[Debian-med-packaging] Bug#1097910: sortmerna: ftbfs with GCC-15
Matthias Klose
doko at debian.org
Mon Feb 17 17:54:20 GMT 2025
Package: src:sortmerna
Version: 4.3.7-2
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/sortmerna_4.3.7-2_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/sortmerna-4.3.7/include/kseq_load.hpp:43:1: note: in expansion of macro ‘KSEQ_INIT’
43 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
[ 74%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/read.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/read.cpp.o -MF CMakeFiles/smr_objs.dir/read.cpp.o.d -o CMakeFiles/smr_objs.dir/read.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/read.cpp
[ 76%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/readfeed.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/readfeed.cpp.o -MF CMakeFiles/smr_objs.dir/readfeed.cpp.o.d -o CMakeFiles/smr_objs.dir/readfeed.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp
[ 77%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/readstats.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/readstats.cpp.o -MF CMakeFiles/smr_objs.dir/readstats.cpp.o.d -o CMakeFiles/smr_objs.dir/readstats.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readstats.cpp
[ 78%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/references.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/references.cpp.o -MF CMakeFiles/smr_objs.dir/references.cpp.o.d -o CMakeFiles/smr_objs.dir/references.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/references.cpp
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp: In member function ‘void Readfeed::init(std::vector<std::__cxx11::basic_string<char> >&, const int&)’:
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp:105:69: warning: unused parameter ‘dbg’ [-Wunused-parameter]
105 | void Readfeed::init(std::vector<std::string>& readfiles, const int& dbg)
| ~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp: In static member function ‘static bool Readfeed::loadReadByIdx(Read&)’:
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp:187:37: warning: unused parameter ‘read’ [-Wunused-parameter]
187 | bool Readfeed::loadReadByIdx(Read & read)
| ~~~~~~~^~~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp: In static member function ‘static bool Readfeed::loadReadById(Read&)’:
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp:271:35: warning: unused parameter ‘read’ [-Wunused-parameter]
271 | bool Readfeed::loadReadById(Read& read)
| ~~~~~~^~~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp: In static member function ‘static bool Readfeed::hasnext(std::ifstream&)’:
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp:553:39: warning: unused parameter ‘ifs’ [-Wunused-parameter]
553 | bool Readfeed::hasnext(std::ifstream& ifs)
| ~~~~~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp: In member function ‘bool Readfeed::define_format(const int&)’:
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp:857:36: warning: comparison is always false due to limited range of data type [-Wtype-limits]
857 | if (str[i] > 127 || str[i] < 0) {
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/read.cpp: In member function ‘void Read::unmarshallJson(KeyValueDatabase&)’:
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/read.cpp:540:46: warning: unused parameter ‘kvdb’ [-Wunused-parameter]
540 | void Read::unmarshallJson(KeyValueDatabase & kvdb)
| ~~~~~~~~~~~~~~~~~~~^~~~
[ 80%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/refstats.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/refstats.cpp.o -MF CMakeFiles/smr_objs.dir/refstats.cpp.o.d -o CMakeFiles/smr_objs.dir/refstats.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/refstats.cpp
In file included from /build/reproducible-path/sortmerna-4.3.7/include/kseq_load.hpp:40,
from /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readstats.cpp:52:
/build/reproducible-path/sortmerna-4.3.7/include/kseq.h:171:20: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function]
171 | static int kseq_read(kseq_t *seq) \
| ^~~~~~~~~
/build/reproducible-path/sortmerna-4.3.7/include/kseq.h:221:9: note: in expansion of macro ‘__KSEQ_READ’
221 | __KSEQ_READ
| ^~~~~~~~~~~
/build/reproducible-path/sortmerna-4.3.7/include/kseq_load.hpp:43:1: note: in expansion of macro ‘KSEQ_INIT’
43 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
[ 81%] Building C object src/sortmerna/CMakeFiles/smr_objs.dir/ssw.c.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/ssw.c.o -MF CMakeFiles/smr_objs.dir/ssw.c.o.d -o CMakeFiles/smr_objs.dir/ssw.c.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/ssw.c
In file included from /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/ssw.c:52:
/build/reproducible-path/sortmerna-4.3.7/include/ssw.h:38:23: error: ‘bool’ cannot be defined via ‘typedef’
38 | typedef unsigned char bool;
| ^~~~
/build/reproducible-path/sortmerna-4.3.7/include/ssw.h:38:23: note: ‘bool’ is a keyword with ‘-std=c23’ onwards
/build/reproducible-path/sortmerna-4.3.7/include/ssw.h:38:1: warning: useless type name in empty declaration
38 | typedef unsigned char bool;
| ^~~~~~~
make[3]: *** [src/sortmerna/CMakeFiles/smr_objs.dir/build.make:334: src/sortmerna/CMakeFiles/smr_objs.dir/ssw.c.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build'
make[2]: *** [CMakeFiles/Makefile2:257: src/sortmerna/CMakeFiles/smr_objs.dir/all] Error 2
make[2]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build'
make[1]: *** [Makefile:159: all] Error 2
make[1]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build'
dh_auto_build: error: cd .pybuild/cpython3_3.13/build && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2
E: pybuild pybuild:389: build: plugin cmake failed with: exit code=25: dh_auto_build --buildsystem=cmake --builddirectory=/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build --
dh_auto_build: error: pybuild --build -i python{version} -p "3.12 3.13" returned exit code 13
make: *** [debian/rules:19: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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