[Debichem-devel] Bug#984199: libpappsomspp: ftbfs with GCC-11
Matthias Klose
doko at debian.org
Wed Mar 3 16:14:50 GMT 2021
Package: src:libpappsomspp
Version: 0.8.15-1
Severity: normal
Tags: sid bookworm
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-11
[This bug is not targeted to the upcoming bullseye 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-11/g++-11, but succeeds to build with gcc-10/g++-10. The
severity of this report will be raised before the bookworm release,
so nothing has to be done for the bullseye release.
The full build log can be found at:
http://people.debian.org/~doko/logs/20210228/filtered/gcc11/libpappsomspp_0.8.15-1_unstable_gcc11.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.
[...]
/<<PKGBUILDDIR>>/src/pappsomspp/processing/tandemwrapper/xtandempresetsaxhandler.cpp:184:72: warning: ‘QXmlParseException’ is deprecated [-Wdeprecated-declarations]
184 | XtandemPresetSaxHandler::fatalError(const QXmlParseException &exception)
| ^
[ 10%] Building CXX object src/CMakeFiles/pappsomspp-shared.dir/pappsomspp/massspectrum/massspectrumid.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DQT_CONCURRENT_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_NO_DEBUG_OUTPUT -DQT_PRINTSUPPORT_LIB -DQT_SQL_LIB -DQT_SVG_LIB -DQT_WIDGETS_LIB -DQT_XML_LIB -DWITHOUT_MZ5 -Dpappsomspp_shared_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/pappsomspp-shared_autogen/include -isystem /usr/include/pwizlite -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtSvg -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtPrintSupport -isystem /usr/include/x86_64-linux-gnu/qt5/QtSql -isystem /usr/include/x86_64-linux-gnu/qt5/QtConcurrent -isystem /usr/include/libalglib -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -fPIC -std=gnu++17 -o CMakeFiles/pappsomspp-shared.dir/pappsomspp/massspectrum/massspectrumid.cpp.o -c /<<PKGBUILDDIR>>/src/pappsomspp/massspectrum/massspectrumid.cpp
In file included from /<<PKGBUILDDIR>>/src/pappsomspp/massspectrum/massspectrumid.cpp:25:
/<<PKGBUILDDIR>>/src/pappsomspp/massspectrum/massspectrumid.h:54:38: error: ‘numeric_limits’ is not a member of ‘std’
54 | std::size_t m_spectrumIndex = std::numeric_limits<std::size_t>::max();
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/pappsomspp/massspectrum/massspectrumid.h:54:64: error: expected primary-expression before ‘>’ token
54 | std::size_t m_spectrumIndex = std::numeric_limits<std::size_t>::max();
| ^
/<<PKGBUILDDIR>>/src/pappsomspp/massspectrum/massspectrumid.h:54:67: error: ‘::max’ has not been declared
54 | std::size_t m_spectrumIndex = std::numeric_limits<std::size_t>::max();
| ^~~
/<<PKGBUILDDIR>>/src/pappsomspp/massspectrum/massspectrumid.h:54:67: note: suggested alternatives:
In file included from /usr/include/c++/11/algorithm:62,
from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:142,
from /usr/include/x86_64-linux-gnu/qt5/QtCore/qchar.h:43,
from /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:49,
from /usr/include/x86_64-linux-gnu/qt5/QtCore/QString:1,
from /<<PKGBUILDDIR>>/src/pappsomspp/massspectrum/massspectrumid.h:27,
from /<<PKGBUILDDIR>>/src/pappsomspp/massspectrum/massspectrumid.cpp:25:
/usr/include/c++/11/bits/stl_algo.h:3467:5: note: ‘std::max’
3467 | max(initializer_list<_Tp> __l, _Compare __comp)
| ^~~
In file included from /<<PKGBUILDDIR>>/src/pappsomspp/massspectrum/../msrun/msrunid.h:37,
from /<<PKGBUILDDIR>>/src/pappsomspp/massspectrum/massspectrumid.h:31,
from /<<PKGBUILDDIR>>/src/pappsomspp/massspectrum/massspectrumid.cpp:25:
/<<PKGBUILDDIR>>/src/pappsomspp/massspectrum/../msrun/../types.h:202:3: note: ‘pappso::XicExtractMethod::max’
202 | max = 2 ///< maximum of intensities
| ^~~
/<<PKGBUILDDIR>>/src/pappsomspp/massspectrum/massspectrumid.cpp: In member function ‘bool pappso::MassSpectrumId::isValid() const’:
/<<PKGBUILDDIR>>/src/pappsomspp/massspectrum/massspectrumid.cpp:127:34: error: ‘numeric_limits’ is not a member of ‘std’
127 | m_spectrumIndex != std::numeric_limits<std::size_t>::max();
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/pappsomspp/massspectrum/massspectrumid.cpp:127:60: error: expected primary-expression before ‘>’ token
127 | m_spectrumIndex != std::numeric_limits<std::size_t>::max();
| ^
/<<PKGBUILDDIR>>/src/pappsomspp/massspectrum/massspectrumid.cpp:127:63: error: ‘::max’ has not been declared
127 | m_spectrumIndex != std::numeric_limits<std::size_t>::max();
| ^~~
/<<PKGBUILDDIR>>/src/pappsomspp/massspectrum/massspectrumid.cpp:127:63: note: suggested alternatives:
In file included from /usr/include/c++/11/algorithm:62,
from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:142,
from /usr/include/x86_64-linux-gnu/qt5/QtCore/qchar.h:43,
from /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:49,
from /usr/include/x86_64-linux-gnu/qt5/QtCore/QString:1,
from /<<PKGBUILDDIR>>/src/pappsomspp/massspectrum/massspectrumid.h:27,
from /<<PKGBUILDDIR>>/src/pappsomspp/massspectrum/massspectrumid.cpp:25:
/usr/include/c++/11/bits/stl_algo.h:3467:5: note: ‘std::max’
3467 | max(initializer_list<_Tp> __l, _Compare __comp)
| ^~~
In file included from /<<PKGBUILDDIR>>/src/pappsomspp/massspectrum/../msrun/msrunid.h:37,
from /<<PKGBUILDDIR>>/src/pappsomspp/massspectrum/massspectrumid.h:31,
from /<<PKGBUILDDIR>>/src/pappsomspp/massspectrum/massspectrumid.cpp:25:
/<<PKGBUILDDIR>>/src/pappsomspp/massspectrum/../msrun/../types.h:202:3: note: ‘pappso::XicExtractMethod::max’
202 | max = 2 ///< maximum of intensities
| ^~~
make[4]: *** [src/CMakeFiles/pappsomspp-shared.dir/build.make:429: src/CMakeFiles/pappsomspp-shared.dir/pappsomspp/massspectrum/massspectrumid.cpp.o] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:332: src/CMakeFiles/pappsomspp-shared.dir/all] Error 2
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [Makefile:174: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j1 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2
make[1]: *** [debian/rules:30: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:15: build] Error 2
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
More information about the Debichem-devel
mailing list