Bug 2048217 - Review Request: maeparser - a parser for Schrodinger Maestro files
Summary: Review Request: maeparser - a parser for Schrodinger Maestro files
Keywords:
Status: CLOSED ERRATA
Alias: None
Product: Fedora
Classification: Fedora
Component: Package Review
Version: rawhide
Hardware: All
OS: Linux
medium
medium
Target Milestone: ---
Assignee: Antonio T. sagitter
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard: Trivial
Depends On:
Blocks:
TreeView+ depends on / blocked
 
Reported: 2022-01-30 09:00 UTC by Mark E. Fuller
Modified: 2022-05-11 17:05 UTC (History)
2 users (show)

Fixed In Version:
Clone Of:
Environment:
Last Closed: 2022-04-25 20:11:19 UTC
Type: ---
Embargoed:
trpost: fedora-review+


Attachments (Terms of Use)

Description Mark E. Fuller 2022-01-30 09:00:06 UTC
Spec URL: https://download.copr.fedorainfracloud.org/results/fuller/test-builds/fedora-rawhide-x86_64/03260075-maeparser/maeparser.spec
SRPM URL: https://download.copr.fedorainfracloud.org/results/fuller/test-builds/fedora-rawhide-x86_64/03260075-maeparser/maeparser-1.2.4-1.fc36.src.rpm
Description: Parser for Schrodinger Maestro file formats, which are used as output from a wide range of proprietary chemistry/life science/material science software packages
Fedora Account System Username: fuller

Comment 1 Antonio T. sagitter 2022-04-24 10:21:56 UTC
This package is useful to resume RDKIT in Fedora

Comment 2 Antonio T. sagitter 2022-04-24 11:03:52 UTC
Package Review
==============

Legend:
[x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated
[ ] = Manual review needed

> rm %{buildroot}/usr/lib/cmake/%{name}*.cmake

Why are you removing *cmake config file? It can be useful.

===== MUST items =====

C/C++:
[x]: Package does not contain kernel modules.
[x]: Package contains no static executables.
[x]: If your application is a C or C++ application you must list a
     BuildRequires against gcc, gcc-c++ or clang.
[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.
[x]: Development (unversioned) .so files in -devel subpackage, if present.

Generic:
[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", "MIT License". 31 files have unknown
     license. Detailed output of licensecheck in
     /home/sagitter/2048217-maeparser/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.
[x]: Useful -debuginfo package or justification otherwise.
[x]: Package is not known to require an ExcludeArch tag.
[-]: Large documentation must go in a -doc subpackage. Large could be size
     (~1MB) or number of files.
     Note: Documentation size is 10240 bytes in 1 files.
[x]: Package complies to the Packaging Guidelines
[x]: Package successfully compiles and builds into binary rpms on at least
     one supported primary architecture.
[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 does not use a name that already exists.
[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

===== SHOULD items =====

Generic:
[-]: If the source package does not include license text(s) as a separate
     file from upstream, the packager SHOULD query upstream to include it.
[x]: Final provides and requires are sane (see attachments).
[ ]: Package functions as described.
[x]: Latest version is packaged.
[x]: Package does not include license text files separate from upstream.
[x]: Sources are verified with gpgverify first in %prep if upstream
     publishes signatures.
     Note: gpgverify is not used.
[x]: Package should compile and build into binary rpms on all supported
     architectures.
[?]: %check is present and all tests pass.
[x]: Packages should try to preserve timestamps of original installed
     files.
[x]: Reviewer should test that the package builds in mock.
[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.
[x]: Spec file according to URL is the same as in SRPM.


Rpmlint
-------
Cannot parse rpmlint output:


Rpmlint (debuginfo)
-------------------
Cannot parse rpmlint output:



Rpmlint (installed packages)
----------------------------
Cannot parse rpmlint output:


Source checksums
----------------
https://github.com/schrodinger/maeparser/archive/refs/tags/v1.2.4.tar.gz :
  CHECKSUM(SHA256) this package     : c62d5846c85a2982cfa8895ffbed8a6ce57678d936ddfebf429546fab4b0a36d
  CHECKSUM(SHA256) upstream package : c62d5846c85a2982cfa8895ffbed8a6ce57678d936ddfebf429546fab4b0a36d


