[Debian-med-packaging] Bug#1012990: librostlab-blast: ftbfs with GCC-12
Matthias Klose
doko at debian.org
Thu Jun 16 13:11:20 BST 2022
Package: src:librostlab-blast
Version: 1.0.1-12
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/librostlab-blast_1.0.1-12_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.
[...]
| ^~~~~~~~
/usr/include/c++/12/ostream:598:5: note: template argument deduction/substitution failed:
/usr/include/rostlab/aux_functions.h:186:43: note: mismatched types ‘const _CharT*’ and ‘rostlab::blast::hit’
186 | { if( v_i != v.begin() ) os << ", "; os << *v_i; }
| ~~~^~~~~~~
/usr/include/c++/12/bits/ostream.tcc:302:5: note: candidate: ‘template<class _CharT, class _Traits> std::basic_ostream<_CharT, _Traits>& std::operator<<(basic_ostream<_CharT, _Traits>&, const char*)’
302 | operator<<(basic_ostream<_CharT, _Traits>& __out, const char* __s)
| ^~~~~~~~
/usr/include/c++/12/bits/ostream.tcc:302:5: note: template argument deduction/substitution failed:
/usr/include/rostlab/aux_functions.h:186:43: note: cannot convert ‘v_i.__gnu_cxx::__normal_iterator<const rostlab::blast::hit*, std::vector<rostlab::blast::hit> >::operator*()’ (type ‘const rostlab::blast::hit’) to type ‘const char*’
186 | { if( v_i != v.begin() ) os << ", "; os << *v_i; }
| ~~~^~~~~~~
/usr/include/c++/12/ostream:615:5: note: candidate: ‘template<class _Traits> std::basic_ostream<char, _Traits>& std::operator<<(basic_ostream<char, _Traits>&, const char*)’
615 | operator<<(basic_ostream<char, _Traits>& __out, const char* __s)
| ^~~~~~~~
/usr/include/c++/12/ostream:615:5: note: template argument deduction/substitution failed:
/usr/include/rostlab/aux_functions.h:186:43: note: cannot convert ‘v_i.__gnu_cxx::__normal_iterator<const rostlab::blast::hit*, std::vector<rostlab::blast::hit> >::operator*()’ (type ‘const rostlab::blast::hit’) to type ‘const char*’
186 | { if( v_i != v.begin() ) os << ", "; os << *v_i; }
| ~~~^~~~~~~
/usr/include/c++/12/ostream:628:5: note: candidate: ‘template<class _Traits> std::basic_ostream<char, _Traits>& std::operator<<(basic_ostream<char, _Traits>&, const signed char*)’
628 | operator<<(basic_ostream<char, _Traits>& __out, const signed char* __s)
| ^~~~~~~~
/usr/include/c++/12/ostream:628:5: note: template argument deduction/substitution failed:
/usr/include/rostlab/aux_functions.h:186:43: note: cannot convert ‘v_i.__gnu_cxx::__normal_iterator<const rostlab::blast::hit*, std::vector<rostlab::blast::hit> >::operator*()’ (type ‘const rostlab::blast::hit’) to type ‘const signed char*’
186 | { if( v_i != v.begin() ) os << ", "; os << *v_i; }
| ~~~^~~~~~~
/usr/include/c++/12/ostream:633:5: note: candidate: ‘template<class _Traits> std::basic_ostream<char, _Traits>& std::operator<<(basic_ostream<char, _Traits>&, const unsigned char*)’
633 | operator<<(basic_ostream<char, _Traits>& __out, const unsigned char* __s)
| ^~~~~~~~
/usr/include/c++/12/ostream:633:5: note: template argument deduction/substitution failed:
/usr/include/rostlab/aux_functions.h:186:43: note: cannot convert ‘v_i.__gnu_cxx::__normal_iterator<const rostlab::blast::hit*, std::vector<rostlab::blast::hit> >::operator*()’ (type ‘const rostlab::blast::hit’) to type ‘const unsigned char*’
