[Debian-med-packaging] Bug#1075213: libtfbs-perl: ftbfs with GCC-14

[Matthias Klose]

Package: src:libtfbs-perl
Version: 0.7.1+ds-3
Severity: important
Tags: sid trixie
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-14

[This bug is targeted to the upcoming trixie release]

Please keep this issue open in the bug tracker for the package it
was filed for.  If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.

The package fails to build in a test rebuild on at least amd64 with
gcc-14/g++-14, but succeeds to build with gcc-13/g++-13. The
severity of this report will be raised before the trixie release.

The full build log can be found at:
http://qa-logs.debian.net/2024/07/01/libtfbs-perl_0.7.1+ds-3_unstable_gccexp.log
The last lines of the build log are at the end of this report.

To build with GCC 14, either set CC=gcc-14 CXX=g++-14 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-14/porting_to.html

[...]
Running Mkbootstrap for pwmsearch ()
chmod 644 "pwmsearch.bs"
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- pwmsearch.bs ../blib/arch/auto/TFBS/Ext/pwmsearch/pwmsearch.bs 644
Skip ../blib/lib/TFBS/Ext/pwmsearch.pm (unchanged)
Skip ../blib/lib/pwm_search.h (unchanged)
cp lib/pwm_searchPFF.c ../blib/lib/pwm_searchPFF.c
cp TFBS/DB/JASPAR6.pm blib/lib/TFBS/DB/JASPAR6.pm
Skip blib/lib/TFBS/PatternGen/YMF/Motif.pm (unchanged)
cp TFBS/Matrix/Alignment.pm blib/lib/TFBS/Matrix/Alignment.pm
Skip blib/lib/TFBS/PatternI.pm (unchanged)
Skip blib/lib/TFBS/PatternGen/SimplePFM.pm (unchanged)
cp TFBS/DB/JASPAR5.pm blib/lib/TFBS/DB/JASPAR5.pm
Skip blib/lib/TFBS/SiteSet.pm (unchanged)
cp TFBS/DB/JASPAR.pm blib/lib/TFBS/DB/JASPAR.pm
cp TFBS/TFFM.pm blib/lib/TFBS/TFFM.pm
Skip blib/lib/TFBS/PatternGen/Elph.pm (unchanged)
cp TFBS/PatternGen.pm blib/lib/TFBS/PatternGen.pm
Skip blib/lib/TFBS/PatternGen/Motif/Matrix.pm (unchanged)
Skip blib/lib/TFBS/Matrix/_Alignment.pm (unchanged)
Skip blib/lib/TFBS/PatternGen/Motif/Word.pm (unchanged)
Skip blib/lib/TFBS/PatternGenI.pm (unchanged)
cp TFBS/Matrix/PFM.pm blib/lib/TFBS/Matrix/PFM.pm
Skip blib/lib/TFBS/Matrix/PWM.pm (unchanged)
cp TFBS/Run/ConservationProfileGenerator.pm blib/lib/TFBS/Run/ConservationProfileGenerator.pm
cp TFBS/MatrixSet.pm blib/lib/TFBS/MatrixSet.pm
Skip blib/lib/TFBS/PatternGen/MEME/Motif.pm (unchanged)
Skip blib/lib/TFBS/Site.pm (unchanged)
Skip blib/lib/TFBS/PatternGen/Gibbs.pm (unchanged)
Skip blib/lib/TFBS/DB.pm (unchanged)
cp TFBS/ConservationProfile.pm blib/lib/TFBS/ConservationProfile.pm
Skip blib/lib/TFBS/SitePairSet.pm (unchanged)
cp TFBS/DB/JASPAR7.pm blib/lib/TFBS/DB/JASPAR7.pm
cp TFBS/DB/JASPAR4.pm blib/lib/TFBS/DB/JASPAR4.pm
Skip blib/lib/TFBS/PatternGen/Gibbs/Motif.pm (unchanged)
cp TFBS/PatternGen/YMF.pm blib/lib/TFBS/PatternGen/YMF.pm
Skip blib/lib/TFBS/PatternGen/AnnSpec/Motif.pm (unchanged)
Skip blib/lib/TFBS/DB/LocalTRANSFAC.pm (unchanged)
cp TFBS/Matrix.pm blib/lib/TFBS/Matrix.pm
cp TFBS/DB/TRANSFAC.pm blib/lib/TFBS/DB/TRANSFAC.pm
Skip blib/lib/TFBS/Tools/SetOperations.pm (unchanged)
cp TFBS/PatternGen/AnnSpec.pm blib/lib/TFBS/PatternGen/AnnSpec.pm
cp TFBS/DB/FlatFileDir.pm blib/lib/TFBS/DB/FlatFileDir.pm
Skip blib/lib/TFBS/PatternGen/Elph/Motif.pm (unchanged)
cp TFBS/SitePair.pm blib/lib/TFBS/SitePair.pm
Skip blib/lib/TFBS/PatternGen/MEME.pm (unchanged)
Skip blib/lib/TFBS/DB/JASPAR2.pm (unchanged)
cp TFBS/README.md blib/lib/TFBS/README.md
cp TFBS/Matrix/ICM.pm blib/lib/TFBS/Matrix/ICM.pm
Please specify prototyping behavior for pwmsearch.xs (see perlxs manual)
mv pwmsearch.xsc pwmsearch.c
x86_64-linux-gnu-gcc -c  -I. -I./lib -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2   -DVERSION=\"0.2\" -DXS_VERSION=\"0.2\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.38/CORE"   pwmsearch.c
Skip blib/lib/TFBS/_Iterator.pm (unchanged)
Skip blib/lib/TFBS/Word/Consensus.pm (unchanged)
cp TFBS/_Iterator/_MatrixSetIterator.pm blib/lib/TFBS/_Iterator/_MatrixSetIterator.pm
Skip blib/lib/TFBS/Word.pm (unchanged)
cp TFBS/_Iterator/_SiteSetIterator.pm blib/lib/TFBS/_Iterator/_SiteSetIterator.pm
In file included from pwmsearch.xs:4:
./lib/pwm_searchPFF.c:303:1: error: return type defaults to ‘int’ [-Wimplicit-int]
  303 | get_sequence(fp,seq_id,sequence)
      | ^~~~~~~~~~~~
./lib/pwm_searchPFF.c:414:1: error: return type defaults to ‘int’ [-Wimplicit-int]
  414 | best_pull(pargs,pbase,pstrand,pscore)
      | ^~~~~~~~~
make[2]: *** [Makefile:324: pwmsearch.o] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>/Ext'
make[1]: *** [Makefile:638: subdirs] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j8 returned exit code 2
make: *** [debian/rules:11: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2