pymol failed to build from source in Fedora rawhide https://koji.fedoraproject.org/koji/taskinfo?taskID=28219856 For details on the mass rebuild see: https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild Please fix pymol at your earliest convenience and set the bug's status to ASSIGNED when you start fixing it. If the bug remains in NEW state for 8 weeks, pymol will be orphaned. Before branching of Fedora 30, pymol will be retired, if it still fails to build. For more details on the FTBFS policy, please visit: https://fedoraproject.org/wiki/Fails_to_build_from_source
Created attachment 1465853 [details] build.log
Created attachment 1465854 [details] root.log file root.log too big, will only attach last 32768 bytes
Created attachment 1465855 [details] state.log
OK, I fixed the immediate issue, yet there is a gcc-c++ build failure on ppc64le. https://koji.fedoraproject.org/koji/taskinfo?taskID=28564602
(In reply to Miro Hrončok from comment #4) > OK, I fixed the immediate issue, yet there is a gcc-c++ build failure on > ppc64le. > > https://koji.fedoraproject.org/koji/taskinfo?taskID=28564602 Yeah, this is where I've been stuck - the error isn't informative and I can't find a good ppc64le build system to test with?
CCing Dan, he might have something for you to debug this on.
(In reply to Tim Fenn from comment #5) > (In reply to Miro Hrončok from comment #4) > > OK, I fixed the immediate issue, yet there is a gcc-c++ build failure on > > ppc64le. > > > > https://koji.fedoraproject.org/koji/taskinfo?taskID=28564602 > > Yeah, this is where I've been stuck - the error isn't informative and I > can't find a good ppc64le build system to test with? all maintainers can use machines from https://fedoraproject.org/wiki/Test_Machine_Resources_For_Package_Maintainers the problem looks like a real problem in pymol (or its bundled libs)
(This is a mass bug update. Forgive me if things are not 100% accurate for this one.) At this moment, your package still requires Python 3.6. This will cause broken upgrades to Fedora 29. Please prioritize this rebuild. Let me know if you need help from the Python maintenance team figuring out why the package FTBFS. Consider orphaning the package if you don't have time for it. Consider retiring the package if upstream is dead and nothing depends on it in Fedora. If you are blocked by other packages (I've recently tried to set the Bugzilla metadata to reflect that), consider helping there as well. Thank you.
Igor, this has been unblocked in comment #4.
This is another friendly reminder. Please take action.
The problem is with the -std=c++0x compiler option. It causes the "unix" preprocessor symbol to be undefined which is them missing in <msgpack/v1/vrefbuffer.hpp> to include <sys/uio.h> that defines "struct iovec". For the record pymol is FTBFS in F-28 too.
-std=c++11 doesn't help either
(In reply to Miro Hrončok from comment #12) > -std=c++11 doesn't help either -std=gnu++0x/gnu++11 helps, feel free to revert my workaround
Thanks Dan.
The needinfo request[s] on this closed bug have been removed as they have been unresolved for 1000 days