[Debian-med-packaging] Bug#1037742: libssw: ftbfs with GCC-13

[Matthias Klose]

Package: src:libssw
Version: 1.1-13
Severity: normal
Tags: sid trixie
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-13

[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-13/g++-13, but succeeds to build with gcc-12/g++-12. 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/2023/05/22/logs/libssw_1.1-13_unstable_gccexp.log
The last lines of the build log are at the end of this report.

To build with GCC 13, either set CC=gcc-13 CXX=g++-13 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-13/porting_to.html

[...]
Query:       907    CCCCTTTCTGCAT-TAT--TTAATGATTTTCTCA-TAT----GTCA-CTCTTAAATGTAC    957

Target:     9707    TGTTGATTGTTTC-CTTT    9723
                    |**|*||| |||| ||||
Query:       958    TTCTAATT-TTTCACTTT    974

make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   create-stamp debian/debhelper-build-stamp
   dh_prep
   debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
sed 's/@DEB_HOST_MULTIARCH@/x86_64-linux-gnu/g' debian/libssw0.install.in > debian/libssw0.install
sed 's/@DEB_HOST_MULTIARCH@/x86_64-linux-gnu/g' debian/libssw-dev.install.in > debian/libssw-dev.install
sed -e 's/@DEB_HOST_MULTIARCH@/x86_64-linux-gnu/g' \
            -e 's/@DEB_JAVA_PKG_VERSION@/1.1/g' debian/libssw-dev.links.in > debian/libssw-dev.links
sed 's/@DEB_HOST_MULTIARCH@/x86_64-linux-gnu/g' debian/libssw-java.install.in > debian/libssw-java.install
sed -e 's/@DEB_HOST_MULTIARCH@/x86_64-linux-gnu/g' \
            -e 's/@DEB_JAVA_PKG_VERSION@/1.1/g' debian/libssw-java.links.in > debian/libssw-java.links
mv src/ssw.jar src/ssw-1.1.jar
dh_auto_install
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_install
   jh_installjavadoc
   dh_installdocs
   dh_installchangelogs
   debian/rules override_dh_installman
make[1]: Entering directory '/<<PKGBUILDDIR>>'
LD_LIBRARY_PATH=`pwd`/src help2man --version-string=' ' --help-option=' ' \
          -I debian/extra-man-info.txt \
          -N -n 'fast Smith-Waterman aligner' \
          --no-discard-stderr src/ssw-align \
            | fgrep -v ERROR > debian/ssw-align.1
dh_installman
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_perl
   dh_link
   jh_installlibs
   jh_classpath
   jh_manifest
   jh_exec
   jh_depends
   mh_installpoms
   mh_linkjars --skip-clean-poms
   dh_strip_nondeterminism
   dh_compress
   dh_fixperms
   dh_missing
   dh_dwz -a
   dh_strip -a
   dh_makeshlibs -a
dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols file: see diff output below
dpkg-gensymbols: warning: debian/libssw0/DEBIAN/symbols doesn't match completely debian/libssw0.symbols
--- debian/libssw0.symbols (libssw0_1.1-13_amd64)
+++ dpkg-gensymbolsRLn4HN	2023-05-22 02:10:01.559468309 +0000
@@ -22,9 +22,9 @@
  _ZNK20StripedSmithWaterman7Aligner5AlignEPKcRKNS_6FilterEPNS_9AlignmentE at Base 1.1
  _ZNK20StripedSmithWaterman7Aligner5AlignEPKcS2_RKiRKNS_6FilterEPNS_9AlignmentE at Base 1.1
  (optional)_ZNSt6vectorIjSaIjEE17_M_realloc_insertIJRKjEEEvN9__gnu_cxx17__normal_iteratorIPjS1_EEDpOT_ at Base 1.1
- _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED0Ev at Base 1.1
- _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED1Ev at Base 1.1
- _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED2Ev at Base 1.1
+#MISSING: 1.1-13# _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED0Ev at Base 1.1
+#MISSING: 1.1-13# _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED1Ev at Base 1.1
+#MISSING: 1.1-13# _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED2Ev at Base 1.1
  align_destroy at Base 1.1
  init_destroy at Base 1.1
  mark_mismatch at Base 1.1
dh_makeshlibs: error: failing due to earlier errors
make: *** [debian/rules:20: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2