[Bug 2081113] New: Review Request: rdkit - Chemical informatics and machine learning toolkit
https://bugzilla.redhat.com/show_bug.cgi?id=2081113
Bug ID: 2081113 Summary: Review Request: rdkit - Chemical informatics and machine learning toolkit Product: Fedora Version: rawhide Hardware: All OS: Linux Status: NEW Component: Package Review Severity: medium Priority: medium Assignee: nobody@fedoraproject.org Reporter: trpost@rocketmail.com QA Contact: extras-qa@fedoraproject.org CC: package-review@lists.fedoraproject.org Target Milestone: --- Classification: Fedora
Spec URL: https://download.copr.fedorainfracloud.org/results/sagitter/ForTesting/fedor...
SRPM URL: https://download.copr.fedorainfracloud.org/results/sagitter/ForTesting/fedor...
Description: This is a review request for unretiring rdkit packge
Fedora Account System Username: sagitter
https://bugzilla.redhat.com/show_bug.cgi?id=2081113
Antonio T. sagitter trpost@rocketmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Blocks| |1862143, 1927163 Doc Type|--- |If docs needed, set a value
Referenced Bugs:
https://bugzilla.redhat.com/show_bug.cgi?id=1862143 [Bug 1862143] New upstream version 2021.03.1 of RDKit is available https://bugzilla.redhat.com/show_bug.cgi?id=1927163 [Bug 1927163] F34FailsToInstall: rdkit-postgresql
https://bugzilla.redhat.com/show_bug.cgi?id=2081113
Mark E. Fuller mark.e.fuller@gmx.de changed:
What |Removed |Added ---------------------------------------------------------------------------- Assignee|nobody@fedoraproject.org |mark.e.fuller@gmx.de CC| |mark.e.fuller@gmx.de
--- Comment #1 from Mark E. Fuller mark.e.fuller@gmx.de --- Taking this review - thanks for getting this building again!
https://bugzilla.redhat.com/show_bug.cgi?id=2081113
Mark E. Fuller mark.e.fuller@gmx.de changed:
What |Removed |Added ---------------------------------------------------------------------------- Flags| |fedora-review? | |needinfo?(trpost@rocketmail | |.com)
--- Comment #2 from Mark E. Fuller mark.e.fuller@gmx.de --- Two initial comments: 1) The SPEC/SRPM here didn't build with fedora-review as the source URL in the spec is https://github.com/rdkit/rdkit/archive/refs/tags/rdkit-%%7Bpkgname%7D.tar.gz, but the tarball should just be %{pkgname}.tar.gz (no leading "rdkit-") 2) Test builds only succeeded for rawhide/x86_64 - everything else failed: https://copr.fedorainfracloud.org/coprs/fuller/test-builds/build/4361857/ Pre-rawhide, this is due to maeparser-devel not being available; otherwise there's failing tests (@sagitter: do you want to be a co-maintainer for maeparser?)
Here's a preliminary review since there likely needs to be another iteration to look at the other Fedora versions and architectures
Package Review ==============
Legend: [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated [ ] = Manual review needed
Issues: ======= - Package does not use a name that already exists. Note: A package with this name already exists. Please check https://src.fedoraproject.org/rpms/rdkit See: https://docs.fedoraproject.org/en-US/packaging- guidelines/Naming/#_conflicting_package_names
===== MUST items =====
C/C++: [?]: Provides: bundled(gnulib) in place as required. Note: Sources not installed [x]: Package does not contain kernel modules. [x]: Package contains no static executables. [?]: Development (unversioned) .so files in -devel subpackage, if present. Note: Unversioned so-files in private %_libdir subdirectory (see attachment). Verify they are not in ld path. [x]: If your application is a C or C++ application you must list a BuildRequires against gcc, gcc-c++ or clang. [x]: Header files in -devel subpackage, if present. [x]: ldconfig not called in %post and %postun for Fedora 28 and later. [x]: Package does not contain any libtool archives (.la) [x]: Rpath absent or only used for internal libs.
