[Bug 1290922] Review Request: moose - Multiscale Neuroscience and Systems Biology Simulator

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https://bugzilla.redhat.com/show_bug.cgi?id=1290922



--- Comment #9 from Zbigniew Jędrzejewski-Szmek <zbyszek@xxxxxxxxx> ---
(In reply to Antonio Trande from comment #8)
> (fedora-review is not reliable in these days)
I run it with '-x CheckOwnDirs' and it's mostly OK...

> Generic:
> [!]: Package is licensed with an open-source compatible license and meets
>      other legal requirements as defined in the legal section of Packaging
>      Guidelines.
> 
> biophysics/VClamp.cpp: *No copyright* LGPL (v3 or later)
> builtins/Func.cpp: *No copyright* LGPL (v3 or later)
> builtins/Function.cpp: *No copyright* LGPL (v3 or later)
> 
> are managed by compiler; i think guidelines for "Mixed Source Licensing
> Scenario" may be imposed here.
> https://fedoraproject.org/wiki/Packaging:LicensingGuidelines?rd=Packaging/
> LicensingGuidelines#Mixed_Source_Licensing_Scenario
I don't think this actually applies: that paragraph talks about the case
where sources have two different licenses, and to satisfy the license you have
to satisfy the constrains from both licenses (e.g. both "no advertising", and
"modifications as patches only"). But in this case we are mixing LGPL and GPL.
GPL is a superset of LGPL, and also, GPL does not allow any additional
restrictions
to be added. So effectively, the binary package is distributed under the terms
of GPL,
and no additional constraints exists and no different licensing is available.

> [!]: License field in the package spec file matches the actual license.
> [!]: License file installed when any subpackage combination is installed.
> 
> None license file is packaged.
Pull request with the license text:
https://github.com/BhallaLab/moose-core/pull/50.


> [x]: Package must own 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.
> [-]: 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.
> [-]: gtk-update-icon-cache is invoked in %postun and %posttrans if package
>      contains icons.
> [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 20480 bytes in 2 files.
> [!]: Package complies to the Packaging Guidelines
> 
> --> See above.
> 
> [x]: Package successfully compiles and builds into binary rpms on at least
>      one supported primary architecture.
> [x]: Rpmlint is run on all rpms the build produces.
> 
> moose.src: W: spelling-error Summary(en_US) Multiscale -> Timescale
> moose.src: W: spelling-error %description -l en_US subcellular -> sub
> cellular, sub-cellular, cellular
> moose.x86_64: W: spelling-error Summary(en_US) Multiscale -> Timescale
> moose.x86_64: W: spelling-error %description -l en_US subcellular -> sub
> cellular, sub-cellular, cellular
> moose.x86_64: W: no-manual-page-for-binary moose
> moose-debuginfo.x86_64: W: spurious-executable-perm
> /usr/src/debug/moose-core-ghevar_3.0.2-beta.2/device/RC.cpp
> moose-debuginfo.x86_64: W: spurious-executable-perm
> /usr/src/debug/moose-core-ghevar_3.0.2-beta.2/utility/strutil.h
> moose-debuginfo.x86_64: W: spurious-executable-perm
> /usr/src/debug/moose-core-ghevar_3.0.2-beta.2/utility/strutil.cpp
> moose-debuginfo.x86_64: W: spurious-executable-perm
> /usr/src/debug/moose-core-ghevar_3.0.2-beta.2/biophysics/MarkovChannel.h
> moose-debuginfo.x86_64: W: spurious-executable-perm
> /usr/src/debug/moose-core-ghevar_3.0.2-beta.2/device/RC.h
Fixed, also https://github.com/BhallaLab/moose-core/pull/51.

> --> Fix 'spurious-executable-perm' warnings.
> 
> [!]: 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.
> 
> --> See above.
The way I understand this point, if the license is missing, it is not supposed
to be included from other sources.

> [-]: Package requires other packages for directories it uses.
> [-]: Package does not own files or directories owned by other packages.
> [!]: All build dependencies are listed in BuildRequires, except for any
>      that are listed in the exceptions section of Packaging Guidelines.
> 
> --> gcc-c++ make can be removed as BR.
That's an error in fedora-review. gcc-g++ might be removed from the default
build root, and this dependency future-proofs against that.

> [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.
> [-]: Package contains desktop file if it is a GUI application.
> [-]: Package installs a %{name}.desktop using desktop-file-install or
>      desktop-file-validate if there is such a file.
> [x]: Dist tag is present.
> [x]: Package does not contain duplicates in %files.
> [x]: Permissions on files are set properly.
> [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:
> [x]: Sources can be downloaded from URI in Source: tag
> [-]: 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 freedv-
>      debuginfo
> [ ]: Package functions as described.
> [x]: Latest version is packaged.
> [?]: Package does not include license text files separate from upstream.
> [!]: Patches link to upstream bugs/comments/lists or are otherwise
>      justified.
> 
> --> Please, leave comments about patches.
> 
> [-]: SourceX tarball generation or download is documented.
> [-]: Description and summary sections in the package spec file contains
>      translations for supported Non-English languages, if available.
> [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]: Packager, Vendor, PreReq, Copyright tags should not be in spec file
> [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]: Uses parallel make %{?_smp_mflags} macro.
> [x]: SourceX is a working URL.
> [x]: Spec use %global instead of %define unless justified.
> 
> ===== EXTRA items =====
> 
> $ checksec --file ./moose
> RELRO  STACK CANARY  NX       PIE      RPATH  RUNPATH      FILE
> Full   Canary found  enabled  enabled  No     No RUNPATH   ./moose
> 
> I suggest to control whith 'checksec' in F22 if it's necessary.
I don't understand: this checksec output looks OK, no?

> >OpenMPI (1.8.x)     OPTIONAL For running moose in parallel on clusters
> 
> An OpenMPI implemented version is available even if optional.

Yeah, but the MPI stuff is pretty new. I would prefer to get the non-MPI
version working reliably first.

Spec URL: https://in.waw.pl/~zbyszek/fedora/moose.spec
SRPM URL: https://in.waw.pl/~zbyszek/fedora/moose-3.0.2-0.4.fc24.beta.2.src.rpm

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