https://bugzilla.redhat.com/show_bug.cgi?id=2166884
Bug ID: 2166884 Summary: Review Request: mepack - A Fortran software library for solving dense Sylvester-like matrix equations Product: Fedora Version: rawhide Hardware: All OS: Linux Status: NEW Component: Package Review Severity: medium Priority: medium Assignee: nobody@fedoraproject.org Reporter: i.ucar86@gmail.com QA Contact: extras-qa@fedoraproject.org CC: package-review@lists.fedoraproject.org Target Milestone: --- Classification: Fedora
Spec URL: https://iucar.fedorapeople.org/pkgs/mepack.spec SRPM URL: https://iucar.fedorapeople.org/pkgs/mepack-1.0.3-1.fc37.src.rpm
Copr build: https://copr.fedorainfracloud.org/coprs/iucar/mepack/build/5430901/
Description: MEPACK is a software library focused on solving dense Sylvester-like matrix equations. The library is written in Fortran and provides interfaces for C, MATLAB and GNU Octave. The development places great emphasis on the fact that the algorithms can be adapted very well to modern CPU architectures by current Fortran compilers. In addition, the algorithms are accelerated through the use of directed acyclic graphs using OpenMP to increase the utility of multicore architectures.
Fedora Account System Username: iucar
https://bugzilla.redhat.com/show_bug.cgi?id=2166884
Benson Muite benson_muite@emailplus.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Doc Type|--- |If docs needed, set a value Status|NEW |ASSIGNED Assignee|nobody@fedoraproject.org |benson_muite@emailplus.org CC| |benson_muite@emailplus.org Flags| |fedora-review?
https://bugzilla.redhat.com/show_bug.cgi?id=2166884
--- Comment #1 from Jakub Kadlčík jkadlcik@redhat.com --- Copr build: https://copr.fedorainfracloud.org/coprs/build/5430987 (succeeded)
Review template: https://download.copr.fedorainfracloud.org/results/@fedora-review/fedora-rev...
Please take a look if any issues were found.
--- This comment was created by the fedora-review-service https://github.com/FrostyX/fedora-review-service
https://bugzilla.redhat.com/show_bug.cgi?id=2166884
--- Comment #2 from Benson Muite benson_muite@emailplus.org --- Package Review ==============
Legend: [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated [ ] = Manual review needed
===== 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]: 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. [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", "*No copyright* GNU General Public License, Version 3", "GNU General Public License v3.0 or later", "GNU Lesser General Public License v2.1 or later", "MIT License", "BSD 2-Clause License", "GNU General Public License v2.0 or later", "BSD 3-Clause License", "GNU Affero General Public License v3.0 or later". 811 files have unknown license. Detailed output of licensecheck in /home/FedoraPackaging/reviews/mepack/review-mepack/licensecheck.txt [x]: License file installed when any subpackage combination is installed. [x]: If the package is under multiple licenses, the licensing breakdown must be documented in the spec. [ ]: Package requires other packages for directories it uses. Note: No known owner of /usr/lib64/gfortran [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. [ ]: 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 40960 bytes in 6 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 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). [x]: Fully versioned dependency in subpackages if applicable. Note: No Requires: %{name}%{?_isa} = %{version}-%{release} in mepack64 [ ]: Package functions as described. [x]: Latest version is packaged. [x]: 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. [x]: Package should compile and build 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: No rpmlint messages. [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: mepack-1.0.3-1.fc38.x86_64.rpm mepack64-1.0.3-1.fc38.x86_64.rpm mepack-devel-1.0.3-1.fc38.x86_64.rpm mepack-debuginfo-1.0.3-1.fc38.x86_64.rpm mepack-debugsource-1.0.3-1.fc38.x86_64.rpm mepack-1.0.3-1.fc38.src.rpm ==================================== rpmlint session starts =================================== rpmlint: 2.4.0 configuration: /usr/lib/python3.11/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/tmpfddskto7')] checks: 31, packages: 6
