[Debian-med-packaging] Bug#1075276: minimac4: ftbfs with GCC-14

[Matthias Klose]

Package: src:minimac4
Version: 4.1.6-1
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/minimac4_4.1.6-1_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

[...]
/usr/bin/c++ -DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.6\"  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -std=gnu++11 -MD -MT CMakeFiles/minimac4.dir/src/hidden_markov_model.cpp.o -MF CMakeFiles/minimac4.dir/src/hidden_markov_model.cpp.o.d -o CMakeFiles/minimac4.dir/src/hidden_markov_model.cpp.o -c /<<PKGBUILDDIR>>/src/hidden_markov_model.cpp
/usr/bin/c++ -DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.6\"  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -std=gnu++11 -MD -MT CMakeFiles/minimac4.dir/src/input_prep.cpp.o -MF CMakeFiles/minimac4.dir/src/input_prep.cpp.o.d -o CMakeFiles/minimac4.dir/src/input_prep.cpp.o -c /<<PKGBUILDDIR>>/src/input_prep.cpp
/usr/bin/c++ -DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.6\"  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -std=gnu++11 -MD -MT CMakeFiles/minimac4.dir/src/recombination.cpp.o -MF CMakeFiles/minimac4.dir/src/recombination.cpp.o.d -o CMakeFiles/minimac4.dir/src/recombination.cpp.o -c /<<PKGBUILDDIR>>/src/recombination.cpp
In file included from /usr/include/c++/14/cassert:44,
                 from /usr/include/savvy/compressed_vector.hpp:12,
                 from /usr/include/savvy/site_info.hpp:10,
                 from /usr/include/savvy/reader.hpp:10,
                 from /<<PKGBUILDDIR>>/src/unique_haplotype.hpp:7,
                 from /<<PKGBUILDDIR>>/src/unique_haplotype.cpp:2:
/usr/include/savvy/compressed_vector.hpp: In member function ‘AggregateT savvy::compressed_vector<T>::dot_slow(const self_type&, AggregateT) const’:
/usr/include/savvy/compressed_vector.hpp:424:7: error: assignment of member ‘savvy::compressed_vector<T>::size_’ in read-only object
  424 |       assert(size_ = other.size_);
      |       ^~~~~~
In file included from /usr/include/c++/14/cassert:44,
                 from /usr/include/savvy/compressed_vector.hpp:12,
                 from /usr/include/savvy/site_info.hpp:10,
                 from /usr/include/savvy/reader.hpp:10,
                 from /<<PKGBUILDDIR>>/src/prog_args.hpp:6,
                 from /<<PKGBUILDDIR>>/src/main.cpp:2:
/usr/include/savvy/compressed_vector.hpp: In member function ‘AggregateT savvy::compressed_vector<T>::dot_slow(const self_type&, AggregateT) const’:
/usr/include/savvy/compressed_vector.hpp:424:7: error: assignment of member ‘savvy::compressed_vector<T>::size_’ in read-only object
  424 |       assert(size_ = other.size_);
      |       ^~~~~~
In file included from /usr/include/c++/14/cassert:44,
                 from /usr/include/savvy/compressed_vector.hpp:12,
                 from /usr/include/savvy/site_info.hpp:10,
                 from /usr/include/savvy/reader.hpp:10,
                 from /<<PKGBUILDDIR>>/src/unique_haplotype.hpp:7,
                 from /<<PKGBUILDDIR>>/src/dosage_writer.hpp:5,
                 from /<<PKGBUILDDIR>>/src/dosage_writer.cpp:1:
/usr/include/savvy/compressed_vector.hpp: In member function ‘AggregateT savvy::compressed_vector<T>::dot_slow(const self_type&, AggregateT) const’:
/usr/include/savvy/compressed_vector.hpp:424:7: error: assignment of member ‘savvy::compressed_vector<T>::size_’ in read-only object
  424 |       assert(size_ = other.size_);
      |       ^~~~~~
In file included from /usr/include/c++/14/cassert:44,
                 from /usr/include/savvy/compressed_vector.hpp:12,
                 from /usr/include/savvy/site_info.hpp:10,
                 from /usr/include/savvy/reader.hpp:10,
                 from /<<PKGBUILDDIR>>/src/unique_haplotype.hpp:7,
                 from /<<PKGBUILDDIR>>/src/hidden_markov_model.hpp:4,
                 from /<<PKGBUILDDIR>>/src/hidden_markov_model.cpp:1:
/usr/include/savvy/compressed_vector.hpp: In member function ‘AggregateT savvy::compressed_vector<T>::dot_slow(const self_type&, AggregateT) const’:
/usr/include/savvy/compressed_vector.hpp:424:7: error: assignment of member ‘savvy::compressed_vector<T>::size_’ in read-only object
  424 |       assert(size_ = other.size_);
      |       ^~~~~~
In file included from /usr/include/c++/14/cassert:44,
                 from /usr/include/savvy/compressed_vector.hpp:12,
                 from /usr/include/savvy/site_info.hpp:10,
                 from /usr/include/savvy/reader.hpp:10,
                 from /<<PKGBUILDDIR>>/src/unique_haplotype.hpp:7,
                 from /<<PKGBUILDDIR>>/src/input_prep.hpp:4,
                 from /<<PKGBUILDDIR>>/src/input_prep.cpp:1:
/usr/include/savvy/compressed_vector.hpp: In member function ‘AggregateT savvy::compressed_vector<T>::dot_slow(const self_type&, AggregateT) const’:
/usr/include/savvy/compressed_vector.hpp:424:7: error: assignment of member ‘savvy::compressed_vector<T>::size_’ in read-only object
  424 |       assert(size_ = other.size_);
      |       ^~~~~~
make[3]: *** [CMakeFiles/minimac4.dir/build.make:135: CMakeFiles/minimac4.dir/src/unique_haplotype.cpp.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: *** [CMakeFiles/minimac4.dir/build.make:93: CMakeFiles/minimac4.dir/src/hidden_markov_model.cpp.o] Error 1
make[3]: *** [CMakeFiles/minimac4.dir/build.make:107: CMakeFiles/minimac4.dir/src/input_prep.cpp.o] Error 1
make[3]: *** [CMakeFiles/minimac4.dir/build.make:149: CMakeFiles/minimac4.dir/src/main.cpp.o] Error 1
make[3]: *** [CMakeFiles/minimac4.dir/build.make:79: CMakeFiles/minimac4.dir/src/dosage_writer.cpp.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:87: CMakeFiles/minimac4.dir/all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[1]: *** [Makefile:169: 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:8: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2