[Debian-med-packaging] Bug#1012953: jellyfish: ftbfs with GCC-12
Matthias Klose
doko at debian.org
Thu Jun 16 13:09:51 BST 2022
Package: src:jellyfish
Version: 2.3.0-13
Severity: normal
Tags: sid bookworm
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-12
[This bug is targeted to the upcoming bookworm 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-12/g++-12, but succeeds to build with gcc-11/g++-11. The
severity of this report will be raised before the bookworm release.
The full build log can be found at:
http://qa-logs.debian.net/2022/06/09/gcc12/jellyfish_2.3.0-13_unstable_gcc12.log
The last lines of the build log are at the end of this report.
To build with GCC 11, either set CC=gcc-11 CXX=g++-11 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-11/porting_to.html
GCC 11 defaults to the GNU++17 standard. If your package installs
header files in /usr/include, please don't work around C++17 issues
by choosing a lower C++ standard for the package build, but fix these
issues to build with the C++17 standard.
[...]
/bin/bash ./libtool --tag=CXX --mode=link g++ -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -version-info 2:0:0 -Wl,-z,relro -Wl,-z,now -lpthread -o libjellyfish-2.0.la -rpath /usr/lib/x86_64-linux-gnu lib/rectangular_binary_matrix.lo lib/mer_dna.lo lib/storage.lo lib/allocators_mmap.lo lib/misc.lo lib/int128.lo lib/thread_exec.lo lib/jsoncpp.lo lib/time.lo lib/generator_manager.lo
libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/12/crtbeginS.o lib/.libs/rectangular_binary_matrix.o lib/.libs/mer_dna.o lib/.libs/storage.o lib/.libs/allocators_mmap.o lib/.libs/misc.o lib/.libs/int128.o lib/.libs/thread_exec.o lib/.libs/jsoncpp.o lib/.libs/time.o lib/.libs/generator_manager.o -lpthread -L/usr/lib/gcc/x86_64-linux-gnu/12 -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/12/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libjellyfish-2.0.so.2 -o .libs/libjellyfish-2.0.so.2.0.0
libtool: link: (cd ".libs" && rm -f "libjellyfish-2.0.so.2" && ln -s "libjellyfish-2.0.so.2.0.0" "libjellyfish-2.0.so.2")
libtool: link: (cd ".libs" && rm -f "libjellyfish-2.0.so" && ln -s "libjellyfish-2.0.so.2.0.0" "libjellyfish-2.0.so")
libtool: link: ar cr .libs/libjellyfish-2.0.a lib/rectangular_binary_matrix.o lib/mer_dna.o lib/storage.o lib/allocators_mmap.o lib/misc.o lib/int128.o lib/thread_exec.o lib/jsoncpp.o lib/time.o lib/generator_manager.o
libtool: link: ranlib .libs/libjellyfish-2.0.a
libtool: link: ( cd ".libs" && rm -f "libjellyfish-2.0.la" && ln -s "../libjellyfish-2.0.la" "libjellyfish-2.0.la" )
/bin/bash ./libtool --tag=CXX --mode=link g++ -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -pthread -L/<<PKGBUILDDIR>>/debian/tmp//usr/lib/x86_64-linux-gnu -lhts -R/<<PKGBUILDDIR>>/debian/tmp//usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o bin/jellyfish sub_commands/jellyfish.o sub_commands/count_main.o sub_commands/info_main.o sub_commands/dump_main.o sub_commands/histo_main.o sub_commands/stats_main.o sub_commands/merge_main.o sub_commands/bc_main.o sub_commands/query_main.o sub_commands/cite_main.o sub_commands/mem_main.o jellyfish/merge_files.o libjellyfish-2.0.la
libtool: link: g++ -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/jellyfish sub_commands/jellyfish.o sub_commands/count_main.o sub_commands/info_main.o sub_commands/dump_main.o sub_commands/histo_main.o sub_commands/stats_main.o sub_commands/merge_main.o sub_commands/bc_main.o sub_commands/query_main.o sub_commands/cite_main.o sub_commands/mem_main.o jellyfish/merge_files.o -L/<<PKGBUILDDIR>>/debian/tmp//usr/lib/x86_64-linux-gnu -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/<<PKGBUILDDIR>>/debian/tmp//usr/lib/x86_64-linux-gnu
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/lib/x86_64-linux-gnu/perl/5.34/CORE -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo `test -f 'swig/perl5/swig_wrap.cpp' || echo './'`swig/perl5/swig_wrap.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/lib/x86_64-linux-gnu/perl/5.34/CORE -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c swig/perl5/swig_wrap.cpp -fPIC -DPIC -o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/lib/x86_64-linux-gnu/perl/5.34/CORE -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c swig/perl5/swig_wrap.cpp -o swig/perl5/swig_perl5_jellyfish_la-swig_wrap.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=link g++ -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.34.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la
libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/12/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -Wl,-rpath -Wl,/<<PKGBUILDDIR>>/.libs -lpthread ./.libs/libjellyfish-2.0.so -L/usr/lib/gcc/x86_64-linux-gnu/12 -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/12/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0
libtool: link: (cd "swig/perl5/.libs" && rm -f "jellyfish.so.0" && ln -s "jellyfish.so.0.0.0" "jellyfish.so.0")
libtool: link: (cd "swig/perl5/.libs" && rm -f "jellyfish.so" && ln -s "jellyfish.so.0.0.0" "jellyfish.so")
libtool: link: ar cr swig/perl5/.libs/jellyfish.a swig/perl5/swig_perl5_jellyfish_la-swig_wrap.o
libtool: link: ranlib swig/perl5/.libs/jellyfish.a
