[Debichem-devel] Bug#1075335: openbabel: ftbfs with GCC-14

Wed Jul 3 13:38:33 BST 2024

Package: src:openbabel
Version: 3.1.1+dfsg-10
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/openbabel_3.1.1+dfsg-10_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

[...]
[ 77%] Built target pubchem
[ 77%] Building CXX object src/formats/CMakeFiles/cmlformat.dir/xml/xml.cpp.o
cd /<<PKGBUILDDIR>>/builddir/src/formats && /usr/bin/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dcmlformat_EXPORTS -I/<<PKGBUILDDIR>>/builddir/include -I/<<PKGBUILDDIR>>/data -I/<<PKGBUILDDIR>>/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/libxml2 -isystem /usr/lib/x86_64-linux-gnu/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fopenmp -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/cmlformat.dir/xml/xml.cpp.o -MF CMakeFiles/cmlformat.dir/xml/xml.cpp.o.d -o CMakeFiles/cmlformat.dir/xml/xml.cpp.o -c /<<PKGBUILDDIR>>/src/formats/xml/xml.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
[ 77%] Built target xmlformat
In file included from /<<PKGBUILDDIR>>/include/openbabel/format.h:22,
                 from /<<PKGBUILDDIR>>/include/openbabel/obconversion.h:37,
                 from /<<PKGBUILDDIR>>/include/openbabel/xml.h:21,
                 from /<<PKGBUILDDIR>>/src/formats/xml/xml.cpp:15:
/<<PKGBUILDDIR>>/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
   41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
      |                                          ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
                 from /usr/include/c++/14/bits/locale_classes.h:40,
                 from /usr/include/c++/14/bits/ios_base.h:41,
                 from /usr/include/c++/14/ios:44,
                 from /usr/include/c++/14/ostream:40,
                 from /usr/include/c++/14/iostream:41,
                 from /<<PKGBUILDDIR>>/include/openbabel/obconversion.h:24:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
make[4]: *** [src/formats/CMakeFiles/pubchemjsonformat.dir/build.make:79: src/formats/CMakeFiles/pubchemjsonformat.dir/json/pubchemjsonformat.cpp.o] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
make[3]: *** [CMakeFiles/Makefile2:4649: src/formats/CMakeFiles/pubchemjsonformat.dir/all] Error 2
[ 77%] Linking CXX shared module ../../lib/x86_64-linux-gnu/chemkinformat.so
cd /<<PKGBUILDDIR>>/builddir/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemkinformat.dir/link.txt --verbose=1
In file included from /<<PKGBUILDDIR>>/include/openbabel/format.h:22,
                 from /<<PKGBUILDDIR>>/include/openbabel/obconversion.h:37,
                 from /<<PKGBUILDDIR>>/include/openbabel/xml.h:21,
                 from /<<PKGBUILDDIR>>/src/formats/xml/xml.cpp:15:
/<<PKGBUILDDIR>>/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
   41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
      |                                          ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
                 from /usr/include/c++/14/bits/locale_classes.h:40,
                 from /usr/include/c++/14/bits/ios_base.h:41,
                 from /usr/include/c++/14/ios:44,
                 from /usr/include/c++/14/ostream:40,
                 from /usr/include/c++/14/iostream:41,
                 from /<<PKGBUILDDIR>>/include/openbabel/obconversion.h:24:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fopenmp -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -shared  -o ../../lib/x86_64-linux-gnu/chemkinformat.so CMakeFiles/chemkinformat.dir/chemkinformat.cpp.o  -lmaeparser -lcoordgen -lm -ldl -lz -lcairo -linchi -lm ../../lib/x86_64-linux-gnu/libopenbabel.so.7.0.0
make[4]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
[ 77%] Built target chemkinformat
[ 77%] Linking CXX shared module ../../lib/x86_64-linux-gnu/cmlreactformat.so
cd /<<PKGBUILDDIR>>/builddir/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmlreactformat.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fopenmp -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -shared  -o ../../lib/x86_64-linux-gnu/cmlreactformat.so CMakeFiles/cmlreactformat.dir/xml/cmlreactformat.cpp.o CMakeFiles/cmlreactformat.dir/xml/xml.cpp.o  -lmaeparser -lcoordgen -lm -ldl -lz -lcairo -linchi -lm -lxml2 ../../lib/x86_64-linux-gnu/libopenbabel.so.7.0.0
make[4]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
[ 77%] Built target cmlreactformat
[ 77%] Linking CXX shared module ../../lib/x86_64-linux-gnu/cmlformat.so
cd /<<PKGBUILDDIR>>/builddir/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmlformat.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fopenmp -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -shared  -o ../../lib/x86_64-linux-gnu/cmlformat.so CMakeFiles/cmlformat.dir/xml/cmlformat.cpp.o CMakeFiles/cmlformat.dir/xml/xml.cpp.o  -lmaeparser -lcoordgen -lm -ldl -lz -lcairo -linchi -lm -lxml2 ../../lib/x86_64-linux-gnu/libopenbabel.so.7.0.0
make[4]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
[ 77%] Built target cmlformat
[ 77%] Linking CXX shared module ../lib/x86_64-linux-gnu/plugin_charges.so
cd /<<PKGBUILDDIR>>/builddir/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/plugin_charges.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fopenmp -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -shared  -o ../lib/x86_64-linux-gnu/plugin_charges.so CMakeFiles/plugin_charges.dir/charges/eem.cpp.o CMakeFiles/plugin_charges.dir/charges/gasteiger.cpp.o CMakeFiles/plugin_charges.dir/charges/none.cpp.o CMakeFiles/plugin_charges.dir/charges/mmff94.cpp.o CMakeFiles/plugin_charges.dir/charges/fromfile.cpp.o CMakeFiles/plugin_charges.dir/charges/eqeq.cpp.o CMakeFiles/plugin_charges.dir/charges/qeq.cpp.o CMakeFiles/plugin_charges.dir/charges/qtpie.cpp.o  -lmaeparser -lcoordgen -lm -ldl -lz ../lib/x86_64-linux-gnu/libopenbabel.so.7.0.0
make[4]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
[ 77%] Built target plugin_charges
make[3]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
make[2]: *** [Makefile:149: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
dh_auto_build: error: cd builddir && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2
make[1]: *** [debian/rules:34: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:28: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2