[Debian-med-packaging] Bug#1133507: jellyfish: ftbfs with GCC-16

[Emanuele Rocca]

Package: src:jellyfish
Version: 2.3.1-5
Severity: important
Tags: sid forky ftbfs
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-16

Hi,

jellyfish fails to build in a test rebuild on at least amd64 and arm64 with
gcc-16/g++-16, but builds properly with gcc-15/g++-15. The severity of this
report will be raised before the forky release.

The full build log can be found at:
https://people.debian.org/~ema/gcc-16-rebuilds/output-1/jellyfish_arm64.build.xz

The last lines of the build log are at the end of this report.

To build with GCC 16, either set CC=gcc-16 CXX=g++-16 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

Common build failures include unused (but set) variables, array subscripts
partly outside array bounds, and new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-16/porting_to.html

Please only close this issue after double-checking that the package can be
built correctly with GCC 16.

Please do not reassign this bug to another package. If a fix in another package
is required, then file a bug for the other package (or clone), and mark this
bug as blocked by the bug in the other package.

[...]


config.status: creating compat.sh
config.status: creating jellyfish-2.0.pc
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
dh_auto_configure --sourcedirectory=swig/perl5
	cd swig/perl5 && /usr/bin/perl Makefile.PL INSTALLDIRS=vendor OPTIMIZE="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2" LD="aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -lpthread"
-I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1
-L/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -lpthread
-L/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu
Warning (mostly harmless): No library found for -ljellyfish-2.0
Generating a Unix-style Makefile
Writing Makefile for jellyfish
Writing MYMETA.yml and MYMETA.json
dh_auto_configure --sourcedirectory=swig/python --buildsystem=pybuild
I: pybuild base:385: python3.14 setup.py config 
running config
I: pybuild base:385: python3.13 setup.py config 
running config
mv /tmp/m4-ax_python_devel.m4 m4
make[1]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1'
   debian/rules override_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/jellyfish-2.3.1'
mkdir -p debian/tmp_save_tests
cp -a tests/* debian/tmp_save_tests
dh_auto_build --no-parallel -- all bin/generate_sequence bin/test_all bin/fastq2sam
	make -j1 all bin/generate_sequence bin/test_all bin/fastq2sam
make[2]: Entering directory '/build/reproducible-path/jellyfish-2.3.1'
/usr/bin/yaggo --license ./header-license -o sub_commands/count_main_cmdline.hpp sub_commands/count_main_cmdline.yaggo
/usr/bin/yaggo --license ./header-license -o sub_commands/info_main_cmdline.hpp sub_commands/info_main_cmdline.yaggo
/usr/bin/yaggo --license ./header-license -o sub_commands/dump_main_cmdline.hpp sub_commands/dump_main_cmdline.yaggo
/usr/bin/yaggo --license ./header-license -o sub_commands/histo_main_cmdline.hpp sub_commands/histo_main_cmdline.yaggo
/usr/bin/yaggo --license ./header-license -o sub_commands/stats_main_cmdline.hpp sub_commands/stats_main_cmdline.yaggo
/usr/bin/yaggo --license ./header-license -o sub_commands/merge_main_cmdline.hpp sub_commands/merge_main_cmdline.yaggo
/usr/bin/yaggo --license ./header-license -o sub_commands/bc_main_cmdline.hpp sub_commands/bc_main_cmdline.yaggo
/usr/bin/yaggo --license ./header-license -o sub_commands/query_main_cmdline.hpp sub_commands/query_main_cmdline.yaggo
/usr/bin/yaggo --license ./header-license -o sub_commands/cite_main_cmdline.hpp sub_commands/cite_main_cmdline.yaggo
/usr/bin/yaggo --license ./header-license -o sub_commands/mem_main_cmdline.hpp sub_commands/mem_main_cmdline.yaggo
/usr/bin/yaggo --license ./header-license -o jellyfish/generate_sequence_cmdline.hpp jellyfish/generate_sequence_cmdline.yaggo
/usr/bin/yaggo --license ./header-license -o jellyfish/fastq2sam_cmdline.hpp jellyfish/fastq2sam_cmdline.yaggo
/usr/bin/yaggo --license ./header-license -o unit_tests/test_main_cmdline.hpp unit_tests/test_main_cmdline.yaggo
/usr/bin/swig -c++ -python -I./../include -o swig/python/swig_wrap.cpp swig/jellyfish.i
/usr/bin/swig -c++ -perl5 -I./../include -o swig/perl5/swig_wrap.cpp swig/jellyfish.i
make  all-am
make[3]: Entering directory '/build/reproducible-path/jellyfish-2.3.1'
g++ -std=gnu++11 -DHAVE_CONFIG_H -I.  -Wall -Wnon-virtual-dtor -I. -I./include  -Wdate-time -D_FORTIFY_SOURCE=2  -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -c -o sub_commands/jellyfish.o sub_commands/jellyfish.cc
g++ -std=gnu++11 -DHAVE_CONFIG_H -I.  -Wall -Wnon-virtual-dtor -I. -I./include  -Wdate-time -D_FORTIFY_SOURCE=2  -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -c -o sub_commands/count_main.o sub_commands/count_main.cc
sub_commands/count_main.cc: In instantiation of ‘void mer_counter_base<MerIteratorType, ParserType>::start(int) [with MerIteratorType = mer_qual_iterator; ParserType = sequence_qual_parser]’:
sub_commands/count_main.cc:152:16:   required from here
  152 |   virtual void start(int thid) {
      |                ^~~~~
sub_commands/count_main.cc:153:12: error: variable ‘count’ set but not used [-Werror=unused-but-set-variable=]
  153 |     size_t count = 0;
      |            ^~~~~
sub_commands/count_main.cc: In instantiation of ‘void mer_counter_base<MerIteratorType, ParserType>::start(int) [with MerIteratorType = jellyfish::mer_iterator<jellyfish::mer_overlap_sequence_parser<jellyfish::stream_manager<__gnu_cxx::__normal_iterator<const char* const*, std::vector<const char*> > > >, jellyfish::mer_dna_ns::mer_base_static<long unsigned int, 0> >; ParserType = jellyfish::mer_overlap_sequence_parser<jellyfish::stream_manager<__gnu_cxx::__normal_iterator<const char* const*, std::vector<const char*> > > >]’:
sub_commands/count_main.cc:152:16:   required from here
  152 |   virtual void start(int thid) {
      |                ^~~~~
sub_commands/count_main.cc:153:12: error: variable ‘count’ set but not used [-Werror=unused-but-set-variable=]
  153 |     size_t count = 0;
      |            ^~~~~
cc1plus: all warnings being treated as errors
make[3]: *** [Makefile:1705: sub_commands/count_main.o] Error 1
make[3]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1'
make[2]: *** [Makefile:1040: all] Error 2
make[2]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1'
dh_auto_build: error: make -j1 all bin/generate_sequence bin/test_all bin/fastq2sam returned exit code 2
make[1]: *** [debian/rules:70: override_dh_auto_build] Error 25
make[1]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1'
make: *** [debian/rules:22: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2