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Bug 1808661 - rdkit fails to build in Fedora 32+
Summary: rdkit fails to build in Fedora 32+
Alias: None
Product: Fedora
Classification: Fedora
Component: rdkit
Version: rawhide
Hardware: Unspecified
OS: Unspecified
Target Milestone: ---
Assignee: Gianluca Sforna
QA Contact: Fedora Extras Quality Assurance
Depends On:
TreeView+ depends on / blocked
Reported: 2020-02-29 09:55 UTC by Miro Hrončok
Modified: 2020-03-04 18:59 UTC (History)
2 users (show)

Fixed In Version:
Doc Type: If docs needed, set a value
Doc Text:
Clone Of:
Last Closed: 2020-03-04 18:56:24 UTC
Type: Bug

Attachments (Terms of Use)

Description Miro Hrončok 2020-02-29 09:55:35 UTC
Description of problem:
Package rdkit fails to build from source in Fedora rawhide and Fedora 32:

[ 39%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o
cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++  -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wl,--as-needed -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC   -std=gnu++11 -o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp
/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/catch_sgroups.cpp: In function 'void ____C_A_T_C_H____T_E_S_T____2()':
/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/catch_sgroups.cpp:212:6: error: could not convert '{{{{{{1.0e+0, 3.0e+0, 0.0}}, {{5.0e+0, 7.0e+0, 0.0}}, {{0.0, 0.0, 0.0}}}}, {{{{2.0e+0, 4.0e+0, 0.0}}, {{6.0e+0, 8.0e+0, 0.0}}, {{0.0, 0.0, 0.0}}}}}}' from '<brace-enclosed initializer list>' to 'std::vector<std::array<std::array<double, 3>, 3> >'
  212 |     }};
      |      ^
      |      |
      |      <brace-enclosed initializer list>

Version-Release number of selected component (if applicable):

Steps to Reproduce:
fedpkg build

Additional info:
This package is tracked by Koschei. See:

This blocks the Python 3.9 rebuild of the package.

Comment 1 Fedora Release Engineering 2020-03-01 04:22:34 UTC
Dear Maintainer,

your package has not been built successfully in 32. Action is required from you.

If you can fix your package to build, perform a build in koji, and either create
an update in bodhi, or close this bug without creating an update, if updating is
not appropriate [1]. If you are working on a fix, set the status to ASSIGNED to
acknowledge this. Following the latest policy for such packages [2], your package
will be orphaned if this bug remains in NEW state more than 8 weeks.

A week before the mass branching of Fedora 33 according to the schedule [3],
any packages not successfully rebuilt at least on Fedora 31 will be
retired regardless of the status of this bug.


Comment 2 Than Ngo 2020-03-04 18:56:24 UTC
it's fixed in rdkit-2019.03.3-5.fc33 and rdkit-2019.03.3-5.fc32

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