mepack-devel.x86_64: W: no-documentation mepack-devel.x86_64: W: files-duplicate /usr/include/mepack64/mepack.h /usr/include/mepack/mepack.h mepack-devel.x86_64: W: files-duplicate /usr/lib64/cmake/mepack64/MEPACK64ConfigVersion.cmake /usr/lib64/cmake/mepack/MEPACKConfigVersion.cmake mepack-devel.x86_64: W: files-duplicate /usr/lib64/gfortran/modules/mepack64/mepack_options_machine_double.mod /usr/lib64/gfortran/modules/mepack/mepack_options_machine_double.mod mepack-devel.x86_64: W: files-duplicate /usr/lib64/gfortran/modules/mepack64/mepack_options_machine_single.mod /usr/lib64/gfortran/modules/mepack/mepack_options_machine_single.mod ===== 6 packages and 0 specfiles checked; 0 errors, 5 warnings, 0 badness; has taken 6.4 s ====
Rpmlint (debuginfo) ------------------- Checking: mepack-debuginfo-1.0.3-1.fc38.x86_64.rpm ==================================== rpmlint session starts =================================== rpmlint: 2.4.0 configuration: /usr/lib/python3.11/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/tmpm2nj3718')] checks: 31, packages: 1
===== 1 packages and 0 specfiles checked; 0 errors, 0 warnings, 0 badness; has taken 1.8 s ====
Rpmlint (installed packages) ---------------------------- ============================ rpmlint session starts ============================ rpmlint: 2.4.0 configuration: /usr/lib/python3.11/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 checks: 31, packages: 5
mepack-devel.x86_64: W: no-documentation mepack-devel.x86_64: W: files-duplicate /usr/include/mepack64/mepack.h /usr/include/mepack/mepack.h mepack-devel.x86_64: W: files-duplicate /usr/lib64/cmake/mepack64/MEPACK64ConfigVersion.cmake /usr/lib64/cmake/mepack/MEPACKConfigVersion.cmake mepack-devel.x86_64: W: files-duplicate /usr/lib64/gfortran/modules/mepack64/mepack_options_machine_double.mod /usr/lib64/gfortran/modules/mepack/mepack_options_machine_double.mod mepack-devel.x86_64: W: files-duplicate /usr/lib64/gfortran/modules/mepack64/mepack_options_machine_single.mod /usr/lib64/gfortran/modules/mepack/mepack_options_machine_single.mod 5 packages and 0 specfiles checked; 0 errors, 5 warnings, 0 badness; has taken 5.7 s
Source checksums ---------------- https://gitlab.mpi-magdeburg.mpg.de/software/mepack-release/-/archive/v1.0.3... : CHECKSUM(SHA256) this package : d7c695988c9d7e086882f8a717a55f01dd3d85fba660d5e9b87de737535aec45 CHECKSUM(SHA256) upstream package : d7c695988c9d7e086882f8a717a55f01dd3d85fba660d5e9b87de737535aec45
Requires -------- mepack (rpmlib, GLIBC filtered): libc.so.6()(64bit) libflexiblas.so.3()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_4.0.0)(64bit) libgfortran.so.5()(64bit) libgfortran.so.5(GFORTRAN_8)(64bit) libgomp.so.1()(64bit) libgomp.so.1(OMP_1.0)(64bit) libm.so.6()(64bit) rtld(GNU_HASH)
mepack64 (rpmlib, GLIBC filtered): libc.so.6()(64bit) libflexiblas64.so.3()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_4.0.0)(64bit) libgfortran.so.5()(64bit) libgfortran.so.5(GFORTRAN_8)(64bit) libgomp.so.1()(64bit) libgomp.so.1(OMP_1.0)(64bit) libm.so.6()(64bit) rtld(GNU_HASH)
mepack-devel (rpmlib, GLIBC filtered): /usr/bin/pkg-config cmake-filesystem(x86-64) gcc-gfortran(x86-64) libmepack.so.1()(64bit) libmepack64.so.1()(64bit) mepack(x86-64) mepack64(x86-64)
mepack-debuginfo (rpmlib, GLIBC filtered):
mepack-debugsource (rpmlib, GLIBC filtered):
Provides -------- mepack: libmepack.so.1()(64bit) mepack mepack(x86-64)
mepack64: libmepack64.so.1()(64bit) mepack64 mepack64(x86-64)
mepack-devel: cmake(MEPACK) cmake(MEPACK64) cmake(mepack) cmake(mepack64) mepack-devel mepack-devel(x86-64) pkgconfig(mepack) pkgconfig(mepack64)
mepack-debuginfo: debuginfo(build-id) libmepack.so.1.0.3-1.0.3-1.fc38.x86_64.debug()(64bit) mepack-debuginfo mepack-debuginfo(x86-64)
mepack-debugsource: mepack-debugsource mepack-debugsource(x86-64)
Generated by fedora-review 0.9.0 (6761b6c) last change: 2022-08-23 Command line :/usr/bin/fedora-review -n mepack Buildroot used: fedora-rawhide-x86_64 Active plugins: Generic, Shell-api, C/C++ Disabled plugins: Ocaml, Ruby, PHP, Java, Python, Perl, fonts, Haskell, R, SugarActivity Disabled flags: EPEL6, EPEL7, DISTTAG, BATCH, EXARCH
Comments: a) Would an additional devel64 package be better than putting all headers in one package? b) Built on all architectures https://copr.fedorainfracloud.org/coprs/fed500/mepack/build/5503628/
https://bugzilla.redhat.com/show_bug.cgi?id=2166884
--- Comment #3 from Iñaki Ucar i.ucar86@gmail.com --- Thanks for the review. About the comments,
a) There is no guideline about this, and different packages do different things. In my opinion, given that packages mepack and mepack64 won't be normally pulled manually (because it's a library, there's no executable or anything in there), I think it's better in this case to keep things simple and have a single -devel package with everything.
