[Debian-med-packaging] Bug#1037689: hhsuite: ftbfs with GCC-13

Wed Jun 14 10:25:33 BST 2023

Package: src:hhsuite
Version: 3.3.0+ds-7
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/hhsuite_3.3.0+ds-7_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

[...]
[  9%] Linking C static library libffindex.a
cd /<<PKGBUILDDIR>>/build_plain/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build_plain/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex.dir/link.txt --verbose=1
make[4]: *** [src/CMakeFiles/A3M_COMPRESS.dir/build.make:79: src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build_plain'
make[3]: *** [CMakeFiles/Makefile2:843: src/CMakeFiles/A3M_COMPRESS.dir/all] Error 2
make[3]: *** Waiting for unfinished jobs....
/usr/bin/ar qc libffindex.a CMakeFiles/ffindex.dir/ffindex.c.o CMakeFiles/ffindex.dir/ffutil.c.o
[ 10%] Generating ../generated/cs219.lib.h
cd /<<PKGBUILDDIR>>/data && mkdir -p /<<PKGBUILDDIR>>/build_plain/generated
cd /<<PKGBUILDDIR>>/data && /<<PKGBUILDDIR>>/cmake/xxdi.pl cs219.lib > /<<PKGBUILDDIR>>/build_plain/generated/cs219.lib.h
/usr/bin/ranlib libffindex.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build_plain'
[ 10%] Built target ffindex
[ 11%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o
cd /<<PKGBUILDDIR>>/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/build_plain/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/build_plain/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -MF CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c /<<PKGBUILDDIR>>/src/cs/as.cc
cd /<<PKGBUILDDIR>>/data && /bin/sed 's!unsigned char!static const unsigned char!' < /<<PKGBUILDDIR>>/build_plain/generated/cs219.lib.h > /<<PKGBUILDDIR>>/build_plain/generated/cs219.lib.h.tmp
cd /<<PKGBUILDDIR>>/data && mv -f /<<PKGBUILDDIR>>/build_plain/generated/cs219.lib.h.tmp /<<PKGBUILDDIR>>/build_plain/generated/cs219.lib.h
[ 12%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o
cd /<<PKGBUILDDIR>>/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/build_plain/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/build_plain/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /<<PKGBUILDDIR>>/src/cs/assert_helpers.cc
[ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o
cd /<<PKGBUILDDIR>>/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/build_plain/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/build_plain/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /<<PKGBUILDDIR>>/src/cs/blosum_matrix.cc
[ 14%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o
cd /<<PKGBUILDDIR>>/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/build_plain/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/build_plain/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /<<PKGBUILDDIR>>/src/cs/getopt_pp.cc
[ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o
cd /<<PKGBUILDDIR>>/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/build_plain/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/build_plain/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /<<PKGBUILDDIR>>/src/cs/log.cc
[ 16%] Linking CXX static library libhhviterbialgorithm_and_ss.a
cd /<<PKGBUILDDIR>>/build_plain/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1
/usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o
/usr/bin/ranlib libhhviterbialgorithm_and_ss.a
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[ 16%] Built target hhviterbialgorithm_and_ss
[ 17%] Linking CXX static library libhhviterbialgorithm_with_celloff.a
cd /<<PKGBUILDDIR>>/build_plain/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake
[ 18%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o
cd /<<PKGBUILDDIR>>/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/build_plain/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/build_plain/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /<<PKGBUILDDIR>>/src/cs/application.cc
cd /<<PKGBUILDDIR>>/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1
/usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o
[ 19%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a
/usr/bin/ranlib libhhviterbialgorithm_with_celloff.a
cd /<<PKGBUILDDIR>>/build_plain/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build_plain'
cd /<<PKGBUILDDIR>>/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1
[ 19%] Built target hhviterbialgorithm_with_celloff
/usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o
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[ 19%] Built target hhviterbialgorithm_with_celloff_and_ss
cd /<<PKGBUILDDIR>>/data && /bin/sed 's!unsigned char!static const unsigned char!' < /<<PKGBUILDDIR>>/build_plain/generated/context_data.lib.h > /<<PKGBUILDDIR>>/build_plain/generated/context_data.lib.h.tmp
cd /<<PKGBUILDDIR>>/data && /bin/sed 's!unsigned char!static const unsigned char!' < /<<PKGBUILDDIR>>/build_plain/generated/context_data.crf.h > /<<PKGBUILDDIR>>/build_plain/generated/context_data.crf.h.tmp
cd /<<PKGBUILDDIR>>/data && mv -f /<<PKGBUILDDIR>>/build_plain/generated/context_data.lib.h.tmp /<<PKGBUILDDIR>>/build_plain/generated/context_data.lib.h
[ 20%] Linking CXX static library libCS_OBJECTS.a
cd /<<PKGBUILDDIR>>/build_plain/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build_plain/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1
/usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o
/usr/bin/ranlib libCS_OBJECTS.a
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cd /<<PKGBUILDDIR>>/data && mv -f /<<PKGBUILDDIR>>/build_plain/generated/context_data.crf.h.tmp /<<PKGBUILDDIR>>/build_plain/generated/context_data.crf.h
[ 20%] Built target CS_OBJECTS
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[ 20%] Built target generated
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build_plain'
make[2]: *** [Makefile:159: all] Error 2
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dh_auto_build: error: cd build_plain && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2
make[1]: *** [debian/rules:67: override_dh_auto_build-arch] Error 25
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dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2