/R/library/S4Vectors/include' -I'/data/user/teo/builds/R-4.2.0-devel/lib/R/library/IRanges/include' -I'/data/user/teo/builds/R-4.2.0-devel/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -c BAB_class.c -o BAB_class.o
gcc -I"/data/user/teo/builds/R-4.2.0-devel/lib/R/include" -DNDEBUG  -I'/data/user/teo/builds/R-4.2.0-devel/lib/R/library/S4Vectors/include' -I'/data/user/teo/builds/R-4.2.0-devel/lib/R/library/IRanges/include' -I'/data/user/teo/builds/R-4.2.0-devel/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -c BitMatrix.c -o BitMatrix.o
BitMatrix.c:9:10: fatal error: S.h: No such file or directory
 #include <S.h> /* for Salloc() */
          ^~~~~
compilation terminated.

Looking at the R-devel changelog I see:

The header ‘S.h’ which has been unsupported since Jan 2016 has been removed. Use ‘R.h’ instead. [Scheduled for Mar 15.]

so this is probably the first release with this problem. I guess just replacing the header in the #include would be enough.

Thank you!

hpages commented 2 years ago

Hi,

I was just notified this morning by the R core team about this change in R 4.2.

Fixed in Biostrings 2.63.2 (see commit c3340745870a88d1558e093a7f892c1aeac784ef). Note that it'll take about 24h for this new version to go thru our daily builds and propagate to the BioC 3.15 repos where is will become available via BiocManager::install().

Cheers, H.