[Debian-med-packaging] Bug#1097435: ncbi-igblast: ftbfs with GCC-15
Matthias Klose
doko at debian.org
Mon Feb 17 17:38:59 GMT 2025
Package: src:ncbi-igblast
Version: 1.19.0-1
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/ncbi-igblast_1.19.0-1_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
[...]
1693 | NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION_TEMPL_ERRNO(CErrnoTemplException<TBase>, CParent)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/ncbi-igblast-1.19.0/c++/include/corelib/ncbiexpt.hpp:1290:20: note: remove the ‘< >’
1290 | exception_class(void) {} \
| ^
/build/reproducible-path/ncbi-igblast-1.19.0/c++/include/corelib/ncbiexpt.hpp:1370:5: note: in expansion of macro ‘NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION_COMMON’
1370 | NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION_COMMON(exception_class, base_class) \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/ncbi-igblast-1.19.0/c++/include/corelib/ncbiexpt.hpp:1693:5: note: in expansion of macro ‘NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION_TEMPL_ERRNO’
1693 | NCBI_EXCEPTION_DEFAULT_IMPLEMENTATION_TEMPL_ERRNO(CErrnoTemplException<TBase>, CParent)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/ncbi-igblast-1.19.0/c++/include/corelib/ncbiexpt.hpp:1696:32: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
1696 | CErrnoTemplException<TBase>(const CDiagCompileInfo& info,
| ^
/build/reproducible-path/ncbi-igblast-1.19.0/c++/include/corelib/ncbiexpt.hpp:1696:32: note: remove the ‘< >’
In file included from /build/reproducible-path/ncbi-igblast-1.19.0/c++/include/util/bitset/ncbi_bitset.hpp:38,
from /build/reproducible-path/ncbi-igblast-1.19.0/c++/include/serial/serialbase.hpp:46,
from /build/reproducible-path/ncbi-igblast-1.19.0/c++/include/serial/impl/stdtypes.hpp:36,
from /build/reproducible-path/ncbi-igblast-1.19.0/c++/include/serial/objectinfo.hpp:40,
from /build/reproducible-path/ncbi-igblast-1.19.0/c++/include/serial/impl/objecttype.hpp:36,
from /build/reproducible-path/ncbi-igblast-1.19.0/c++/include/serial/objhook.hpp:37,
from /build/reproducible-path/ncbi-igblast-1.19.0/c++/include/serial/objistr.hpp:42,
from /build/reproducible-path/ncbi-igblast-1.19.0/c++/src/serial/typeinfo.cpp:38:
/build/reproducible-path/ncbi-igblast-1.19.0/c++/include/util/bitset/bm.h: In member function ‘bm::bvector<A>::bulk_insert_iterator& bm::bvector<A>::bulk_insert_iterator::operator=(const bm::bvector<A>::bulk_insert_iterator&)’:
/build/reproducible-path/ncbi-igblast-1.19.0/c++/include/util/bitset/bm.h:526:32: error: ‘bm::bvector<A>::bulk_insert_iterator::bvector_type’ has no member named ‘allocate_tempblock’ [-Wtemplate-body]
526 | buf_ = bvect_->allocate_tempblock();
| ^~~~~~~~~~~~~~~~~~
/build/reproducible-path/ncbi-igblast-1.19.0/c++/include/util/bitset/bm.h: In member function ‘bm::bvector<A>::bulk_insert_iterator& bm::bvector<A>::bulk_insert_iterator::operator=(bm::bvector<A>::bulk_insert_iterator&&)’:
/build/reproducible-path/ncbi-igblast-1.19.0/c++/include/util/bitset/bm.h:537:25: error: ‘bm::bvector<A>::bulk_insert_iterator::bvector_type’ has no member named ‘free_tempblock’ [-Wtemplate-body]
537 | bvect_->free_tempblock(buf_);
| ^~~~~~~~~~~~~~
/build/reproducible-path/ncbi-igblast-1.19.0/c++/include/serial/objhook.hpp: At global scope:
/build/reproducible-path/ncbi-igblast-1.19.0/c++/include/serial/objhook.hpp:614:9: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
614 | CSerial_FilterObjectsHook<TObject>* processor)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/ncbi-igblast-1.19.0/c++/include/serial/objhook.hpp:614:9: note: remove the ‘< >’
make[6]: *** [/build/reproducible-path/ncbi-igblast-1.19.0/c++/GCC1501-Release64/build/Makefile.rules:88: typeinfo.o] Error 1
information for /build/reproducible-path/ncbi-igblast-1.19.0/c++/src/serial/objistrasn.cpp.
Updating dependency information for /build/reproducible-path/ncbi-igblast-1.19.0/c++/src/serial/objostrasnb.cpp.
Updating dependency information for /build/reproducible-path/ncbi-igblast-1.19.0/c++/src/serial/objistrasnb.cpp.
Updating dependency information for /build/reproducible-path/ncbi-igblast-1.19.0/c++/src/serial/objostrxml.cpp.
