[Bug 1231427] Review Request: COPASI - Biochemical network simulator

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https://bugzilla.redhat.com/show_bug.cgi?id=1231427



--- Comment #14 from Antonio Trande <anto.trande@xxxxxxxxx> ---
(In reply to Dave Johansen from comment #13)
> Issues:
> =======
> [!]: Development (unversioned) .so files in -devel subpackage, if present.
>   Several .so files in %_libdir. Are these ok?

Yes, they are in private %_libdir sub-directories.

> [!]: Package is licensed with an open-source compatible license and meets
>      other legal requirements as defined in the legal section of Packaging
>      Guidelines.
>   license.txt does not appear to be Artistic 2.0 and states "You cannot
> redistribute this test version."
> [!]: License field in the package spec file matches the actual license.
>   Several licenses found by licensecheck. Here's the list:
>     BSD (2 clause)
>     --------------
>    
> COPASI-192df43f09810b4416c7c59bec08ed63a2c22186/copasi/randomGenerator/
> Cmt19937.cpp
>    
> COPASI-192df43f09810b4416c7c59bec08ed63a2c22186/copasi/randomGenerator/
> Cmt19937.h
>     GPL (v2 or later)
>     -----------------
>    
> COPASI-192df43f09810b4416c7c59bec08ed63a2c22186/copasi/model/
> CChemEqParser_yacc.cpp
>    
> COPASI-192df43f09810b4416c7c59bec08ed63a2c22186/copasi/model/
> CChemEqParser_yacc.hpp
>     GPL (v2 or later) GPL (v2 or later) (with incorrect FSF address)
>     ----------------------------------------------------------------
>    
> COPASI-192df43f09810b4416c7c59bec08ed63a2c22186/copasi/MIRIAM/
> WebServicesIssues/stdsoap2.cpp
>    
> COPASI-192df43f09810b4416c7c59bec08ed63a2c22186/copasi/MIRIAM/
> WebServicesIssues/stdsoap2.h
>     GPL (v3 or later)
>     -----------------
>    
> COPASI-192df43f09810b4416c7c59bec08ed63a2c22186/copasi/function/
> CEvaluationParser_yacc.cpp
>    
> COPASI-192df43f09810b4416c7c59bec08ed63a2c22186/copasi/function/
> CEvaluationParser_yacc.hpp
>     LGPL
>     ----
>     COPASI-192df43f09810b4416c7c59bec08ed63a2c22186/copasi/sbml/IdList.h
>     MIT/X11 (BSD like)
>     ------------------
>     COPASI-192df43f09810b4416c7c59bec08ed63a2c22186/copasi/GL/glext.h

Fixed.

> [!]: Package must own all directories that it creates.
>      Note: Directories without known owners:
>      /usr/lib/perl5/vendor_perl/auto, /usr/lib/perl5,
>      /usr/lib/perl5/vendor_perl, /usr/lib/mono, /usr/share/copasi,
>      /usr/share/java

Only /usr/share/copasi must be owned by this package.

> [!]: Useful -debuginfo package or justification otherwise.
>   Missing -debuginfo.

Disabled.
There is still the debugedit error.

> [!]: Fully versioned dependency in subpackages if applicable.
>   I'm not sure which of these are appropriate, but:
>      Note: No Requires: %{name}%{?_isa} = %{version}-%{release} in COPASI-
>      gui , COPASI-data , python-COPASI , python3-COPASI , java-COPASI ,
>      perl-COPASI , R-COPASI , COPASI-sharp , COPASI-doc

Only COPASI and COPASI-gui need COPASI-data.
All the others are stand-alone package.

> [!]: Patches link to upstream bugs/comments/lists or are otherwise
>      justified.
>   Needs to be fixed

All patches are commented.

> 
> Other Issues:
> =======
> [!]: examples are in -data but would it make sense for them to be somewhere
> else?
> 
> [!]: I would recommend making the .desktop and .appdata.xml sources to
> simplify the .spec file.

It's not need to me.

