[Debian-med-packaging] Bug#925714: hilive: ftbfs with GCC-9

[Matthias Klose]

Package: src:hilive
Version: 1.1-2
Severity: normal
Tags: sid bullseye
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-9

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-9/g++-9, but succeeds to build with gcc-8/g++-8. The
severity of this report will be raised before the bullseye release,
so nothing has to be done for the buster release.

The full build log can be found at:
http://people.debian.org/~doko/logs/gcc9-20190321/hilive_1.1-2_unstable_gcc9.log
The last lines of the build log are at the end of this report.

To build with GCC 9, either set CC=gcc-9 CXX=g++-9 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-9/porting_to.html

GCC 9 also passes the linker option --as-needed by default; typical
build issues are passing libraries before object files to the linker,
or underlinking of convenience libraries built from the same source.

[...]
/usr/bin/c++  -DHiLive_VERSION_MAJOR=1 -DHiLive_VERSION_MINOR=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>>/lib  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2    -o CMakeFiles/HiLiveLibs.dir/lib/argument_parser.cpp.o -c /<<PKGBUILDDIR>>/lib/argument_parser.cpp
[ 60%] Linking CXX static library libHiLiveLibs.a
/usr/bin/cmake -P CMakeFiles/HiLiveLibs.dir/cmake_clean_target.cmake
/usr/bin/cmake -E cmake_link_script CMakeFiles/HiLiveLibs.dir/link.txt --verbose=1
/usr/bin/ar qc libHiLiveLibs.a  CMakeFiles/HiLiveLibs.dir/lib/tools_static.cpp.o CMakeFiles/HiLiveLibs.dir/lib/tools.cpp.o CMakeFiles/HiLiveLibs.dir/lib/alnread.cpp.o CMakeFiles/HiLiveLibs.dir/lib/alnstream.cpp.o CMakeFiles/HiLiveLibs.dir/lib/illumina_parsers.cpp.o CMakeFiles/HiLiveLibs.dir/lib/kindex.cpp.o CMakeFiles/HiLiveLibs.dir/lib/parallel.cpp.o CMakeFiles/HiLiveLibs.dir/lib/argument_parser.cpp.o
/usr/bin/ranlib libHiLiveLibs.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 60%] Built target HiLiveLibs
make -f CMakeFiles/hilive.dir/build.make CMakeFiles/hilive.dir/depend
make -f CMakeFiles/hilive-build.dir/build.make CMakeFiles/hilive-build.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/hilive.dir/DependInfo.cmake --color=
make -f CMakeFiles/hilive-out.dir/build.make CMakeFiles/hilive-out.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/hilive-build.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/hilive-out.dir/DependInfo.cmake --color=
Scanning dependencies of target hilive
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make -f CMakeFiles/hilive.dir/build.make CMakeFiles/hilive.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
Scanning dependencies of target hilive-build
Scanning dependencies of target hilive-out
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make -f CMakeFiles/hilive-build.dir/build.make CMakeFiles/hilive-build.dir/build
make -f CMakeFiles/hilive-out.dir/build.make CMakeFiles/hilive-out.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 66%] Building CXX object CMakeFiles/hilive.dir/tools/hilive.cpp.o
/usr/bin/c++  -DHiLive_VERSION_MAJOR=1 -DHiLive_VERSION_MINOR=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>>/lib  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2    -o CMakeFiles/hilive.dir/tools/hilive.cpp.o -c /<<PKGBUILDDIR>>/tools/hilive.cpp
[ 73%] Building CXX object CMakeFiles/hilive-out.dir/tools/hilive_out.cpp.o
/usr/bin/c++  -DHiLive_VERSION_MAJOR=1 -DHiLive_VERSION_MINOR=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>>/lib  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2    -o CMakeFiles/hilive-out.dir/tools/hilive_out.cpp.o -c /<<PKGBUILDDIR>>/tools/hilive_out.cpp
[ 80%] Building CXX object CMakeFiles/hilive-build.dir/tools/build_index.cpp.o
/usr/bin/c++  -DHiLive_VERSION_MAJOR=1 -DHiLive_VERSION_MINOR=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>>/lib  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2    -o CMakeFiles/hilive-build.dir/tools/build_index.cpp.o -c /<<PKGBUILDDIR>>/tools/build_index.cpp
[ 86%] Linking CXX executable hilive-build
/usr/bin/cmake -E cmake_link_script CMakeFiles/hilive-build.dir/link.txt --verbose=1
/usr/bin/c++  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/hilive-build.dir/tools/build_index.cpp.o  -o hilive-build libHiLiveLibs.a -lz -llz4 -Wl,-Bstatic -lboost_system -lboost_filesystem -lboost_program_options -Wl,-Bdynamic -lrt -lz -llz4 -Wl,-Bstatic -lboost_system -lboost_filesystem -lboost_program_options -Wl,-Bdynamic -lrt 
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 86%] Built target hilive-build
[ 93%] Linking CXX executable hilive-out
/usr/bin/cmake -E cmake_link_script CMakeFiles/hilive-out.dir/link.txt --verbose=1
