[Debian-med-packaging] Bug#1037863: spades: ftbfs with GCC-13
Matthias Klose
doko at debian.org
Wed Jun 14 10:31:35 BST 2023
Package: src:spades
Version: 3.15.5+dfsg-2
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/spades_3.15.5+dfsg-2_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
[...]
5 | safe_mutex_lock(pthread_mutex_t *mutex);
| ^~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c:8:
/<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined
8 | safe_mutex_unlock(pthread_mutex_t *mutex);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined
5 | safe_mutex_lock(pthread_mutex_t *mutex);
| ^~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c:7:
/<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined
240 | unpackInt16(const uint8_t* buffer);
| ^~~~~~~~~~~
[ 38%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/<<PKGBUILDDIR>>/assembler/src/include -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/include -I/<<PKGBUILDDIR>>/assembler/src -I/<<PKGBUILDDIR>>/assembler/src/common -I/<<PKGBUILDDIR>>/assembler/ext/src/bamtools -I/<<PKGBUILDDIR>>/assembler/ext/src/bamtools/src -isystem /<<PKGBUILDDIR>>/assembler/src/../ext/include -isystem /<<PKGBUILDDIR>>/assembler/ext/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o -c /<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.c
[ 39%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/<<PKGBUILDDIR>>/assembler/src/include -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/include -I/<<PKGBUILDDIR>>/assembler/src -I/<<PKGBUILDDIR>>/assembler/src/common -I/<<PKGBUILDDIR>>/assembler/ext/src/bamtools -I/<<PKGBUILDDIR>>/assembler/ext/src/bamtools/src -isystem /<<PKGBUILDDIR>>/assembler/src/../ext/include -isystem /<<PKGBUILDDIR>>/assembler/ext/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o -c /<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c
[ 39%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/<<PKGBUILDDIR>>/assembler/src/include -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/include -I/<<PKGBUILDDIR>>/assembler/src -I/<<PKGBUILDDIR>>/assembler/src/common -I/<<PKGBUILDDIR>>/assembler/ext/src/bamtools -I/<<PKGBUILDDIR>>/assembler/ext/src/bamtools/src -isystem /<<PKGBUILDDIR>>/assembler/src/../ext/include -isystem /<<PKGBUILDDIR>>/assembler/ext/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -c /<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api/internal/sam/SamFormatParser_p.cpp
[ 39%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/<<PKGBUILDDIR>>/assembler/src/include -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/include -I/<<PKGBUILDDIR>>/assembler/src -I/<<PKGBUILDDIR>>/assembler/src/common -I/<<PKGBUILDDIR>>/assembler/ext/src/bamtools -I/<<PKGBUILDDIR>>/assembler/ext/src/bamtools/src -isystem /<<PKGBUILDDIR>>/assembler/src/../ext/include -isystem /<<PKGBUILDDIR>>/assembler/ext/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -c /<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api/internal/sam/SamFormatPrinter_p.cpp
[ 39%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/<<PKGBUILDDIR>>/assembler/src/include -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/include -I/<<PKGBUILDDIR>>/assembler/src -I/<<PKGBUILDDIR>>/assembler/src/common -I/<<PKGBUILDDIR>>/assembler/ext/src/bamtools -I/<<PKGBUILDDIR>>/assembler/ext/src/bamtools/src -isystem /<<PKGBUILDDIR>>/assembler/src/../ext/include -isystem /<<PKGBUILDDIR>>/assembler/ext/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -c /<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api/internal/sam/SamHeaderValidator_p.cpp
[ 39%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/<<PKGBUILDDIR>>/assembler/src/include -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/include -I/<<PKGBUILDDIR>>/assembler/src -I/<<PKGBUILDDIR>>/assembler/src/common -I/<<PKGBUILDDIR>>/assembler/ext/src/bamtools -I/<<PKGBUILDDIR>>/assembler/ext/src/bamtools/src -isystem /<<PKGBUILDDIR>>/assembler/src/../ext/include -isystem /<<PKGBUILDDIR>>/assembler/ext/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -c /<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api/internal/utils/BamException_p.cpp
In file included from /<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.h:11,
from /<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c:10:
/<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined
8 | safe_mutex_unlock(pthread_mutex_t *mutex);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined
5 | safe_mutex_lock(pthread_mutex_t *mutex);
| ^~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c:7:
/<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined
240 | unpackInt16(const uint8_t* buffer);
| ^~~~~~~~~~~
[ 39%] Building CXX object common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/<<PKGBUILDDIR>>/assembler/src/include -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/include -I/<<PKGBUILDDIR>>/assembler/src -I/<<PKGBUILDDIR>>/assembler/src/common -I/<<PKGBUILDDIR>>/assembler/src/common/io/binary -isystem /<<PKGBUILDDIR>>/assembler/src/../ext/include -isystem /<<PKGBUILDDIR>>/assembler/ext/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o -MF CMakeFiles/binary_io.dir/genomic_info.cpp.o.d -o CMakeFiles/binary_io.dir/genomic_info.cpp.o -c /<<PKGBUILDDIR>>/assembler/src/common/io/binary/genomic_info.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:1380: ext/llvm/CMakeFiles/llvm-support.dir/all] Error 2
[ 40%] Linking CXX static library libBamTools.a
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cmake -P CMakeFiles/BamTools.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cmake -E cmake_link_script CMakeFiles/BamTools.dir/link.txt --verbose=1
/usr/bin/ar qc libBamTools.a CMakeFiles/BamTools.dir/BamAlignment.cpp.o CMakeFiles/BamTools.dir/BamMultiReader.cpp.o CMakeFiles/BamTools.dir/BamReader.cpp.o CMakeFiles/BamTools.dir/BamWriter.cpp.o CMakeFiles/BamTools.dir/SamHeader.cpp.o CMakeFiles/BamTools.dir/SamProgram.cpp.o CMakeFiles/BamTools.dir/SamProgramChain.cpp.o CMakeFiles/BamTools.dir/SamReadGroup.cpp.o CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o CMakeFiles/BamTools.dir/SamSequence.cpp.o CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o
/usr/bin/ranlib libBamTools.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 40%] Built target BamTools
[ 40%] Linking CXX static library libbinary_io.a
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake -P CMakeFiles/binary_io.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake -E cmake_link_script CMakeFiles/binary_io.dir/link.txt --verbose=1
/usr/bin/ar qc libbinary_io.a CMakeFiles/binary_io.dir/graph_pack.cpp.o CMakeFiles/binary_io.dir/genomic_info.cpp.o
/usr/bin/ranlib libbinary_io.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 40%] Built target binary_io
[ 40%] Linking CXX static library libConsensusCore.a
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/cmake -P CMakeFiles/ConsensusCore.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/cmake -E cmake_link_script CMakeFiles/ConsensusCore.dir/link.txt --verbose=1
/usr/bin/ar qc libConsensusCore.a CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o CMakeFiles/ConsensusCore.dir/Coverage.cpp.o CMakeFiles/ConsensusCore.dir/Mutation.cpp.o CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o CMakeFiles/ConsensusCore.dir/Sequence.cpp.o CMakeFiles/ConsensusCore.dir/Utils.cpp.o CMakeFiles/ConsensusCore.dir/Version.cpp.o CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o
/usr/bin/ranlib libConsensusCore.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 40%] Built target ConsensusCore
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [Makefile:169: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" all debruijn_test include_test VERBOSE=1 returned exit code 2
make[1]: *** [debian/rules:29: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:14: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
More information about the Debian-med-packaging
mailing list