[Debian-med-packaging] Bug#984212: libvcflib: ftbfs with GCC-11
Matthias Klose
doko at debian.org
Wed Mar 3 16:15:02 GMT 2021
Package: src:libvcflib
Version: 1.0.2+dfsg-2
Severity: normal
Tags: sid bookworm
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-11
[This bug is not targeted to the upcoming bullseye 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-11/g++-11, but succeeds to build with gcc-10/g++-10. The
severity of this report will be raised before the bookworm release,
so nothing has to be done for the bullseye release.
The full build log can be found at:
http://people.debian.org/~doko/logs/20210228/filtered/gcc11/libvcflib_1.0.2+dfsg-2_unstable_gcc11.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.
[...]
/usr/include/c++/11/bits/stl_algo.h:3449:5: note: template argument deduction/substitution failed:
In file included from /<<PKGBUILDDIR>>/src/BedReader.h:21,
from /<<PKGBUILDDIR>>/src/vcf2dag.cpp:11:
/<<PKGBUILDDIR>>/intervaltree/IntervalTree.h:271:103: note: candidate expects 1 argument, 0 provided
271 | std::numeric_limits<Scalar>::min() }};
| ^
In file included from /usr/include/c++/11/algorithm:62,
from /usr/include/smithwaterman/SmithWatermanGotoh.h:4,
from /<<PKGBUILDDIR>>/src/Variant.h:30,
from /<<PKGBUILDDIR>>/src/vcf2dag.cpp:10:
/usr/include/c++/11/bits/stl_algo.h:3455:5: note: candidate: ‘template<class _Tp, class _Compare> _Tp std::min(std::initializer_list<_Tp>, _Compare)’
3455 | min(initializer_list<_Tp> __l, _Compare __comp)
| ^~~
/usr/include/c++/11/bits/stl_algo.h:3455:5: note: template argument deduction/substitution failed:
In file included from /<<PKGBUILDDIR>>/src/BedReader.h:21,
from /<<PKGBUILDDIR>>/src/vcf2dag.cpp:11:
/<<PKGBUILDDIR>>/intervaltree/IntervalTree.h:271:103: note: candidate expects 2 arguments, 0 provided
271 | std::numeric_limits<Scalar>::min() }};
| ^
[ 12%] Linking CXX executable vcfsample2info
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsample2info.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -o vcfsample2info -Wl,-rpath,/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
/<<PKGBUILDDIR>>/intervaltree/IntervalTree.h: In instantiation of ‘std::pair<bool, std::pair<_FIter, _FIter> > IntervalTree<Scalar, Value>::is_valid() const [with Scalar = long unsigned int; Value = BedTarget*]’:
/<<PKGBUILDDIR>>/intervaltree/IntervalTree.h:115:13: required from ‘IntervalTree<Scalar, Value>::IntervalTree(IntervalTree<Scalar, Value>::interval_vector&&, std::size_t, std::size_t, std::size_t, Scalar, Scalar) [with Scalar = long unsigned int; Value = BedTarget*; IntervalTree<Scalar, Value>::interval_vector = std::vector<Interval<long unsigned int, BedTarget*> >; std::size_t = long unsigned int]’
/<<PKGBUILDDIR>>/src/BedReader.h:163:118: required from here
/<<PKGBUILDDIR>>/intervaltree/IntervalTree.h:270:52: error: could not convert ‘{true, {<expression error>, <expression error>}}’ from ‘<brace-enclosed initializer list>’ to ‘std::pair<bool, std::pair<long unsigned int, long unsigned int> >’
270 | std::pair<bool, std::pair<Scalar, Scalar>> result = {true, { std::numeric_limits<Scalar>::max(),
| ^~~~~~
| |
| <brace-enclosed initializer list>
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 12%] Built target vcfsample2info
make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/depend
make[4]: 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/vcfgenosamplenames.dir/DependInfo.cmake --color=
Dependee "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/vcfgenosamplenames.dir/DependInfo.cmake" is newer than depender "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/vcfgenosamplenames.dir/depend.internal".
Dependee "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/vcfgenosamplenames.dir/depend.internal".
Scanning dependencies of target vcfgenosamplenames
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 13%] Building CXX object CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/intervaltree -I/<<PKGBUILDDIR>>/multichoose -I/<<PKGBUILDDIR>>/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -c /<<PKGBUILDDIR>>/src/vcfgenosamplenames.cpp
make[4]: *** [CMakeFiles/vcf2dag.dir/build.make:85: CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:372: CMakeFiles/vcf2dag.dir/all] Error 2
make[3]: *** Waiting for unfinished jobs....
[ 13%] Linking CXX executable vcfgeno2alleles
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgeno2alleles.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -o vcfgeno2alleles -Wl,-rpath,/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 13%] Built target vcfgeno2alleles
[ 13%] Linking CXX executable vcfgenosamplenames
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosamplenames.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -o vcfgenosamplenames -Wl,-rpath,/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 13%] Built target vcfgenosamplenames
[ 13%] Linking CXX executable vcfcombine
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcombine.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -o vcfcombine -Wl,-rpath,/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 13%] Built target vcfcombine
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [Makefile:163: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2
make[1]: *** [debian/rules:26: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:12: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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