Your message dated Mon, 04 Jan 2021 22:05:02 +0000 with message-id <e1kwxyi-000iib...@fasolo.debian.org> and subject line Bug#978194: fixed in openms 2.6.0+cleaned1-2 has caused the Debian Bug report #978194, regarding openms: FTBFS: glpk.h:36:16: error: using typedef-name ‘glp_prob’ after ‘struct’ 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.) -- 978194: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=978194 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: openms Version: 2.6.0+cleaned1-1 Severity: serious Justification: FTBFS on amd64 Tags: bullseye sid ftbfs Usertags: ftbfs-20201226 ftbfs-bullseye Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/openms && /usr/bin/c++ > -DBOOST_ALL_NO_LIB -DOpenMS_EXPORTS -DQT_CORE_LIB -DQT_NETWORK_LIB > -DQT_NO_DEBUG -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/openms > -I/<<PKGBUILDDIR>>/src/openms > -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/openms/OpenMS_autogen/include > -I/<<PKGBUILDDIR>>/src/openms/include > -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/openms/include -isystem /usr/lib > -isystem /usr/lib/x86_64-linux-gnu/include -isystem > /<<PKGBUILDDIR>>/src/openms/thirdparty/evergreen/src -isystem > /usr/include/hdf5/serial -isystem /usr/include/libsvm -isystem > /usr/include/eigen3 -isystem /usr/include/libwildmagic -isystem > /<<PKGBUILDDIR>>/src/openswathalgo/include -isystem > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/openswathalgo/include -isystem > /<<PKGBUILDDIR>>/src/openswathalgo/thirdparty/MIToolbox/include -isystem > /<<PKGBUILDDIR>>/src/openswathalgo/thirdparty/MIToolbox/src -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/QtNetwork -isystem > /<<PKGBUILDDIR>>/src/openms/thirdparty/eol-bspline -isystem > /<<PKGBUILDDIR>>/src/openms/thirdparty/IsoSpec -isystem > /<<PKGBUILDDIR>>/src/openms/thirdparty/json -g -O2 > -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC > -fvisibility=hidden -fvisibility-inlines-hidden -Wall -Wextra > -Wno-non-virtual-dtor -Wno-unknown-pragmas -Wno-long-long > -Wno-unused-function -Wno-variadic-macros -fPIC -fopenmp -o > CMakeFiles/OpenMS.dir/source/DATASTRUCTURES/LPWrapper.cpp.o -c > /<<PKGBUILDDIR>>/src/openms/source/DATASTRUCTURES/LPWrapper.cpp > In file included from > /<<PKGBUILDDIR>>/src/openms/source/DATASTRUCTURES/LPWrapper.cpp:63: > /usr/include/glpk.h:36:16: error: using typedef-name ‘glp_prob’ after ‘struct’ > 36 | typedef struct glp_prob glp_prob; > | ^~~~~~~~ > In file included from > /<<PKGBUILDDIR>>/src/openms/source/DATASTRUCTURES/LPWrapper.cpp:37: > /<<PKGBUILDDIR>>/src/openms/include/OpenMS/DATASTRUCTURES/LPWrapper.h:58:3: > note: ‘glp_prob’ has a previous declaration here > 58 | } glp_prob; > | ^~~~~~~~ > In file included from > /<<PKGBUILDDIR>>/src/openms/source/DATASTRUCTURES/LPWrapper.cpp:63: > /usr/include/glpk.h:36:25: error: conflicting declaration ‘typedef int > glp_prob’ > 36 | typedef struct glp_prob glp_prob; > | ^~~~~~~~ > In file included from > /<<PKGBUILDDIR>>/src/openms/source/DATASTRUCTURES/LPWrapper.cpp:37: > /<<PKGBUILDDIR>>/src/openms/include/OpenMS/DATASTRUCTURES/LPWrapper.h:58:3: > note: previous declaration as ‘typedef struct glp_prob glp_prob’ > 58 | } glp_prob; > | ^~~~~~~~ > /<<PKGBUILDDIR>>/src/openms/source/DATASTRUCTURES/LPWrapper.cpp: In member > function ‘void OpenMS::LPWrapper::readProblem(const OpenMS::String&, const > OpenMS::String&)’: > /<<PKGBUILDDIR>>/src/openms/source/DATASTRUCTURES/LPWrapper.cpp:472:69: > warning: unused parameter ‘format’ [-Wunused-parameter] > 472 | void LPWrapper::readProblem(const String& filename, const String& > format) // format=(LP,MPS,GLPK) > | > ~~~~~~~~~~~~~~^~~~~~ > /<<PKGBUILDDIR>>/src/openms/source/DATASTRUCTURES/LPWrapper.cpp: In member > function ‘OpenMS::Int > OpenMS::LPWrapper::solve(OpenMS::LPWrapper::SolverParam&, OpenMS::Size)’: > /<<PKGBUILDDIR>>/src/openms/source/DATASTRUCTURES/LPWrapper.cpp:529:37: > warning: unused parameter ‘solver_param’ [-Wunused-parameter] > 529 | Int LPWrapper::solve(SolverParam& solver_param, const Size > | ~~~~~~~~~~~~~^~~~~~~~~~~~ > make[5]: *** [src/openms/CMakeFiles/OpenMS.dir/build.make:1168: > src/openms/CMakeFiles/OpenMS.dir/source/DATASTRUCTURES/LPWrapper.cpp.o] Error > 1 The full build log is available from: http://qa-logs.debian.net/2020/12/26/openms_2.6.0+cleaned1-1_unstable.log A list of current common problems and possible solutions is available at http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! If you reassign this bug to another package, please marking it as 'affects'-ing this package. See https://www.debian.org/Bugs/server-control#affects If you fail to reproduce this, please provide a build log and diff it with me so that we can identify if something relevant changed in the meantime. About the archive rebuild: The rebuild was done on EC2 VM instances from Amazon Web Services, using a clean, minimal and up-to-date chroot. Every failed build was retried once to eliminate random failures.
