Bug 2310390 (mstore) - Review Request: mstore - Molecular structure store for testing
Summary: Review Request: mstore - Molecular structure store for testing
Keywords:
Status: CLOSED ERRATA
Alias: mstore
Product: Fedora
Classification: Fedora
Component: Package Review
Version: rawhide
Hardware: All
OS: Linux
medium
medium
Target Milestone: ---
Assignee: Peter Lemenkov
QA Contact: Fedora Extras Quality Assurance
URL: https://github.com/grimme-lab/mstore
Whiteboard:
Depends On:
Blocks: multicharge dftd4
TreeView+ depends on / blocked
 
Reported: 2024-09-06 10:43 UTC by Susi Lehtola
Modified: 2024-09-23 01:24 UTC (History)
3 users (show)

Fixed In Version:
Clone Of:
Environment:
Last Closed: 2024-09-23 00:15:28 UTC
Type: ---
Embargoed:
lemenkov: fedora-review+


Attachments (Terms of Use)

Description Susi Lehtola 2024-09-06 10:43:23 UTC
Spec URL: https://jussilehtola.fedorapeople.org/mstore.spec
SRPM URL: https://jussilehtola.fedorapeople.org/mstore-0.3.0-1.fc40.src.rpm
Fedora Account System Username: jussilehtola

Description:
Molecular structure store for testing

Comment 1 Fedora Review Service 2024-09-06 10:47:57 UTC
Copr build:
https://copr.fedorainfracloud.org/coprs/build/7988967
(succeeded)

Review template:
https://download.copr.fedorainfracloud.org/results/@fedora-review/fedora-review-2310390-mstore/fedora-rawhide-x86_64/07988967-mstore/fedora-review/review.txt

Found issues:

- No gcc, gcc-c++ or clang found in BuildRequires
  Read more: https://docs.fedoraproject.org/en-US/packaging-guidelines/C_and_C++/

Please know that there can be false-positives.

---
This comment was created by the fedora-review-service
https://github.com/FrostyX/fedora-review-service

If you want to trigger a new Copr build, add a comment containing new
Spec and SRPM URLs or [fedora-review-service-build] string.

Comment 2 Peter Lemenkov 2024-09-07 08:52:20 UTC
I'll review it

Comment 3 Peter Lemenkov 2024-09-07 09:27:22 UTC
Looks very clean and straightforward. I see only a couple of issues.

* The first one is mostly cosmetic - lack of versioning in a %changelog. At least rpmlint doesn't like it - please address it before uploading.
* Regarding 2nd one I'm not sure so I do not consider it as a blocker. Please report upstream that rpmlint believes that the final library is linked against libraries it does not use (see rpmlint messages below). Perhaps it's the false positive, perhaps not - I do not know a lot about Fortran libraries internals to say for certain.

I can't find any other issues so here is my formal

Package Review
==============

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

Issues:
=======
- If your application is a C or C++ application you must list a
  BuildRequires against gcc, gcc-c++ or clang.
  Note: No gcc, gcc-c++ or clang found in BuildRequires
  See: https://docs.fedoraproject.org/en-US/packaging-guidelines/C_and_C++/

^^^ This is a false positive. We do have gcc-gfortran as a build dependency listed.