Generic: [x]: Package successfully compiles and builds into binary rpms on at least one supported primary architecture. Note: Using prebuilt packages [x]: Package is licensed with an open-source compatible license and meets other legal requirements as defined in the legal section of Packaging Guidelines. [x]: License field in the package spec file matches the actual license. Note: Checking patched sources after %prep for licenses. Licenses found: "Unknown or generated". 1 files have unknown license. Detailed output of licensecheck in /var/lib/copr- rpmbuild/results/rdkit/licensecheck.txt [x]: License file installed when any subpackage combination is installed. [x]: %build honors applicable compiler flags or justifies otherwise. [x]: Package contains no bundled libraries without FPC exception. [x]: Changelog in prescribed format. [x]: Sources contain only permissible code or content. [-]: Package contains desktop file if it is a GUI application. [x]: Development files must be in a -devel package [x]: Package uses nothing in %doc for runtime. [x]: Package consistently uses macros (instead of hard-coded directory names). [x]: Package is named according to the Package Naming Guidelines. [x]: Package does not generate any conflict. [x]: Package obeys FHS, except libexecdir and /usr/target. [-]: If the package is a rename of another package, proper Obsoletes and Provides are present. [x]: Requires correct, justified where necessary. [x]: Spec file is legible and written in American English. [-]: Package contains systemd file(s) if in need. [?]: Useful -debuginfo package or justification otherwise. [!]: Package is not known to require an ExcludeArch tag. [x]: Large documentation must go in a -doc subpackage. Large could be size (~1MB) or number of files. Note: Documentation size is 317440 bytes in 2 files. [x]: Package complies to the Packaging Guidelines [x]: Package installs properly. [x]: Rpmlint is run on all rpms the build produces. Note: There are rpmlint messages (see attachment). [x]: If (and only if) the source package includes the text of the license(s) in its own file, then that file, containing the text of the license(s) for the package is included in %license. [x]: Package requires other packages for directories it uses. [x]: Package must own all directories that it creates. [x]: Package does not own files or directories owned by other packages. [x]: Package uses either %{buildroot} or $RPM_BUILD_ROOT [x]: Package does not run rm -rf %{buildroot} (or $RPM_BUILD_ROOT) at the beginning of %install. [x]: Macros in Summary, %description expandable at SRPM build time. [x]: Dist tag is present. [x]: Package does not contain duplicates in %files. [x]: Permissions on files are set properly. [x]: Package must not depend on deprecated() packages. [x]: Package use %makeinstall only when make install DESTDIR=... doesn't work. [x]: Package is named using only allowed ASCII characters. [x]: Package is not relocatable. [x]: Sources used to build the package match the upstream source, as provided in the spec URL. [x]: Spec file name must match the spec package %{name}, in the format %{name}.spec. [x]: File names are valid UTF-8. [x]: Packages must not store files under /srv, /opt or /usr/local
Python: [?]: Binary eggs must be removed in %prep Note: Cannot find any build in BUILD directory (--prebuilt option?) [?]: Python eggs must not download any dependencies during the build process. [?]: A package which is used by another package via an egg interface should provide egg info. [?]: Package meets the Packaging Guidelines::Python [x]: Package contains BR: python2-devel or python3-devel [x]: Packages MUST NOT have dependencies (either build-time or runtime) on packages named with the unversioned python- prefix unless no properly versioned package exists. Dependencies on Python packages instead MUST use names beginning with python2- or python3- as appropriate. [x]: Python packages must not contain %{pythonX_site(lib|arch)}/* in %files
===== SHOULD items =====
Generic: [!]: Reviewer should test that the package builds in mock. [ ]: Avoid bundling fonts in non-fonts packages. Note: Package contains font files [ ]: If the source package does not include license text(s) as a separate file from upstream, the packager SHOULD query upstream to include it. [ ]: Final provides and requires are sane (see attachments). [ ]: Package functions as described. [ ]: Latest version is packaged. [ ]: Package does not include license text files separate from upstream. [ ]: Sources are verified with gpgverify first in %prep if upstream publishes signatures. Note: gpgverify is not used. [ ]: Package should compile and build into binary rpms on all supported architectures. [ ]: %check is present and all tests pass. [ ]: Packages should try to preserve timestamps of original installed files. [x]: Buildroot is not present [x]: Package has no %clean section with rm -rf %{buildroot} (or $RPM_BUILD_ROOT) [x]: No file requires outside of /etc, /bin, /sbin, /usr/bin, /usr/sbin. [x]: Fully versioned dependency in subpackages if applicable. [x]: Packager, Vendor, PreReq, Copyright tags should not be in spec file [x]: Sources can be downloaded from URI in Source: tag [x]: SourceX is a working URL. [x]: Spec use %global instead of %define unless justified.
===== EXTRA items =====
Generic: [x]: Rpmlint is run on debuginfo package(s). Note: There are rpmlint messages (see attachment). [x]: Rpmlint is run on all installed packages. Note: There are rpmlint messages (see attachment). [x]: Large data in /usr/share should live in a noarch subpackage if package is arched.