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--- Begin Message ---Source: openms Source-Version: 2.6.0+cleaned1-2 Done: Filippo Rusconi <lopi...@debian.org> We believe that the bug you reported is fixed in the latest version of openms, 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 978...@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 openms 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: Mon, 04 Jan 2021 20:12:34 +0100 Source: openms Architecture: source Version: 2.6.0+cleaned1-2 Distribution: unstable Urgency: low Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org> Changed-By: Filippo Rusconi <lopi...@debian.org> Closes: 978194 Changes: openms (2.6.0+cleaned1-2) unstable; urgency=low . * Implement the patch by Logan Rosen <lo...@ubuntu.com> to fix the GLPK version check that doesn't account for major version, fixing FTBFS against GLPK 5. Thanks, Logan! Closes: #978194. Patch suggested upstream. Checksums-Sha1: e0cda83a360fa189dd105962e1a42212a613fb5e 2988 openms_2.6.0+cleaned1-2.dsc 80175d35933a8efe60adc9016e9f587ca385f344 22276 openms_2.6.0+cleaned1-2.debian.tar.xz 08213417420af0a28e055bd5ed5ea80044f451f4 18500 openms_2.6.0+cleaned1-2_amd64.buildinfo Checksums-Sha256: 38cc9915cf7d5e694b0b25479b3e27d0daeaf73d3aad8cbcb71f1ab7bb5be18a 2988 openms_2.6.0+cleaned1-2.dsc eccb4f004f9efbeca0508064a3a6ac51784ef4d1a0f0eefde0f90928ee5a7836 22276 openms_2.6.0+cleaned1-2.debian.tar.xz 9312571026316d522050db7b2fe2078b32ad85d7363421dfa773aff0a8f30a5b 18500 openms_2.6.0+cleaned1-2_amd64.buildinfo Files: 91eca50a523068785f209fb758f87cea 2988 science optional openms_2.6.0+cleaned1-2.dsc 8f911a400219959f8fbd48edc1fccbe9 22276 science optional openms_2.6.0+cleaned1-2.debian.tar.xz 42a1cb5cfe0cfa84d442c5b1174cd9bc 18500 science optional openms_2.6.0+cleaned1-2_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEsFMwThfW1Bndm0ZRQatITXaUz0IFAl/zi04ACgkQQatITXaU z0L0qg//RdQ+GrxnJz7zTRAjurwBBVcH44nneNZ7p0JT0q2cjHxLAjx4mDAcSUw9 0N32iUi1vPtMJvpeoVIDC1R/EN14OJbc9a/RmVcBNo3JPhttSF4lnp9yeJsV0PcD /rxAkBZneIg/QvQGKJgNqS1l+ZZjsylfGJPImDevjk7/fmNGknRbikAaUyuG+lY4 4gIYvBrFtPEdTb0qFV0GOK7OhiVWCvNw1bv7s8v/P3jPrjd1LNakNbhX0qgFW62+ EIiKmDEDVFbGaKMslvw1EoxcJYdMdDn6nOT2JfojtSLBRfypWr4m4NW16f5ZcSWM wuGYvt2TP4PxLr7pbHWxGcgv8SoMdZGxRchKwNbYF381dHrTsMpFUq150A2oApCi XgK4ffhlJbVObm6pPIFbZzuxswghdphDNSv14nvd80mRlESkwBya5LT1GFUyAnYt BYs1fE0T8+lkokbV70kkdve902Ruo93bi6TrfNJ2Qh0bBACzENwe/LoemAhCNmkM ABhwzG773Pi5ZW1uIwy3E5nS95oHhW47RgUKSx99WFxtY0TA9sdNFMY9xsA8/Yxo 2DE0pAK+rtgpMKCEQEmJK7JDc60a6R2dLgSoUGNQQkSUtop+qGRAW4AHqSAqaylC vjIc4LGwT4N/AW39f60bQ0DgFqywCXzNeQXbYWjpYag3l7cGb9U= =k4cr -----END PGP SIGNATURE-----
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