[R-pkg-team] Bug#1009467: r-bioc-biostrings: FTBFS: BitMatrix.c:9:10: fatal error: S.h: No such file or directory

[Lucas Nussbaum]

Source: r-bioc-biostrings
Version: 2.62.0-1
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20220412 ftbfs-bookworm

Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.


Relevant part (hopefully):
> gcc -I"/usr/share/R/include" -DNDEBUG  -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include'    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-uzEjFP/r-base-4.1.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c BitMatrix.c -o BitMatrix.o
> BitMatrix.c:9:10: fatal error: S.h: No such file or directory
>     9 | #include <S.h> /* for Salloc() */
>       |          ^~~~~
> compilation terminated.
> make[1]: *** [/usr/lib/R/etc/Makeconf:168: BitMatrix.o] Error 1


The full build log is available from:
http://qa-logs.debian.net/2022/04/12/r-bioc-biostrings_2.62.0-1_unstable.log

All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20220412;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20220412&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects

If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.