[Debian-med-packaging] Bug#1096367: bifrost: ftbfs with GCC-15

Mon Feb 17 17:04:59 GMT 2025

Package: src:bifrost
Version: 1.3.1-1
Severity: important
Tags: sid forky
User: debian-gcc at lists.debian.org
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/bifrost_1.3.1-1_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

[...]
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/bifrost-1.3.1 /build/reproducible-path/bifrost-1.3.1/src /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src/CMakeFiles/bifrost_static.dir/DependInfo.cmake "--color="
make[3]: Entering directory '/build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu'
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/bifrost-1.3.1 /build/reproducible-path/bifrost-1.3.1/src /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src/CMakeFiles/bifrost_dynamic.dir/DependInfo.cmake "--color="
make[3]: Leaving directory '/build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu'
make  -f src/CMakeFiles/bifrost_static.dir/build.make src/CMakeFiles/bifrost_static.dir/build
make[3]: Leaving directory '/build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu'
make  -f src/CMakeFiles/bifrost_dynamic.dir/build.make src/CMakeFiles/bifrost_dynamic.dir/build
make[3]: Entering directory '/build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu'
make[3]: Entering directory '/build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu'
[ 12%] Building CXX object src/CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o
[ 12%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o
[ 12%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o
[ 12%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o
[ 15%] Building CXX object src/CMakeFiles/bifrost_static.dir/BitContainer.cpp.o
[ 18%] Building CXX object src/CMakeFiles/bifrost_static.dir/ColorSet.cpp.o
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/BitContainer.cpp
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o -MF CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o.d -o CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/BitContainer.cpp.o -MF CMakeFiles/bifrost_static.dir/BitContainer.cpp.o.d -o CMakeFiles/bifrost_static.dir/BitContainer.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/BitContainer.cpp
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/ColorSet.cpp.o -MF CMakeFiles/bifrost_static.dir/ColorSet.cpp.o.d -o CMakeFiles/bifrost_static.dir/ColorSet.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/ColorSet.cpp
[ 25%] Building CXX object src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o
[ 25%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o -MF CMakeFiles/bifrost_static.dir/Bifrost.cpp.o.d -o CMakeFiles/bifrost_static.dir/Bifrost.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/ColorSet.cpp
In file included from /build/reproducible-path/bifrost-1.3.1/src/DataManager.hpp:10,
                 from /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.hpp:10,
                 from /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:2:
/build/reproducible-path/bifrost-1.3.1/src/DataStorage.tcc: In copy constructor ‘DataStorage<Unitig_data_t>::DataStorage(const DataStorage<Unitig_data_t>&)’:
/build/reproducible-path/bifrost-1.3.1/src/DataStorage.tcc:81:69: error: ‘const class DataStorage<Unitig_data_t>’ has no member named ‘sz_link’ [-Wtemplate-body]
   81 |         for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] = o.sz_link[i].load();
      |                                                                     ^~~~~~~
In file included from /build/reproducible-path/bifrost-1.3.1/src/DataManager.hpp:10,
                 from /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.hpp:10,
                 from /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:2:
/build/reproducible-path/bifrost-1.3.1/src/DataStorage.tcc: In copy constructor ‘DataStorage<Unitig_data_t>::DataStorage(const DataStorage<Unitig_data_t>&)’:
/build/reproducible-path/bifrost-1.3.1/src/DataStorage.tcc:81:69: error: ‘const class DataStorage<Unitig_data_t>’ has no member named ‘sz_link’ [-Wtemplate-body]
   81 |         for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] = o.sz_link[i].load();
      |                                                                     ^~~~~~~
[ 28%] Building CXX object src/CMakeFiles/bifrost_static.dir/CompressedCoverage.cpp.o
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/CompressedCoverage.cpp.o -MF CMakeFiles/bifrost_static.dir/CompressedCoverage.cpp.o.d -o CMakeFiles/bifrost_static.dir/CompressedCoverage.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp
[ 31%] Building CXX object src/CMakeFiles/bifrost_static.dir/CompressedSequence.cpp.o
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/CompressedSequence.cpp.o -MF CMakeFiles/bifrost_static.dir/CompressedSequence.cpp.o.d -o CMakeFiles/bifrost_static.dir/CompressedSequence.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/CompressedSequence.cpp
[ 34%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp
[ 37%] Building CXX object src/CMakeFiles/bifrost_static.dir/FASTX_Parser.cpp.o
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/FASTX_Parser.cpp.o -MF CMakeFiles/bifrost_static.dir/FASTX_Parser.cpp.o.d -o CMakeFiles/bifrost_static.dir/FASTX_Parser.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.cpp
[ 40%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/CompressedSequence.cpp.o
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/CompressedSequence.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/CompressedSequence.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/CompressedSequence.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/CompressedSequence.cpp
[ 43%] Building CXX object src/CMakeFiles/bifrost_static.dir/GFA_Parser.cpp.o
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/GFA_Parser.cpp.o -MF CMakeFiles/bifrost_static.dir/GFA_Parser.cpp.o.d -o CMakeFiles/bifrost_static.dir/GFA_Parser.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/GFA_Parser.cpp
[ 46%] Building CXX object src/CMakeFiles/bifrost_static.dir/Kmer.cpp.o
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/Kmer.cpp.o -MF CMakeFiles/bifrost_static.dir/Kmer.cpp.o.d -o CMakeFiles/bifrost_static.dir/Kmer.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/Kmer.cpp
make[3]: *** [src/CMakeFiles/bifrost_static.dir/build.make:82: src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o] Error 1
make[3]: *** Waiting for unfinished jobs....
[ 50%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/FASTX_Parser.cpp.o
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/FASTX_Parser.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/FASTX_Parser.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/FASTX_Parser.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.cpp
make[3]: *** [src/CMakeFiles/bifrost_dynamic.dir/build.make:82: src/CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: Leaving directory '/build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:147: src/CMakeFiles/bifrost_dynamic.dir/all] Error 2
make[2]: *** Waiting for unfinished jobs....
make[3]: Leaving directory '/build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:115: src/CMakeFiles/bifrost_static.dir/all] Error 2
make[2]: Leaving directory '/build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu'
make[1]: *** [Makefile:139: all] Error 2
make[1]: Leaving directory '/build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2
make: *** [debian/rules:8: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2