b) Thanks for checking this.
https://bugzilla.redhat.com/show_bug.cgi?id=2166884
--- Comment #4 from Iñaki Ucar i.ucar86@gmail.com --- Just a kind reminder. :)
https://bugzilla.redhat.com/show_bug.cgi?id=2166884
--- Comment #5 from Benson Muite benson_muite@emailplus.org --- a) One further issue raised is: No known owner of /usr/lib64/gfortran
Maybe should use: Requires: gcc-gfortran%{_isa} https://docs.fedoraproject.org/en-US/packaging-guidelines/Fortran/#_packagin...
b) Perhaps add kernel-tools-libs-devel as a build requirement to provide libcpupower.so and cpufreq.h c) Can the documentation be build and packaged? It uses doxygen which can generate manpages if the doxyfile is modified slightly to turn off html documentation and turn on man page generation. This will add doxygen as a build requirement.
https://bugzilla.redhat.com/show_bug.cgi?id=2166884
--- Comment #6 from Iñaki Ucar i.ucar86@gmail.com --- (In reply to Benson Muite from comment #5)
a) One further issue raised is: No known owner of /usr/lib64/gfortran
Maybe should use: Requires: gcc-gfortran%{_isa} https://docs.fedoraproject.org/en-US/packaging-guidelines/Fortran/ #_packaging_of_fortran_programs
I already do that (line 44 of the SPEC), so I don't understand this warning. I believe it's a false positive.
b) Perhaps add kernel-tools-libs-devel as a build requirement to provide libcpupower.so and cpufreq.h
I asked the upstream maintainer about this and other libraries not found. He told me that it's fine, they are not needed, they are just for some advanced upstream testing.
c) Can the documentation be build and packaged? It uses doxygen which can generate manpages if the doxyfile is modified slightly to turn off html documentation and turn on man page generation. This will add doxygen as a build requirement.
The same, I asked the upstream maintainer about the docs, because doxygen HTML docs are a nightmare when it comes to the additional licenses that are included as a result of the build. He told me to ignore the docs, and that he prefers to just maintain an online version.
https://bugzilla.redhat.com/show_bug.cgi?id=2166884
--- Comment #7 from Benson Muite benson_muite@emailplus.org --- a) Trying to understand why. Checking other Fortran packages.
b) Ok on not adding kernel-tools-lib-devel
c) Man pages are helpful, may not always be online when using the package. Before doing the build could add:
sed -i `s/GENERATE_HTML = YES/GENERATE_HTML = NO/g' doc/Doxyfile.in sed -i `s/GENERATE_MAN = NO/GENERATE_MAN = YES/g' doc/Doxyfile.in
Then in the CMake configure section add
-DDOC=ON
After the build, within the build directory there will be
doc/man/man3
This will need to be installed manually, so add
install doc/man/man3 %{_mandir}/man3
https://bugzilla.redhat.com/show_bug.cgi?id=2166884
--- Comment #8 from Iñaki Ucar i.ucar86@gmail.com --- Spec URL: https://iucar.fedorapeople.org/pkgs/mepack.spec SRPM URL: https://iucar.fedorapeople.org/pkgs/mepack-1.0.3-1.fc37.src.rpm
I didn't know it was so easy to build man pages, thanks. Updated above, with docs. Build: https://copr.fedorainfracloud.org/coprs/iucar/mepack/build/5566175/
About a), gfortran owns %_fmoddir, and that expands to /usr/lib64/gfortran/modules, so nobody owns /usr/lib64/gfortran. It should be owned by gfortran too.
https://bugzilla.redhat.com/show_bug.cgi?id=2166884
--- Comment #9 from Jakub Kadlčík jkadlcik@redhat.com --- Created attachment 1946365 --> https://bugzilla.redhat.com/attachment.cgi?id=1946365&action=edit The .spec file difference from Copr build 5430987 to 5566266
https://bugzilla.redhat.com/show_bug.cgi?id=2166884
Jakub Kadlčík jkadlcik@redhat.com changed:
What |Removed |Added ---------------------------------------------------------------------------- URL| |https://www.mpi-magdeburg.m | |pg.de/projects/%{name}
--- Comment #10 from Jakub Kadlčík jkadlcik@redhat.com --- Copr build: https://copr.fedorainfracloud.org/coprs/build/5566266 (succeeded)
Review template: https://download.copr.fedorainfracloud.org/results/@fedora-review/fedora-rev...
Please take a look if any issues were found.