Requires
--------
maeparser (rpmlib, GLIBC filtered):
    libboost_iostreams.so.1.76.0()(64bit)
    libc.so.6()(64bit)
    libgcc_s.so.1()(64bit)
    libgcc_s.so.1(GCC_3.0)(64bit)
    libgcc_s.so.1(GCC_3.3.1)(64bit)
    libstdc++.so.6()(64bit)
    libstdc++.so.6(CXXABI_1.3)(64bit)
    rtld(GNU_HASH)

maeparser-devel (rpmlib, GLIBC filtered):
    maeparser(x86-64)

maeparser-debuginfo (rpmlib, GLIBC filtered):

maeparser-debugsource (rpmlib, GLIBC filtered):



Provides
--------
maeparser:
    libmaeparser.so.1()(64bit)
    maeparser
    maeparser(x86-64)

maeparser-devel:
    maeparser-devel
    maeparser-devel(x86-64)

maeparser-debuginfo:
    debuginfo(build-id)
    maeparser-debuginfo
    maeparser-debuginfo(x86-64)

maeparser-debugsource:
    maeparser-debugsource
    maeparser-debugsource(x86-64)



Generated by fedora-review 0.8.0 (e988316) last change: 2022-04-07
Command line :/usr/bin/fedora-review -m fedora-rawhide-x86_64 -b 2048217
Buildroot used: fedora-rawhide-x86_64
Active plugins: C/C++, Generic, Shell-api
Disabled plugins: Python, R, Perl, Ocaml, Java, PHP, SugarActivity, fonts, Haskell
Disabled flags: EPEL6, EPEL7, DISTTAG, BATCH, EXARCH

Comment 3 Mark E. Fuller 2022-04-24 16:43:49 UTC
Spec URL: https://download.copr.fedorainfracloud.org/results/fuller/test-builds/fedora-rawhide-x86_64/04307487-maeparser/maeparser.spec
SRPM URL: https://download.copr.fedorainfracloud.org/results/fuller/test-builds/fedora-rawhide-x86_64/04307487-maeparser/maeparser-1.2.4-1.fc37.src.rpm

I updated to not remove the cmake config file and yes, my goal (on hold) was to get RDKIT and some other chemistry software into Fedora

Thank you

Comment 4 Antonio T. sagitter 2022-04-24 16:57:29 UTC
> %{_prefix}/lib/cmake/%{name}*.cmake

This is wrong for x86_64

Patch the CMakeLists.txt file:

```
--- CMakeLists.origin.txt	2020-10-13 19:18:02.000000000 +0200
+++ CMakeLists.txt	2022-04-24 18:55:46.282345739 +0200
@@ -78,7 +78,7 @@
 
 INSTALL(EXPORT maeparser-targets
     FILE ${PROJECT_NAME}-config.cmake
-    DESTINATION lib/cmake)
+    DESTINATION lib${LIB_SUFFIX}/cmake)
 
 file(GLOB mae_headers "*.hpp")
 install(FILES ${mae_headers} DESTINATION include/maeparser)

```

> my goal (on hold) was to get RDKIT and some other chemistry software into Fedora

Okay, let me know when you decide to resume rdkit please.

Comment 5 Mark E. Fuller 2022-04-24 20:16:38 UTC
Spec URL: https://download.copr.fedorainfracloud.org/results/fuller/test-builds/fedora-rawhide-x86_64/04307606-maeparser/maeparser.spec
SRPM URL: https://download.copr.fedorainfracloud.org/results/fuller/test-builds/fedora-rawhide-x86_64/04307606-maeparser/maeparser-1.2.4-1.fc37.src.rpm

Thank you for the patch!
I opened a PR for this (https://github.com/schrodinger/maeparser/pull/73) and amended the SPEC and rebuilt the SRPM accordingly

If you are interested in coordinating on rdkit, I would be happy to look at it again. Otherwise, since I just left the group for which it was relevant, it might be a while before I think about it again

Comment 6 Antonio T. sagitter 2022-04-25 10:31:39 UTC
Package approved.

> If you are interested in coordinating on rdkit

Okay. I will recover RDKIT as soon as possible.

Comment 7 Gwyn Ciesla 2022-04-25 19:30:41 UTC
(fedscm-admin):  The Pagure repository was created at https://src.fedoraproject.org/rpms/maeparser

Comment 8 Fedora Update System 2022-04-25 20:09:34 UTC
FEDORA-2022-5dacb6b3c6 has been submitted as an update to Fedora 37. https://bodhi.fedoraproject.org/updates/FEDORA-2022-5dacb6b3c6

Comment 9 Fedora Update System 2022-04-25 20:11:19 UTC
FEDORA-2022-5dacb6b3c6 has been pushed to the Fedora 37 stable repository.
If problem still persists, please make note of it in this bug report.


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