Your message dated Wed, 10 Nov 2021 23:03:50 +0000 with message-id <e1mkwdc-0001vk...@fasolo.debian.org> and subject line Bug#984199: fixed in libpappsomspp 0.8.39-1 has caused the Debian Bug report #984199, regarding libpappsomspp: ftbfs with GCC-11 to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 984199: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=984199 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: src:libpappsomspp Version: 0.8.15-1 Severity: normal Tags: sid bookworm User: debian-...@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/x 86_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
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--- Begin Message ---Source: libpappsomspp Source-Version: 0.8.39-1 Done: Filippo Rusconi <lopi...@debian.org> We believe that the bug you reported is fixed in the latest version of libpappsomspp, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 984...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Filippo Rusconi <lopi...@debian.org> (supplier of updated libpappsomspp package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 10 Nov 2021 16:32:10 +0100 Source: libpappsomspp Architecture: source Version: 0.8.39-1 Distribution: unstable Urgency: low Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org> Changed-By: Filippo Rusconi <lopi...@debian.org> Closes: 984199 Changes: libpappsomspp (0.8.39-1) unstable; urgency=low . * New upstream version (see below). . * Fixes to the build by adding #include <limits> where required (build with g++ v 11.2.0). . Many thanks to Adrian Bunk <b...@debian.org> for the patch (although not applied as-is). Closes: #984199. . * Bump-up Standards to 4.6.0 . * Add watch file that points to the forgemia GitLab repos instance. Checksums-Sha1: 349e284327b5720269ffbb6ba3aa283095229384 2680 libpappsomspp_0.8.39-1.dsc ce64a7a35d4f06a046842637d55c3c827bcedb77 902068 libpappsomspp_0.8.39.orig.tar.gz 49c6d619b1eaf2453ab6d3e62cd3f93d53432189 9860 libpappsomspp_0.8.39-1.debian.tar.xz a8b3df1f0811ce56a61eb59b2450e816fb7c090d 14006 libpappsomspp_0.8.39-1_amd64.buildinfo Checksums-Sha256: d8a4b23e545ed40324d229fd08af42954f34ec61062fa5c96901f0c239820a9d 2680 libpappsomspp_0.8.39-1.dsc 21750af5a6fc3511456a35ce8d7735b21a1f04f57db8b25d8a6f880b987929b8 902068 libpappsomspp_0.8.39.orig.tar.gz f29d7d2fb7a4cd82729a0b998367636bc4f537efa0a8ae3e02edaed25c9b1dd3 9860 libpappsomspp_0.8.39-1.debian.tar.xz 3ff8eb84ab25ce1cf6d0411d8edc9293f0c513ca0a9c8da28236ce286f57f11a 14006 libpappsomspp_0.8.39-1_amd64.buildinfo Files: 181a2671afd3222842a5fe71b2f12bc9 2680 libs optional libpappsomspp_0.8.39-1.dsc 342ef13fe2dfad841a82fad00dbbfaf9 902068 libs optional libpappsomspp_0.8.39.orig.tar.gz 1d18cbf231f0b9cd2baea4d19e54e913 9860 libs optional libpappsomspp_0.8.39-1.debian.tar.xz 34aa121683cd242dc1163febb3b9a7f4 14006 libs optional libpappsomspp_0.8.39-1_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEsFMwThfW1Bndm0ZRQatITXaUz0IFAmGMS7YACgkQQatITXaU z0IhqQ/9EwM71wVs5zekJ9Cpa7kYQsf8fjuWhEVaakEOcapYdEE39rjRmUUJTmlm D3sAmvrNcGWqTPIoq8+r4qLvfnuL0PLadKwS+PX0EPykf3iOUJ7OnD1cIxqmTp0g o3qX/PDbKDJmL0cwKrhXsRhSULJNuxA0JYul1CjV2NhIrVR63zT+IgyQX0OJ4TWW qw/xurzY2BSp8jdQ9ySQMEZTh+CUQ22qVZUfRWGUdrP0EEtT0Bc/AF+ePmnxpac6 HUmSWzo1i7Tz6M4RrIp9IXGnopCEKDoLW99Ak9YCZoAxlpM6aFle4nl1G3KpiZC4 aRV7n5pbSeoF7CZg/l2vbfrvKByuEHbWCQE08bZygEffVR5wYTyQeLfjgh6SaYXy 3qQ1VxG6Sdr5dHO49RHCKqgxTqKqPKUH7hxQJQmx7bCDmDiZTmuYOwd2o0C7fri8 vSdQKvMmFOW4H2wV5OXZlRC3J3f8GLRr1jjcnYOgHeODEJi680l1cYY+yn1u/B1E 7kfaKBH7PN76sIf32jFP4POB0FfhAProieee+T1nUzgcJBUkvr2FXg71ezyXCjxO 2NnQRfwL6biBbmlAVssf2CxDR425caldQHKwcUOSzTCuvRkXWvzp1IoSDVBg4T3I XjYwqPjzuPhRgWnh3uRTa67yE8DTX9y3SLFGdV4jP9pfBIX0lbg= =4bsi -----END PGP SIGNATURE-----
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