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I've tried re-build rdkit against new PostgreSQL 9.6.0 (soon in rawhide), but the build failed on PostgreSQL unrelated issue: make -C _build/latex all-pdf make[1]: Entering directory '/builddir/build/BUILD/rdkit-Release_2016_03_2/python2/Docs/Book/_build/latex' pdflatex 'RDKit.tex' This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=pdflatex) restricted \write18 enabled. kpathsea: Running mktexfmt pdflatex.fmt mktexfmt: mktexfmt is using the following fmtutil.cnf files (in precedence order): mktexfmt: mktexfmt is using the following fmtutil.cnf file for writing changes: mktexfmt: /builddir/.cache/texlive/texmf-config/web2c/fmtutil.cnf mktexfmt [INFO]: writing formats under /builddir/.cache/texlive/texmf-var/web2c mktexfmt [INFO]: did not find entry for byfmt=pdflatex, skipped mktexfmt [INFO]: Total formats: 0 mktexfmt [INFO]: exiting with status 0 I can't find the format file `pdflatex.fmt'! make[1]: *** [Makefile:66: RDKit.pdf] Error 1 Full log is here: https://copr-be.cloud.fedoraproject.org/results/@db-sig/postgresql-9.6-rebuild/fedora-rawhide-i386/00463003-rdkit/build.log.gz Note that your package provides PostgreSQL plugin, please merge commit 9680b42a9af83cd3cb9d6e2b71b2684d2c3c1d2c from private-praiskup-postgresql-9.6.0-rebuild branch. Thanks!
Yeah, it seems tex packaging in rawhide is somewhat in flux and I have no clue about how to fix this. Will ask in fedora-devel. Thanks for the patch, if you have any recommendations for upstream about the cartridge, just let me know and I will forward the info.
Ok, here is the issue with tex: https://bugzilla.redhat.com/show_bug.cgi?id=1382447
This bug appears to have been reported against 'rawhide' during the Fedora 26 development cycle. Changing version to '26'.
I tried to rebuild rdkit again, now against PostgreSQL 10, and it seems to have issues again (on non-x86_64 architectures): https://koji.fedoraproject.org/koji/packageinfo?packageID=22955
Is this bug the reason for (on F27): # dnf install python2-rdkit Last metadata expiration check: 0:26:32 ago on Tue 07 Nov 2017 11:06:32 AM EST. Error: Problem: conflicting requests - nothing provides libboost_system.so.1.63.0()(64bit) needed by python2-rdkit-2016.09.4-2.fc26.x86_64
I don't think so, Tim. The issue I talk about is about F28 only. There we updated postgresql package and because of this some subpackage of rdkit is not installable together with newer postgresql. To fix this, we need rdkit rebuild (for F28), but that can not be done easily. So here is the bug report...
(In reply to Pavel Raiskup from comment #6) > I don't think so, Tim. The issue I talk about is about F28 only. There > we updated postgresql package and because of this some subpackage of > rdkit is not installable together with newer postgresql. To fix this, we > need rdkit rebuild (for F28), but that can not be done easily. So here > is the bug report... OK - should I file a new report for the F27 build issues? I don't see a viable F27 rdkit rpm...
Sorry, the FTBFS is there also for F27 so the only available version of rdkit for you is the version from F26 -- but that was built against different set of libraries (and thus is not installable now on F27). I don't think new bug report is needed. There are different sets of issues, depending on the architecture: ================================================ on ppc64/ppc64le/aarch64: 62: **** 62: Test Assert 62: Expression Failed:_ 62: Violation occurred on line 456 in file /builddir/build/BUILD/rdkit-Release_2017_03_3/python2/Code/GraphMol/Descriptors/test3D.cpp 62: Failed Expression: fabs(val) < 1e-4 62: **** 62:_ 62: terminate called after throwing an instance of 'Invar::Invariant' 62: what(): Test Assert 62/117 Test #62: test3D .............................***Exception: Other 0.62 sec ================================================ On i686: The following tests FAILED: >------- 20 - pyForceFieldConstraints (SEGFAULT) >------- 36 - pyDepictor (SEGFAULT) >------- 50 - pyChemReactions (SEGFAULT) >------- 51 - pyChemReactionEnumerations (SEGFAULT) >------- 52 - pyChemReactionSanitize (SEGFAULT) >------- 57 - pyFilterCatalog (SEGFAULT) >------- 59 - pyFragCatalog (SEGFAULT) >------- 63 - pyMolDescriptors (SEGFAULT) >------- 66 - pyPartialCharges (SEGFAULT) >------- 68 - pyMolTransforms (SEGFAULT) >------- 72 - pyForceFieldHelpers (SEGFAULT) >------- 74 - pyDistGeom (SEGFAULT) >------- 76 - pyMolAlign (SEGFAULT) >------- 78 - pyChemicalFeatures (SEGFAULT) >------- 80 - pyShapeHelpers (SEGFAULT) >------- 82 - pyMolCatalog (SEGFAULT) >------- 84 - pyMolDraw2D (SEGFAULT) >------- 86 - pyFMCS (SEGFAULT) >------- 89 - pyMolHash (SEGFAULT) >------- 91 - pyMMPA (SEGFAULT) >------- 93 - pyStructChecker (SEGFAULT) >------- 95 - pyReducedGraphs (SEGFAULT) >------- 98 - pySLNParse (SEGFAULT) >------- 99 - pyGraphMolWrap (SEGFAULT) >-------100 - pyTestConformerWrap (SEGFAULT) >-------101 - pyTestTrajectory (SEGFAULT) >-------102 - pyTestThreads (SEGFAULT) >-------110 - pyFeatures (SEGFAULT) >-------111 - pythonTestDbCLI (Failed) >-------112 - pythonTestDirML (Failed) >-------113 - pythonTestDirDataStructs (Failed) >-------115 - pythonTestDirSimDivFilters (Failed) >-------116 - pythonTestDirVLib (Failed) >-------117 - pythonTestDirChem (SEGFAULT) Errors while running CTest ================================================ On s390x: 94% tests passed, 7 tests failed out of 115 Total Test time (real) = 340.78 sec The following tests FAILED: 5 - testFPB (OTHER_FAULT) 6 - testMultiFPB (OTHER_FAULT) 10 - pyFPB (SEGFAULT) 47 - testReaction (OTHER_FAULT) 51 - pyChemReactionEnumerations (Failed) 62 - test3D (OTHER_FAULT) 111 - pythonTestDirDataStructs (Failed) Errors while running CTest
This bug appears to have been reported against 'rawhide' during the Fedora 28 development cycle. Changing version to '28'.
Created attachment 1444122 [details] build.log
Created attachment 1444125 [details] root.log
Created attachment 1444129 [details] state.log
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