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

C/C++:
[x]: Package does not contain kernel modules.
[x]: ldconfig not called in %post and %postun for Fedora 28 and later.
[x]: Package does not contain any libtool archives (.la)
[x]: Package contains no static executables.
[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 (Apache 2.0).
[x]: License file installed when any subpackage combination is installed.
[x]: Package requires other packages for directories it uses.
[x]: Package owns all directories that it creates.
[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 does not contain desktop file (not a GUI application).
[x]: Development files placed 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.
[-]: The package is not a rename of another package.
[x]: Requires correct, justified where necessary.
[x]: Spec file is legible and written in American English.
[-]: Package does not contains systemd file(s).
[x]: Useful -debuginfo package or justification otherwise.
[x]: Package is not known to require an ExcludeArch tag.
[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]: The License field must be a valid SPDX expression.
[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]: Large documentation must go in a -doc subpackage. Large could be size
     (~1MB) or number of files.
     Note: Documentation size is 4119 bytes in 1 files.
[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).
[-]: Not necessary to have a fully versioned dependency in subpackages.
[?]: I did not test if the package functions as described.
[x]: Latest version is packaged (0.3.0).
[x]: Package does not include license text files separate from upstream.
[-]: Sources weren't verified with gpgverify (upstream does not publish
     signatures).
[?]: I did not test if the package compiles and builds into binary rpms
     on all supported architectures.
[x]: %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]: Packager, Vendor, PreReq, Copyright tags should not be in spec file
[x]: The placement of pkgconfig(.pc) files are correct.
[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
-------
Checking: mstore-0.3.0-1.fc42.x86_64.rpm
          mstore-devel-0.3.0-1.fc42.x86_64.rpm
          mstore-debuginfo-0.3.0-1.fc42.x86_64.rpm
          mstore-debugsource-0.3.0-1.fc42.x86_64.rpm
          mstore-0.3.0-1.fc42.src.rpm
========================================================================================================================================= rpmlint session starts ========================================================================================================================================
rpmlint: 2.5.0
configuration:
    /usr/lib/python3.12/site-packages/rpmlint/configdefaults.toml
    /etc/xdg/rpmlint/fedora-legacy-licenses.toml
    /etc/xdg/rpmlint/fedora-spdx-licenses.toml
    /etc/xdg/rpmlint/fedora.toml
    /etc/xdg/rpmlint/scoring.toml
    /etc/xdg/rpmlint/users-groups.toml
    /etc/xdg/rpmlint/warn-on-functions.toml
rpmlintrc: [PosixPath('/tmp/tmp0egtvdjm')]
checks: 32, packages: 5

mstore.src: W: no-version-in-last-changelog
mstore.x86_64: W: no-version-in-last-changelog
mstore-debuginfo.x86_64: W: no-version-in-last-changelog
mstore-debugsource.x86_64: W: no-version-in-last-changelog
mstore-devel.x86_64: W: no-version-in-last-changelog


^^^ See my note at the top of my comment.


mstore.x86_64: W: no-manual-page-for-binary mstore-info
mstore-devel.x86_64: W: no-documentation
=================================================================================================== 5 packages and 0 specfiles checked; 0 errors, 7 warnings, 37 filtered, 0 badness; has taken 1.8 s ===================================================================================================




Rpmlint (debuginfo)
-------------------
Checking: mstore-debuginfo-0.3.0-1.fc42.x86_64.rpm
========================================================================================================================================= rpmlint session starts ========================================================================================================================================
rpmlint: 2.5.0
configuration:
    /usr/lib/python3.12/site-packages/rpmlint/configdefaults.toml
    /etc/xdg/rpmlint/fedora-legacy-licenses.toml
    /etc/xdg/rpmlint/fedora-spdx-licenses.toml
    /etc/xdg/rpmlint/fedora.toml
    /etc/xdg/rpmlint/scoring.toml
    /etc/xdg/rpmlint/users-groups.toml
    /etc/xdg/rpmlint/warn-on-functions.toml
rpmlintrc: [PosixPath('/tmp/tmptw4zaqxs')]
checks: 32, packages: 1

mstore-debuginfo.x86_64: W: no-version-in-last-changelog
=================================================================================================== 1 packages and 0 specfiles checked; 0 errors, 1 warnings, 12 filtered, 0 badness; has taken 0.5 s ===================================================================================================





