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.
