--- Begin Message ---
Package: src:hilive
Version: 1.1-2
Severity: normal
Tags: sid bullseye
User: debian-...@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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:76: CMakeFiles/hilive.dir/all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[1]: *** [Makefile:87: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
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
--- End Message ---