Rpmlint (installed packages)
----------------------------
============================ rpmlint session starts ============================
rpmlint: 2.5.0
configuration:
    /usr/lib/python3.13/site-packages/rpmlint/configdefaults.toml
    /etc/xdg/rpmlint/fedora-spdx-licenses.toml
    /etc/xdg/rpmlint/fedora.toml
    /etc/xdg/rpmlint/scoring.toml
    /etc/xdg/rpmlint/users-groups.toml
    /etc/xdg/rpmlint/warn-on-functions.toml
checks: 32, packages: 4

mstore.x86_64: W: unused-direct-shlib-dependency /usr/bin/mstore-info /lib64/libm.so.6
mstore.x86_64: W: unused-direct-shlib-dependency /usr/bin/mstore-info /lib64/libgcc_s.so.1
mstore.x86_64: E: unused-direct-shlib-dependency /usr/lib64/libmstore.so.0.3.0 /lib64/libm.so.6
mstore.x86_64: E: unused-direct-shlib-dependency /usr/lib64/libmstore.so.0.3.0 /lib64/libgcc_s.so.1

^^^ Please report upstream about it. Can we get rid of these or these are also false positives?

mstore-debugsource.x86_64: W: no-version-in-last-changelog
mstore.x86_64: W: no-version-in-last-changelog
mstore-debuginfo.x86_64: W: no-version-in-last-changelog
mstore-devel.x86_64: W: no-version-in-last-changelog



^^^ See my note at the top of my comment.



mstore.x86_64: W: no-manual-page-for-binary mstore-info
mstore-devel.x86_64: W: no-documentation
 4 packages and 0 specfiles checked; 2 errors, 8 warnings, 35 filtered, 2 badness; has taken 1.8 s 



Source checksums
----------------
https://github.com/grimme-lab/mstore/archive/v0.3.0/mstore-0.3.0.tar.gz :
  CHECKSUM(SHA256) this package     : 56b3d778629eb74b8a515cd53c727d04609f858a07f8d3555fd5fd392a206dcc
  CHECKSUM(SHA256) upstream package : 56b3d778629eb74b8a515cd53c727d04609f858a07f8d3555fd5fd392a206dcc


Requires
--------
mstore (rpmlib, GLIBC filtered):
    libc.so.6()(64bit)
    libgcc_s.so.1()(64bit)
    libgfortran.so.5()(64bit)
    libgfortran.so.5(GFORTRAN_8)(64bit)
    libm.so.6()(64bit)
    libmctc-lib.so.0()(64bit)
    libmstore.so.0()(64bit)
    rtld(GNU_HASH)

mstore-devel (rpmlib, GLIBC filtered):
    /usr/bin/pkg-config
    libmstore.so.0()(64bit)
    pkgconfig(mctc-lib)

mstore-debuginfo (rpmlib, GLIBC filtered):

mstore-debugsource (rpmlib, GLIBC filtered):



Provides
--------
mstore:
    libmstore.so.0()(64bit)
    mstore
    mstore(x86-64)

mstore-devel:
    mstore-devel
    mstore-devel(x86-64)
    pkgconfig(mstore)

mstore-debuginfo:
    debuginfo(build-id)
    libmstore.so.0.3.0-0.3.0-1.fc42.x86_64.debug()(64bit)
    mstore-debuginfo
    mstore-debuginfo(x86-64)

mstore-debugsource:
    mstore-debugsource
    mstore-debugsource(x86-64)



Generated by fedora-review 0.10.0 (e79b66b) last change: 2023-07-24
Command line :/usr/bin/fedora-review -b 2310390
Buildroot used: fedora-rawhide-x86_64
Active plugins: Shell-api, Generic, C/C++
Disabled plugins: Ocaml, Java, SugarActivity, fonts, Haskell, Python, R, Perl, PHP
Disabled flags: EXARCH, EPEL6, EPEL7, DISTTAG, BATCH


This package is

================
=== APPROVED ===
================

Comment 4 Fedora Admin user for bugzilla script actions 2024-09-07 11:07:53 UTC
The Pagure repository was created at https://src.fedoraproject.org/rpms/mstore

Comment 5 Susi Lehtola 2024-09-07 11:17:35 UTC
Thanks for the review! It looks like the libm and libgcc_s dependencies are never explicitly linked in in the build recipes; instead, these are probably normal requirements for Fortran projects since the Fortran language itself has intrinsic math operations and support for data types which are actually implemented in libm and libgcc_s and therefore these libraries are always linked in. Anyway, that's a aesthetical issue, only.