Rpmlint ------- Nothing flagged
Unversioned so-files -------------------- python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/Draw/rdMolDraw2D.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/MolStandardize/rdMolStandardize.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/Scaffolds/rdScaffoldNetwork.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdAbbreviations.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdCIPLabeler.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdChemReactions.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdChemicalFeatures.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdDepictor.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdDeprotect.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdDistGeom.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdFMCS.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdFingerprintGenerator.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdForceFieldHelpers.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdMHFPFingerprint.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdMMPA.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdMolAlign.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdMolCatalog.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdMolChemicalFeatures.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdMolDescriptors.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdMolEnumerator.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdMolHash.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdMolTransforms.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdPartialCharges.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdRGroupDecomposition.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdReducedGraphs.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdSLNParse.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdShapeHelpers.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdSubstructLibrary.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdTautomerQuery.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdchem.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdfiltercatalog.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdfragcatalog.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdinchi.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdmolfiles.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdmolops.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdqueries.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Chem/rdtrajectory.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/DataManip/Metric/rdMetricMatrixCalc.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/DataStructs/cDataStructs.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/DistanceGeometry/DistGeom.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/ForceField/rdForceField.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Geometry/rdGeometry.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/ML/Cluster/Clustering.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/ML/Data/cQuantize.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/ML/InfoTheory/rdInfoTheory.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/Numerics/rdAlignment.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/SimDivFilters/rdSimDivPickers.so python3-rdkit: /usr/lib64/python3.10/site-packages/rdkit/rdBase.so rdkit-postgresql: /usr/lib64/pgsql/rdkit.so
https://bugzilla.redhat.com/show_bug.cgi?id=2081113
Antonio T. sagitter trpost@rocketmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Flags|needinfo?(trpost@rocketmail | |.com) |
--- Comment #3 from Antonio T. sagitter trpost@rocketmail.com --- (In reply to Mark E. Fuller from comment #2)
Two initial comments:
- The SPEC/SRPM here didn't build with fedora-review as the source URL in
the spec is https://github.com/rdkit/rdkit/archive/refs/tags/rdkit-%%7Bpkgname%7D.tar.gz, but the tarball should just be %{pkgname}.tar.gz (no leading "rdkit-") 2) Test builds only succeeded for rawhide/x86_64 - everything else failed: https://copr.fedorainfracloud.org/coprs/fuller/test-builds/build/4361857/ Pre-rawhide, this is due to maeparser-devel not being available; otherwise there's failing tests
Yes, i know; probably due to to swig-4: https://github.com/rdkit/rdkit/issues/5252
(@sagitter: do you want to be a co-maintainer for maeparser?)
Yes.
https://bugzilla.redhat.com/show_bug.cgi?id=2081113
--- Comment #4 from Mark E. Fuller mark.e.fuller@gmx.de --- I updated the SPEC: https://fuller.fedorapeople.org/rdkit.spec and the SRPM: https://fuller.fedorapeople.org/rdkit-2022.03.3-1.fc35.src.rpm but there are still failing tests (https://copr.fedorainfracloud.org/coprs/fuller/review-june-2022/build/454820...) despite issue #5252 being closed in the new release
Product: Fedora Version: rawhide Component: Package Review
Antonio T. sagitter trpost@rocketmail.com has canceled Package Review package-review@lists.fedoraproject.org's request for Mark E. Fuller mark.e.fuller@gmx.de's needinfo: Bug 2081113: Review Request: rdkit - Chemical informatics and machine learning toolkit https://bugzilla.redhat.com/show_bug.cgi?id=2081113
--- Comment #6 from Antonio T. sagitter trpost@rocketmail.com --- I'm testing latest release
https://bugzilla.redhat.com/show_bug.cgi?id=2081113
Antonio T. sagitter trpost@rocketmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Flags|needinfo?(mark.e.fuller@gmx | |.de) |
--- Comment #6 from Antonio T. sagitter trpost@rocketmail.com --- I'm testing latest release
https://bugzilla.redhat.com/show_bug.cgi?id=2081113
Antonio T. sagitter trpost@rocketmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Flags| |needinfo?(mark.e.fuller@gmx | |.de)
--- Comment #7 from Antonio T. sagitter trpost@rocketmail.com --- Spec URL: https://download.copr.fedorainfracloud.org/results/sagitter/ForTesting/fedor... SRPM URL: https://download.copr.fedorainfracloud.org/results/sagitter/ForTesting/fedor...
Hi Mark.
This is a new release of RDKIT, we can restart this review if you can.
package-review@lists.fedoraproject.org
-
bugzilla＠redhat.com