/usr/bin/c++  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/hilive-out.dir/tools/hilive_out.cpp.o  -o hilive-out libHiLiveLibs.a -lz -llz4 -Wl,-Bstatic -lboost_system -lboost_filesystem -lboost_program_options -Wl,-Bdynamic -lrt -lz -llz4 -Wl,-Bstatic -lboost_system -lboost_filesystem -lboost_program_options -Wl,-Bdynamic -lrt 
/usr/bin/ld: CMakeFiles/hilive-out.dir/tools/hilive_out.cpp.o: in function `std::thread::thread<Task (AlnOut::*)(), AlnOut*, void>(Task (AlnOut::*&&)(), AlnOut*&&)':
/usr/include/c++/9/thread:130: undefined reference to `pthread_create'
/usr/bin/ld: /usr/include/c++/9/thread:130: undefined reference to `pthread_create'
/usr/bin/ld: libHiLiveLibs.a(alnstream.cpp.o): in function `std::thread::thread<std::__future_base::_Async_state_impl<std::thread::_Invoker<std::tuple<seqan::basic_bgzf_streambuf<char, std::char_traits<char>, std::allocator<char>, char, std::allocator<char> >::CompressionThread> >, void>::_Async_state_impl(std::thread::_Invoker<std::tuple<seqan::basic_bgzf_streambuf<char, std::char_traits<char>, std::allocator<char>, char, std::allocator<char> >::CompressionThread> >&&)::{lambda()#1}, , void>(std::__future_base::_Async_state_impl<std::thread::_Invoker<std::tuple<seqan::basic_bgzf_streambuf<char, std::char_traits<char>, std::allocator<char>, char, std::allocator<char> >::CompressionThread> >, void>::_Async_state_impl(std::thread::_Invoker<std::tuple<seqan::basic_bgzf_streambuf<char, std::char_traits<char>, std::allocator<char>, char, std::allocator<char> >::CompressionThread> >&&)::{lambda()#1}&&)':
/usr/include/c++/9/thread:130: undefined reference to `pthread_create'
collect2: error: ld returned 1 exit status
make[3]: *** [CMakeFiles/hilive-out.dir/build.make:96: hilive-out] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:187: CMakeFiles/hilive-out.dir/all] Error 2
make[2]: *** Waiting for unfinished jobs....
[100%] Linking CXX executable hilive
/usr/bin/cmake -E cmake_link_script CMakeFiles/hilive.dir/link.txt --verbose=1
/usr/bin/c++  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/hilive.dir/tools/hilive.cpp.o  -o hilive libHiLiveLibs.a -lz -llz4 -Wl,-Bstatic -lboost_system -lboost_filesystem -lboost_program_options -Wl,-Bdynamic -lrt -lz -llz4 -Wl,-Bstatic -lboost_system -lboost_filesystem -lboost_program_options -Wl,-Bdynamic -lrt 
/usr/bin/ld: CMakeFiles/hilive.dir/tools/hilive.cpp.o: in function `std::thread::thread<void (&)(TaskQueue&, TaskQueue&, TaskQueue&, KixRun*, std::deque<AlnOut, std::allocator<AlnOut> >&, std::atomic<unsigned short>&, bool&), std::reference_wrapper<TaskQueue>, std::reference_wrapper<TaskQueue>, std::reference_wrapper<TaskQueue>, KixRun*&, std::reference_wrapper<std::deque<AlnOut, std::allocator<AlnOut> > >, std::reference_wrapper<std::atomic<unsigned short> >, std::reference_wrapper<bool>, void>(void (&)(TaskQueue&, TaskQueue&, TaskQueue&, KixRun*, std::deque<AlnOut, std::allocator<AlnOut> >&, std::atomic<unsigned short>&, bool&), std::reference_wrapper<TaskQueue>&&, std::reference_wrapper<TaskQueue>&&, std::reference_wrapper<TaskQueue>&&, KixRun*&, std::reference_wrapper<std::deque<AlnOut, std::allocator<AlnOut> > >&&, std::reference_wrapper<std::atomic<unsigned short> >&&, std::reference_wrapper<bool>&&)':
/usr/include/c++/9/thread:130: undefined reference to `pthread_create'
/usr/bin/ld: libHiLiveLibs.a(alnstream.cpp.o): in function `std::thread::thread<std::__future_base::_Async_state_impl<std::thread::_Invoker<std::tuple<seqan::basic_bgzf_streambuf<char, std::char_traits<char>, std::allocator<char>, char, std::allocator<char> >::CompressionThread> >, void>::_Async_state_impl(std::thread::_Invoker<std::tuple<seqan::basic_bgzf_streambuf<char, std::char_traits<char>, std::allocator<char>, char, std::allocator<char> >::CompressionThread> >&&)::{lambda()#1}, , void>(std::__future_base::_Async_state_impl<std::thread::_Invoker<std::tuple<seqan::basic_bgzf_streambuf<char, std::char_traits<char>, std::allocator<char>, char, std::allocator<char> >::CompressionThread> >, void>::_Async_state_impl(std::thread::_Invoker<std::tuple<seqan::basic_bgzf_streambuf<char, std::char_traits<char>, std::allocator<char>, char, std::allocator<char> >::CompressionThread> >&&)::{lambda()#1}&&)':
/usr/include/c++/9/thread:130: undefined reference to `pthread_create'
collect2: error: ld returned 1 exit status
make[3]: *** [CMakeFiles/hilive.dir/build.make:96: hilive] Error 1
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make[1]: *** [Makefile:87: all] Error 2
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dh_auto_build: cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" returned exit code 2
make: *** [debian/rules:8: build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2