[Debian-med-packaging] Bug#1037702: jellyfish: ftbfs with GCC-13

[Matthias Klose]

Package: src:jellyfish
Version: 2.3.0-15
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/jellyfish_2.3.0-15_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

[...]
# SKIP:  2
# XFAIL: 0
# FAIL:  1
# XPASS: 0
# ERROR: 0

.. contents:: :depth: 2

SKIP: tests/big
===============

Skip big test
SKIP tests/big.sh (exit status: 77)

SKIP: tests/swig_ruby
=====================

SKIP tests/swig_ruby.sh (exit status: 77)

FAIL: tests/swig_perl
=====================

Test test_mer_file.t
ok 1 - require jellyfish;
ok 2 - Histogram
ok 3 - Dump
ok 4 - Query identical to read
1..4
Test test_hash_counter.t
ok 1 - require jellyfish;
ok 2 - mer_dna k
ok 3 - Hash size
ok 4 - Hash value length
not ok 5 - Adding to new mer
#   Failed test 'Adding to new mer'
#   at /<<PKGBUILDDIR>>/swig/perl5/t/test_hash_counter.t line 31.
not ok 6 - Adding mer to hash
#   Failed test 'Adding mer to hash'
#   at /<<PKGBUILDDIR>>/swig/perl5/t/test_hash_counter.t line 48.
1..6
# Looks like you failed 2 tests of 6.
FAIL tests/swig_perl.sh (exit status: 2)

============================================================================
Testsuite summary for jellyfish 2.3.0
============================================================================
# TOTAL: 15
# PASS:  12
# SKIP:  2
# XFAIL: 0
# FAIL:  1
# XPASS: 0
# ERROR: 0
============================================================================
See ./test-suite.log
Please report to gmarcais at umd.edu
============================================================================
make[5]: *** [Makefile:2348: test-suite.log] Error 1
make[5]: Leaving directory '/<<PKGBUILDDIR>>'
make[4]: *** [Makefile:2456: check-TESTS] Error 2
make[4]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: *** [Makefile:2661: check-am] Error 2
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: *** [Makefile:2663: check] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test: error: make -j8 check "TESTSUITEFLAGS=-j8 --verbose" VERBOSE=1 returned exit code 2
make[1]: *** [debian/rules:103: override_dh_auto_test] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:22: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2