186 | { if( v_i != v.begin() ) os << ", "; os << *v_i; }
| ~~~^~~~~~~
/usr/include/c++/12/ostream:754:5: note: candidate: ‘template<class _Ostream, class _Tp> _Ostream&& std::operator<<(_Ostream&&, const _Tp&)’
754 | operator<<(_Ostream&& __os, const _Tp& __x)
| ^~~~~~~~
/usr/include/c++/12/ostream:754:5: note: template argument deduction/substitution failed:
/usr/include/c++/12/ostream: In substitution of ‘template<class _Ostream, class _Tp> _Ostream&& std::operator<<(_Ostream&&, const _Tp&) [with _Ostream = std::basic_ostream<char>&; _Tp = rostlab::blast::hit]’:
/usr/include/rostlab/aux_functions.h:186:43: required from ‘std::ostream& rostlab::operator<<(std::ostream&, const std::vector<_Tp, _Alloc>&) [with _Tp = blast::hit; _Alloc = std::allocator<blast::hit>; std::ostream = std::basic_ostream<char>]’
./rostlab/blast-result.h:247:66: required from here
/usr/include/c++/12/ostream:754:5: error: no type named ‘type’ in ‘struct std::enable_if<false, void>’
/usr/include/rostlab/aux_functions.h: In instantiation of ‘std::ostream& rostlab::operator<<(std::ostream&, const std::vector<_Tp, _Alloc>&) [with _Tp = blast::hit; _Alloc = std::allocator<blast::hit>; std::ostream = std::basic_ostream<char>]’:
./rostlab/blast-result.h:247:66: required from here
rostlab/blast-parser-location.h:158:3: note: candidate: ‘template<class YYChar> std::basic_ostream<YYChar>& rostlab::blast::operator<<(std::basic_ostream<YYChar>&, const position&)’
158 | operator<< (std::basic_ostream<YYChar>& ostr, const position& pos)
| ^~~~~~~~
rostlab/blast-parser-location.h:158:3: note: template argument deduction/substitution failed:
/usr/include/rostlab/aux_functions.h:186:43: note: cannot convert ‘v_i.__gnu_cxx::__normal_iterator<const rostlab::blast::hit*, std::vector<rostlab::blast::hit> >::operator*()’ (type ‘const rostlab::blast::hit’) to type ‘const rostlab::blast::position&’
186 | { if( v_i != v.begin() ) os << ", "; os << *v_i; }
| ~~~^~~~~~~
rostlab/blast-parser-location.h:286:3: note: candidate: ‘template<class YYChar> std::basic_ostream<YYChar>& rostlab::blast::operator<<(std::basic_ostream<YYChar>&, const location&)’
286 | operator<< (std::basic_ostream<YYChar>& ostr, const location& loc)
| ^~~~~~~~
rostlab/blast-parser-location.h:286:3: note: template argument deduction/substitution failed:
/usr/include/rostlab/aux_functions.h:186:43: note: cannot convert ‘v_i.__gnu_cxx::__normal_iterator<const rostlab::blast::hit*, std::vector<rostlab::blast::hit> >::operator*()’ (type ‘const rostlab::blast::hit’) to type ‘const rostlab::blast::location&’
186 | { if( v_i != v.begin() ) os << ", "; os << *v_i; }
| ~~~^~~~~~~
make[5]: *** [Makefile:575: librostlab_blast_la-librostlab_blast_la-blast-parser-scanner.lo] Error 1
make[5]: Leaving directory '/<<PKGBUILDDIR>>/lib'
make[4]: *** [Makefile:445: all] Error 2
make[4]: Leaving directory '/<<PKGBUILDDIR>>/lib'
make[3]: *** [Makefile:484: all-recursive] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: *** [Makefile:395: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j8 returned exit code 2
make[1]: *** [debian/rules:23: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:8: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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