[Debian-med-packaging] Bug#1012983: libpdb-redo: ftbfs with GCC-12
Matthias Klose
doko at debian.org
Thu Jun 16 13:11:09 BST 2022
Package: src:libpdb-redo
Version: 2.0.3-1
Severity: normal
Tags: sid bookworm
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-12
[This bug is targeted to the upcoming bookworm 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-12/g++-12, but succeeds to build with gcc-11/g++-11. The
severity of this report will be raised before the bookworm release.
The full build log can be found at:
http://qa-logs.debian.net/2022/06/09/gcc12/libpdb-redo_2.0.3-1_unstable_gcc12.log
The last lines of the build log are at the end of this report.
To build with GCC 11, either set CC=gcc-11 CXX=g++-11 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-11/porting_to.html
GCC 11 defaults to the GNU++17 standard. If your package installs
header files in /usr/include, please don't work around C++17 issues
by choosing a lower C++ standard for the package build, but fix these
issues to build with the C++17 standard.
[...]
| ^~~~~~
[ 75%] Building CXX object CMakeFiles/pdb-redo.dir/src/Symmetry-2.cpp.o
/usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_REGEX_DYN_LINK -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>>/PRIVATE -I/<<PKGBUILDDIR>>/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -fPIC -std=gnu++17 -MD -MT CMakeFiles/pdb-redo.dir/src/Symmetry-2.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Symmetry-2.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Symmetry-2.cpp.o -c /<<PKGBUILDDIR>>/src/Symmetry-2.cpp
In file included from /<<PKGBUILDDIR>>/src/DistanceMap.cpp:34:
/<<PKGBUILDDIR>>/include/pdb-redo/Symmetry-2.hpp: At global scope:
/<<PKGBUILDDIR>>/include/pdb-redo/Symmetry-2.hpp:61:50: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
61 | class SymmetryAtomIterator : public std::iterator<std::forward_iterator_tag, const mmcif::Atom>
| ^~~~~~~~
In file included from /usr/include/c++/12/string:45,
from /usr/include/c++/12/stdexcept:39,
from /usr/include/c++/12/system_error:41,
from /usr/include/c++/12/mutex:41,
from /<<PKGBUILDDIR>>/src/DistanceMap.cpp:28:
/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here
127 | struct _GLIBCXX17_DEPRECATED iterator
| ^~~~~~~~
/<<PKGBUILDDIR>>/include/pdb-redo/Symmetry-2.hpp:64:30: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
64 | typedef std::iterator<std::forward_iterator_tag, const mmcif::Atom> baseType;
| ^~~~~~~~
/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here
127 | struct _GLIBCXX17_DEPRECATED iterator
| ^~~~~~~~
make[3]: *** [CMakeFiles/pdb-redo.dir/build.make:79: CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: *** [CMakeFiles/pdb-redo.dir/build.make:93: CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o] Error 1
make[3]: *** [CMakeFiles/pdb-redo.dir/build.make:107: CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o] Error 1
In file included from /usr/include/cif++/Structure.hpp:32,
from /<<PKGBUILDDIR>>/include/pdb-redo/ClipperWrapper.hpp:29,
from /<<PKGBUILDDIR>>/src/Symmetry-2.cpp:33:
/usr/include/cif++/Cif++.hpp: In static member function ‘static int cif::detail::ItemReference::item_value_as<char [N]>::compare(const cif::detail::ItemReference&, const char (&)[N], bool)’:
/usr/include/cif++/Cif++.hpp:548:81: error: ‘strcmp’ is not a member of ‘std’
548 | return icase ? cif::icompare(ref.c_str(), value) : std::strcmp(ref.c_str(), value);
| ^~~~~~
/usr/include/cif++/Cif++.hpp: In static member function ‘static int cif::detail::ItemReference::item_value_as<const char*>::compare(const cif::detail::ItemReference&, const char*, bool)’:
/usr/include/cif++/Cif++.hpp:562:81: error: ‘strcmp’ is not a member of ‘std’
562 | return icase ? cif::icompare(ref.c_str(), value) : std::strcmp(ref.c_str(), value);
| ^~~~~~
/usr/include/cif++/Cif++.hpp: In static member function ‘static int cif::detail::ItemReference::item_value_as<std::__cxx11::basic_string<char> >::compare(const cif::detail::ItemReference&, const std::string&, bool)’:
/usr/include/cif++/Cif++.hpp:576:81: error: ‘strcmp’ is not a member of ‘std’
576 | return icase ? cif::icompare(ref.c_str(), value) : std::strcmp(ref.c_str(), value.c_str());
| ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/Symmetry-2.cpp:34:
/<<PKGBUILDDIR>>/include/pdb-redo/Symmetry-2.hpp: At global scope:
/<<PKGBUILDDIR>>/include/pdb-redo/Symmetry-2.hpp:61:50: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
61 | class SymmetryAtomIterator : public std::iterator<std::forward_iterator_tag, const mmcif::Atom>
| ^~~~~~~~
In file included from /usr/include/c++/12/string:45,
from /usr/include/c++/12/stdexcept:39,
from /usr/include/c++/12/system_error:41,
from /usr/include/c++/12/mutex:41,
from /<<PKGBUILDDIR>>/src/Symmetry-2.cpp:28:
/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here
127 | struct _GLIBCXX17_DEPRECATED iterator
| ^~~~~~~~
/<<PKGBUILDDIR>>/include/pdb-redo/Symmetry-2.hpp:64:30: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
64 | typedef std::iterator<std::forward_iterator_tag, const mmcif::Atom> baseType;
| ^~~~~~~~
/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here
127 | struct _GLIBCXX17_DEPRECATED iterator
| ^~~~~~~~
make[3]: *** [CMakeFiles/pdb-redo.dir/build.make:177: CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o] Error 1
make[3]: *** [CMakeFiles/pdb-redo.dir/build.make:191: CMakeFiles/pdb-redo.dir/src/Symmetry-2.cpp.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:845: CMakeFiles/pdb-redo.dir/all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[1]: *** [Makefile:149: 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:11: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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