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If you want to trigger a new Copr build, add a comment containing new Spec and SRPM URLs or [fedora-review-service-build] string.
https://bugzilla.redhat.com/show_bug.cgi?id=2166884
--- Comment #11 from Benson Muite benson_muite@emailplus.org --- Co-ownership of directories is possible, though here seems not needed: https://docs.fedoraproject.org/en-US/packaging-guidelines/#_the_directory_is...
Made a pull request: https://src.fedoraproject.org/rpms/gcc/pull-request/39
https://bugzilla.redhat.com/show_bug.cgi?id=2166884
--- Comment #12 from Iñaki Ucar i.ucar86@gmail.com --- Nice, thanks. Any other issues here?
https://bugzilla.redhat.com/show_bug.cgi?id=2166884
--- Comment #13 from Benson Muite benson_muite@emailplus.org --- Can the files doc/naming.md and doc/tuning.md be packaged?
The source also includes a library of additional helper routines, libcscutils. Given that these are used in the examples, maybe it is helpful to also package them. Some modifications are needed to obtain shared libraries, in particular a static library liblua.a is created, even if one sets CMake to create shared libraries. Checking what is needed to change this.
https://bugzilla.redhat.com/show_bug.cgi?id=2166884
--- Comment #14 from Iñaki Ucar i.ucar86@gmail.com --- (In reply to Benson Muite from comment #13)
Can the files doc/naming.md and doc/tuning.md be packaged?
These are part of the documentation, so they are included now as man pages.
The source also includes a library of additional helper routines, libcscutils. Given that these are used in the examples, maybe it is helpful to also package them. Some modifications are needed to obtain shared libraries, in particular a static library liblua.a is created, even if one sets CMake to create shared libraries. Checking what is needed to change this.
This is a helper library they use for many projects and should not be packaged according to the maintainer.
https://bugzilla.redhat.com/show_bug.cgi?id=2166884
--- Comment #15 from Benson Muite benson_muite@emailplus.org --- cscutils is used in several of their other projects: https://gitlab.mpi-magdeburg.mpg.de/mess/cmess-releases/-/tree/master/libcsc... https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release/-/tree/master...
Maybe it should be packaged separately? Almost all examples use matrices stored in hdf5 format.
The code does run, but have not checked correctness. Instructions for using it from Fortran without CMake would be helpful, for example
gfortran mepack_example.f90 -I /usr/lib64/gfortran/modules/mepack/ -L /usr/lib64/ -lmepack -llapack -lblas
The main reference: M. Köhler. 2021. Approximate Solution of Non-Symmetric Generalized Eigenvalue Problems and Linear Matrix Equation on HPC Platforms. Dissertation. Logos Verlag Berlin, Magdeburg, Germany.
does not seem to be available for download, though one of the cited references Gardiner et al. is available: https://doi.org/10.1145/146847.146930
https://bugzilla.redhat.com/show_bug.cgi?id=2166884
Benson Muite benson_muite@emailplus.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |POST Flags|fedora-review? |fedora-review+
--- Comment #16 from Benson Muite benson_muite@emailplus.org --- Package is approved. Though it could be made easier to use. Octave interface may be a useful addition for some users.
https://bugzilla.redhat.com/show_bug.cgi?id=2166884
--- Comment #17 from Iñaki Ucar i.ucar86@gmail.com --- Thanks! Yes, I offered to package this libcscutils independently in the past, but they told me that they make an adhoc use of this, different projects may bundle slightly different versions for testing purposes, and they do not release it separately. So given that this is only for development purposes and won't end up in any user system, I agree with them that it makes little sense to waste downstream time in this.
I also asked about the Octave interface, and it is not yet available as an Octave package, so that is why I don't build it. I'll look into it if this changes and improves.
https://bugzilla.redhat.com/show_bug.cgi?id=2166884
--- Comment #18 from Fedora Admin user for bugzilla script actions fedora-admin-xmlrpc@fedoraproject.org --- The Pagure repository was created at https://src.fedoraproject.org/rpms/mepack
https://bugzilla.redhat.com/show_bug.cgi?id=2166884
Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|POST |MODIFIED
--- Comment #19 from Fedora Update System updates@fedoraproject.org --- FEDORA-2023-923ad1c218 has been submitted as an update to Fedora 39. https://bodhi.fedoraproject.org/updates/FEDORA-2023-923ad1c218
https://bugzilla.redhat.com/show_bug.cgi?id=2166884
Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|MODIFIED |CLOSED Resolution|--- |ERRATA Last Closed| |2023-03-08 06:35:05
--- Comment #20 from Fedora Update System updates@fedoraproject.org --- FEDORA-2023-923ad1c218 has been pushed to the Fedora 39 stable repository. If problem still persists, please make note of it in this bug report.
package-review@lists.fedoraproject.org