Subject: spades: ftbfs with GCC-15

From: Matthias Klose <[email-masked]>
Date: Mon, 17 Feb 2025 17:54:26 +0000

Package: src:spades
Version: 3.15.5+dfsg-8
Severity: important
Tags: sid forky
User: [email-masked]
Usertags: ftbfs-gcc-15

[This bug is NOT 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-15/g++-15, but succeeds to build with gcc-14/g++-14. The
severity of this report will be raised before the forky release.

The full build log can be found at:
http://qa-logs.debian.net/2025/02/16/amd64exp/spades_3.15.5+dfsg-8_unstable_gccexp.log.gz
The last lines of the build log are at the end of this report.

To build with GCC 15, either set CC=gcc-15 CXX=g++-15 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

GCC 15 now defaults to the C23/C++23 standards, exposing many FTBFS.
Other 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-15/porting_to.html

[...]
/build/reproducible-path/spades-3.15.5+dfsg/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);
      | ^~~~~~~~~~~~~~~
[ 40%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o
[ 41%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o
[ 41%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o
In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c:8:
/build/reproducible-path/spades-3.15.5+dfsg/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);
      | ^~~~~~~~~~~~~~~~~
/build/reproducible-path/spades-3.15.5+dfsg/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 /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c:7:
/build/reproducible-path/spades-3.15.5+dfsg/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);
      |           ^~~~~~~~~~~
[ 41%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o
[ 43%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o
[ 43%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o
In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.h:11,
                 from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c:10:
/build/reproducible-path/spades-3.15.5+dfsg/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);
      | ^~~~~~~~~~~~~~~~~
/build/reproducible-path/spades-3.15.5+dfsg/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 /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c:7:
/build/reproducible-path/spades-3.15.5+dfsg/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);
      |           ^~~~~~~~~~~
[ 43%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o
[ 43%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o
[ 43%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o
[ 43%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o
[ 43%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o
[ 44%] Linking CXX static library libBamTools.a
cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cmake -P CMakeFiles/BamTools.dir/cmake_clean_target.cmake
cd /build/reproducible-path/spades-3.15.5+dfsg/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 '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu'
[ 44%] Built target BamTools
[ 44%] Linking CXX static library libllvm-support.a
cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -P CMakeFiles/llvm-support.dir/cmake_clean_target.cmake
cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -E cmake_link_script CMakeFiles/llvm-support.dir/link.txt --verbose=1
/usr/bin/ranlib libllvm-support.a
make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu'
[ 44%] Built target llvm-support
make[3]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu'
make[2]: *** [Makefile:169: all] Error 2
make[2]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/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 '/build/reproducible-path/spades-3.15.5+dfsg'
make: *** [debian/rules:14: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2