[Debian-med-packaging] Bug#1075273: mindthegap: ftbfs with GCC-14
Matthias Klose
doko at debian.org
Wed Jul 3 13:36:31 BST 2024
Package: src:mindthegap
Version: 2.3.0-3
Severity: important
Tags: sid trixie
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-14
[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-14/g++-14, but succeeds to build with gcc-13/g++-13. 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/2024/07/01/mindthegap_2.3.0-3_unstable_gccexp.log
The last lines of the build log are at the end of this report.
To build with GCC 14, either set CC=gcc-14 CXX=g++-14 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-14/porting_to.html
[...]
695 | position + 1, //switch to 1-based
| ~~~~~~~~~~~~
| |
| uint64_t {aka long unsigned int}
/<<PKGBUILDDIR>>/src/FindBreakpoints.hpp: In instantiation of ‘void FindBreakpoints<span>::writeBreakpoint(int, std::string&, uint64_t, std::string&, std::string&, int, std::string, bool, bool) [with long unsigned int span = 32; std::string = std::__cxx11::basic_string<char>; uint64_t = long unsigned int]’:
/<<PKGBUILDDIR>>/src/FindHeteroInsertion.hpp:145:57: required from ‘bool FindHeteroInsertion<span>::update() [with long unsigned int span = 32]’
145 | this->_find->writeBreakpoint(this->_find->breakpoint_id(), this->_find->chrom_name(), this->_find->position() - 1 + i, kmer_begin_str, kmer_end_str, i, STR_HET_TYPE, this->_find->het_kmer_history(this->_find->het_kmer_begin_index() + i).is_repeated, this->_find->kmer_end_is_repeated());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/FindHeteroInsertion.hpp:48:6: required from here
48 | bool FindHeteroInsertion<span>::update()
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/FindBreakpoints.hpp:642:63: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 5 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=]
642 | fprintf(this->finder->_breakpoint_file,">bkpt%i_%s_pos_%lli_fuzzy_%i_%s %s left_kmer\n%s\n>bkpt%i_%s_pos_%lli_fuzzy_%i_%s %s right_kmer\n%s\n",
| ~~~^
| |
| long long int
| %li
......
645 | position+1, //switch to 1-based
| ~~~~~~~~~~
| |
| uint64_t {aka long unsigned int}
/<<PKGBUILDDIR>>/src/FindBreakpoints.hpp:642:113: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 12 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=]
642 | fprintf(this->finder->_breakpoint_file,">bkpt%i_%s_pos_%lli_fuzzy_%i_%s %s left_kmer\n%s\n>bkpt%i_%s_pos_%lli_fuzzy_%i_%s %s right_kmer\n%s\n",
| ~~~^
| |
| long long int
| %li
......
652 | position+1, //switch to 1-based
| ~~~~~~~~~~
| |
| uint64_t {aka long unsigned int}
/<<PKGBUILDDIR>>/src/FindBreakpoints.hpp: In instantiation of ‘void FindBreakpoints<span>::writeVcfVariant(int, std::string&, uint64_t, char*, char*, int, std::string) [with long unsigned int span = 32; std::string = std::__cxx11::basic_string<char>; uint64_t = long unsigned int]’:
/<<PKGBUILDDIR>>/src/FindDeletion.hpp:158:30: required from ‘bool FindDeletion<span>::update() [with long unsigned int span = 32]’
158 | this->_find->writeVcfVariant(this->_find->breakpoint_id(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
159 | this->_find->chrom_name(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
160 | del_start_pos, del_sequence, alt_char, repeat_size, STR_DEL_TYPE);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/FindDeletion.hpp:62:6: required from here
62 | bool FindDeletion<span>::update()
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/FindBreakpoints.hpp:668:49: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 4 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=]
668 | fprintf(this->finder->_vcf_file,"%s\t%lli\tbkpt%i\t%s\t%s\t.\tPASS\tTYPE=%s;LEN=%i;FUZZY=%i\tGT\t1/1\n",
| ~~~^
| |
| long long int
| %li
669 | chrom_name.c_str(),
670 | position+1, //switch to 1-based
| ~~~~~~~~~~
| |
| uint64_t {aka long unsigned int}
[ 90%] Linking CXX executable bin/nwalign
/usr/bin/cmake -E cmake_link_script CMakeFiles/nwalign.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/nwalign.dir/src/nwAlign/nwalign.cpp.o -o bin/nwalign -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial -lgatbcore -lhdf5
make[3]: *** [CMakeFiles/MindTheGap.dir/build.make:107: CMakeFiles/MindTheGap.dir/src/Finder.cpp.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 90%] Built target nwalign
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:88: CMakeFiles/MindTheGap.dir/all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[1]: *** [Makefile:159: all] Error 2
make[1]: 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" VERBOSE=1 returned exit code 2
make: *** [debian/rules:9: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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