Updating dependency information for /build/reproducible-path/ncbi-igblast-1.19.0/c++/src/serial/objistrxml.cpp.
Updating dependency information for /build/reproducible-path/ncbi-igblast-1.19.0/c++/src/serial/objostrjson.cpp.
Updating dependency information for /build/reproducible-path/ncbi-igblast-1.19.0/c++/src/serial/objistrjson.cpp.
Updating dependency information for /build/reproducible-path/ncbi-igblast-1.19.0/c++/src/serial/serializable.cpp.
Updating dependency information for /build/reproducible-path/ncbi-igblast-1.19.0/c++/src/serial/serialobject.cpp.
Updating dependency information for /build/reproducible-path/ncbi-igblast-1.19.0/c++/src/serial/pathhook.cpp.
Updating dependency information for /build/reproducible-path/ncbi-igblast-1.19.0/c++/src/serial/rpcbase.cpp.
/usr/bin/g++ -std=gnu++17 -msse4.2 -c -Wall -Wno-format-y2k -O2 -ffile-prefix-map=/build/reproducible-path/ncbi-igblast-1.19.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -DNCBI_WITHOUT_MT -I/build/reproducible-path/ncbi-igblast-1.19.0/c++/GCC1501-Release64/inc -I/build/reproducible-path/ncbi-igblast-1.19.0/c++/include /build/reproducible-path/ncbi-igblast-1.19.0/c++/src/serial/hookdata.cpp -o hookdata.o
/usr/bin/g++ -std=gnu++17 -msse4.2 -c -Wall -Wno-format-y2k -O2 -ffile-prefix-map=/build/reproducible-path/ncbi-igblast-1.19.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -DNCBI_WITHOUT_MT -I/build/reproducible-path/ncbi-igblast-1.19.0/c++/GCC1501-Release64/inc -I/build/reproducible-path/ncbi-igblast-1.19.0/c++/include /build/reproducible-path/ncbi-igblast-1.19.0/c++/src/serial/hookdatakey.cpp -o hookdatakey.o
/usr/bin/g++ -std=gnu++17 -msse4.2 -c -Wall -Wno-format-y2k -O2 -ffile-prefix-map=/build/reproducible-path/ncbi-igblast-1.19.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -DNCBI_WITHOUT_MT -I/build/reproducible-path/ncbi-igblast-1.19.0/c++/GCC1501-Release64/inc -I/build/reproducible-path/ncbi-igblast-1.19.0/c++/include /build/reproducible-path/ncbi-igblast-1.19.0/c++/src/serial/typeinfo.cpp -o typeinfo.o
make[6]: Leaving directory '/build/reproducible-path/ncbi-igblast-1.19.0/c++/GCC1501-Release64/build/serial'
FAILED: src/serial/Makefile.serial.lib
make[6]: Entering directory '/build/reproducible-path/ncbi-igblast-1.19.0/c++/GCC1501-Release64/build/serial'
/bin/rm -f libxser.a .xser.dep .libxser.a.stamp
/bin/rm -f /build/reproducible-path/ncbi-igblast-1.19.0/c++/GCC1501-Release64/lib/libxser.a /build/reproducible-path/ncbi-igblast-1.19.0/c++/GCC1501-Release64/status/.xser.dep \
/build/reproducible-path/ncbi-igblast-1.19.0/c++/GCC1501-Release64/lib/libxser-static.a /build/reproducible-path/ncbi-igblast-1.19.0/c++/GCC1501-Release64/status/.xser-static.dep
make[6]: Leaving directory '/build/reproducible-path/ncbi-igblast-1.19.0/c++/GCC1501-Release64/build/serial'
make[5]: *** [/build/reproducible-path/ncbi-igblast-1.19.0/c++/src/build-system/Makefile.meta_l:328: all.nonusr] Error 2
make[5]: Leaving directory '/build/reproducible-path/ncbi-igblast-1.19.0/c++/GCC1501-Release64/build/serial'
make[4]: *** [/build/reproducible-path/ncbi-igblast-1.19.0/c++/src/build-system/Makefile.meta_l:286: all_l.real] Error 2
make[4]: Leaving directory '/build/reproducible-path/ncbi-igblast-1.19.0/c++/GCC1501-Release64/build/serial'
make[3]: *** [/build/reproducible-path/ncbi-igblast-1.19.0/c++/src/build-system/Makefile.meta_r:41: all_r.real] Error 5
make[3]: Leaving directory '/build/reproducible-path/ncbi-igblast-1.19.0/c++/GCC1501-Release64/build'
make[2]: *** [Makefile:24: all] Error 2
make[2]: Leaving directory '/build/reproducible-path/ncbi-igblast-1.19.0/c++'
make[1]: *** [debian/rules:21: override_dh_auto_build] Error 2
make[1]: Leaving directory '/build/reproducible-path/ncbi-igblast-1.19.0'
make: *** [debian/rules:4: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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