Comment 6 Fedora Update System 2024-09-07 11:26:11 UTC
FEDORA-2024-6c86dae71d (mstore-0.3.0-1.fc41) has been submitted as an update to Fedora 41.
https://bodhi.fedoraproject.org/updates/FEDORA-2024-6c86dae71d

Comment 7 Fedora Update System 2024-09-07 11:26:11 UTC
FEDORA-2024-06971018f5 (mstore-0.3.0-1.fc40) has been submitted as an update to Fedora 40.
https://bodhi.fedoraproject.org/updates/FEDORA-2024-06971018f5

Comment 8 Felix Wang 2024-09-07 15:35:47 UTC
> [ ]: Fully versioned dependency in subpackages if applicable.
>      Note: No Requires: %{name}%{?_isa} = %{version}-%{release} in mstore-
>      devel

For mstore-devel subpackage, the `Requires: %{name}%{?_isa} = %{version}-%{release}` was missing.

Comment 9 Susi Lehtola 2024-09-07 17:19:44 UTC
(In reply to Felix Wang from comment #8)
> > [ ]: Fully versioned dependency in subpackages if applicable.
> >      Note: No Requires: %{name}%{?_isa} = %{version}-%{release} in mstore-
> >      devel
> 
> For mstore-devel subpackage, the `Requires: %{name}%{?_isa} =
> %{version}-%{release}` was missing.

Cheers, fixed in mstore-0.3.0-2

Comment 10 Fedora Update System 2024-09-09 02:07:14 UTC
FEDORA-2024-4be227e78d has been pushed to the Fedora 41 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2024-4be227e78d`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2024-4be227e78d

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.

Comment 11 Fedora Update System 2024-09-09 19:25:18 UTC
FEDORA-2024-a26e2b1b4c has been pushed to the Fedora 40 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2024-a26e2b1b4c`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2024-a26e2b1b4c

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.

Comment 12 Fedora Update System 2024-09-12 02:19:49 UTC
FEDORA-2024-4be227e78d has been pushed to the Fedora 41 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2024-4be227e78d`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2024-4be227e78d

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.

Comment 13 Fedora Update System 2024-09-12 02:43:29 UTC
FEDORA-2024-a26e2b1b4c has been pushed to the Fedora 40 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2024-a26e2b1b4c`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2024-a26e2b1b4c

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.

Comment 14 Fedora Update System 2024-09-14 02:29:09 UTC
FEDORA-2024-4be227e78d has been pushed to the Fedora 41 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2024-4be227e78d`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2024-4be227e78d

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.

Comment 15 Fedora Update System 2024-09-14 03:16:17 UTC
FEDORA-2024-a26e2b1b4c has been pushed to the Fedora 40 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2024-a26e2b1b4c`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2024-a26e2b1b4c

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.

Comment 16 Fedora Update System 2024-09-15 02:16:08 UTC
FEDORA-2024-4be227e78d has been pushed to the Fedora 41 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2024-4be227e78d`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2024-4be227e78d

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.

Comment 17 Fedora Update System 2024-09-15 12:14:01 UTC
FEDORA-2024-a26e2b1b4c has been pushed to the Fedora 40 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2024-a26e2b1b4c`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2024-a26e2b1b4c

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.

Comment 18 Fedora Update System 2024-09-23 00:15:28 UTC
FEDORA-2024-4be227e78d (dftd4-3.7.0-4.fc41, mstore-0.3.0-2.fc41, and 2 more) has been pushed to the Fedora 41 stable repository.
If problem still persists, please make note of it in this bug report.

Comment 19 Fedora Update System 2024-09-23 01:24:11 UTC
FEDORA-2024-a26e2b1b4c (dftd4-3.7.0-4.fc40, mstore-0.3.0-2.fc40, and 2 more) has been pushed to the Fedora 40 stable repository.
If problem still persists, please make note of it in this bug report.


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