libtool: link: ( cd "swig/perl5/.libs" && rm -f "jellyfish.la" && ln -s "../jellyfish.la" "jellyfish.la" )
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I/usr/include/python3.10 -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo `test -f 'swig/python/swig_wrap.cpp' || echo './'`swig/python/swig_wrap.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/include/python3.10 -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c swig/python/swig_wrap.cpp -fPIC -DPIC -o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/include/python3.10 -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c swig/python/swig_wrap.cpp -o swig/python/swig_python__dna_jellyfish_la-swig_wrap.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=link g++ -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3/dist-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la
libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/12/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -Wl,-rpath -Wl,/<<PKGBUILDDIR>>/.libs -lpthread ./.libs/libjellyfish-2.0.so -L/usr/lib/gcc/x86_64-linux-gnu/12 -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/12/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,_dna_jellyfish.so.0 -o swig/python/.libs/_dna_jellyfish.so.0.0.0
libtool: link: (cd "swig/python/.libs" && rm -f "_dna_jellyfish.so.0" && ln -s "_dna_jellyfish.so.0.0.0" "_dna_jellyfish.so.0")
libtool: link: (cd "swig/python/.libs" && rm -f "_dna_jellyfish.so" && ln -s "_dna_jellyfish.so.0.0.0" "_dna_jellyfish.so")
libtool: link: ar cr swig/python/.libs/_dna_jellyfish.a swig/python/swig_python__dna_jellyfish_la-swig_wrap.o
libtool: link: ranlib swig/python/.libs/_dna_jellyfish.a
libtool: link: ( cd "swig/python/.libs" && rm -f "_dna_jellyfish.la" && ln -s "../_dna_jellyfish.la" "_dna_jellyfish.la" )
/usr/bin/python3 -c 'import py_compile, sys; py_compile.compile(sys.argv[1], sys.argv[2])' swig/python/dna_jellyfish.py swig/python/__init__.pyc
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o jellyfish/generate_sequence.o jellyfish/generate_sequence.cc
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o jellyfish/mersenne.o jellyfish/mersenne.cpp
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o jellyfish/backtrace.o jellyfish/backtrace.cc
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o jellyfish/dbg.o jellyfish/dbg.cc
/bin/bash ./libtool --tag=CXX --mode=link g++ -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -pthread -L/<<PKGBUILDDIR>>/debian/tmp//usr/lib/x86_64-linux-gnu -lhts -R/<<PKGBUILDDIR>>/debian/tmp//usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o bin/generate_sequence jellyfish/generate_sequence.o jellyfish/mersenne.o jellyfish/backtrace.o jellyfish/dbg.o libjellyfish-2.0.la
libtool: link: g++ -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/generate_sequence jellyfish/generate_sequence.o jellyfish/mersenne.o jellyfish/backtrace.o jellyfish/dbg.o -L/<<PKGBUILDDIR>>/debian/tmp//usr/lib/x86_64-linux-gnu -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/<<PKGBUILDDIR>>/debian/tmp//usr/lib/x86_64-linux-gnu
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_main.o `test -f 'unit_tests/test_main.cc' || echo './'`unit_tests/test_main.cc
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_misc.o `test -f 'unit_tests/test_misc.cc' || echo './'`unit_tests/test_misc.cc
In file included from unit_tests/test_misc.cc:6:
unit_tests/test_misc.cc: In member function ‘virtual void {anonymous}::BinarySearchFirst_Int_Test::TestBody()’:
unit_tests/test_misc.cc:73:68: error: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = less<int>; _Tp = int]’ is deprecated: use 'std::bind' instead [-Werror=deprecated-declarations]
73 | std::bind2nd(std::less<int>(), i)));
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
./unit_tests/gtest/gtest.h:19418:52: note: in definition of macro ‘GTEST_ASSERT_’
19418 | if (const ::testing::AssertionResult gtest_ar = (expression)) \
| ^~~~~~~~~~
./unit_tests/gtest/gtest.h:19503:3: note: in expansion of macro ‘GTEST_PRED_FORMAT2_’
19503 | GTEST_PRED_FORMAT2_(pred_format, v1, v2, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~~~~~
./unit_tests/gtest/gtest.h:19748:3: note: in expansion of macro ‘EXPECT_PRED_FORMAT2’
19748 | EXPECT_PRED_FORMAT2(::testing::internal:: \
| ^~~~~~~~~~~~~~~~~~~
unit_tests/test_misc.cc:72:5: note: in expansion of macro ‘EXPECT_EQ’
72 | EXPECT_EQ(i, *jellyfish::binary_search_first_false(jellyfish::pointer_integer<int>(0), jellyfish::pointer_integer<int>(size),
| ^~~~~~~~~
In file included from /usr/include/c++/12/bits/stl_function.h:1438,
from /usr/include/c++/12/functional:49,
from unit_tests/test_misc.cc:4:
/usr/include/c++/12/backward/binders.h:172:5: note: declared here
172 | bind2nd(const _Operation& __fn, const _Tp& __x)
| ^~~~~~~
cc1plus: all warnings being treated as errors
make[2]: *** [Makefile:1784: unit_tests/bin_test_all-test_misc.o] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j1 all bin/generate_sequence bin/test_all bin/fastq2sam returned exit code 2
make[1]: *** [debian/rules:85: override_dh_auto_build] 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
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