> 
> ===== MUST items =====
> 
> C/C++:
> [x]: Package does not contain kernel modules.
> [x]: Package contains no static executables.
> [x]: Package does not contain any libtool archives (.la)
> [x]: Rpath absent or only used for internal libs.
> 
> Generic:
> [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.
> [-]: 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]: gtk-update-icon-cache is invoked in %postun and %posttrans if package
>      contains icons.
> [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]: Package requires other packages for directories it uses.
> [x]: Package does not own files or directories owned by other packages.
> [x]: All build dependencies are listed in BuildRequires, except for any
>      that are listed in the exceptions section of Packaging Guidelines.
> [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]: Package contains desktop file if it is a GUI application.
> [x]: 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]: Large documentation must go in a -doc subpackage. Large could be size
>      (~1MB) or number of files.
>      Note: Documentation size is 0 bytes in 0 files.
> [x]: Packages must not store files under /srv, /opt or /usr/local
> 
> Java:
> [x]: Bundled jar/class files should be removed before build
> 
> Python:
> [-]: 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.
> [x]: Package meets the Packaging Guidelines::Python
> [x]: Package contains BR: python2-devel or python3-devel
> [x]: Binary eggs must be removed in %prep
> 
> ===== 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]: Scriptlets must be sane, if used.
> [-]: Description and summary sections in the package spec file contains
>      translations for supported Non-English languages, if available.
> [?]: Package should compile and build into binary rpms on all supported
>      architectures.
> [x]: %check is present and all tests pass.
>   NOTE: Tests are of packaging and not of COPASI itself
> [x]: Packages should try to preserve timestamps of original installed
>      files.
> [x]: Packager, Vendor, PreReq, Copyright tags should not be in spec file
> [x]: Sources can be downloaded from URI in Source: tag
> [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 =====
> 
> Generic:
> [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: COPASI-4.16.101-8.20150707git192df4.fc23.i686.rpm
>           COPASI-gui-4.16.101-8.20150707git192df4.fc23.i686.rpm
>           COPASI-data-4.16.101-8.20150707git192df4.fc23.noarch.rpm
>           python-COPASI-4.16.101-8.20150707git192df4.fc23.i686.rpm
>           python3-COPASI-4.16.101-8.20150707git192df4.fc23.i686.rpm
>           java-COPASI-4.16.101-8.20150707git192df4.fc23.i686.rpm
>           perl-COPASI-4.16.101-8.20150707git192df4.fc23.i686.rpm
>           R-COPASI-4.16.101-8.20150707git192df4.fc23.i686.rpm
>           COPASI-sharp-4.16.101-8.20150707git192df4.fc23.i686.rpm
>           COPASI-doc-4.16.101-8.20150707git192df4.fc23.noarch.rpm
>           COPASI-4.16.101-8.20150707git192df4.fc23.src.rpm
> COPASI.i686: W: spelling-error %description -l en_US customizable ->
> customization
> COPASI.i686: W: unstripped-binary-or-object /usr/bin/CopasiSE
> COPASI.i686: W: no-documentation
> COPASI.i686: W: no-manual-page-for-binary CopasiSE
> COPASI-gui.i686: W: spelling-error %description -l en_US customizable ->
> customization
> COPASI-gui.i686: W: unstripped-binary-or-object /usr/bin/CopasiUI
> COPASI-gui.i686: W: no-documentation
> COPASI-gui.i686: W: no-manual-page-for-binary CopasiUI
> COPASI-data.noarch: W: no-documentation
> python-COPASI.i686: W: unstripped-binary-or-object
> /usr/lib/python2.7/site-packages/copasi/_COPASI.so
> python-COPASI.i686: W: no-documentation
> python3-COPASI.i686: W: unstripped-binary-or-object
> /usr/lib/python3.4/site-packages/copasi/_COPASI.so
> python3-COPASI.i686: W: no-documentation
> java-COPASI.i686: W: unstripped-binary-or-object
> /usr/lib/copasi/libCopasiJava.so
> java-COPASI.i686: W: no-documentation
> perl-COPASI.i686: W: unstripped-binary-or-object
> /usr/lib/perl5/vendor_perl/auto/COPASI/COPASI.so
> perl-COPASI.i686: W: no-documentation
> R-COPASI.i686: W: unstripped-binary-or-object
> /usr/lib/R/library/COPASI/libs/COPASI.so
> R-COPASI.i686: W: no-documentation
> R-COPASI.i686: E: zero-length /usr/lib/R/library/COPASI/help/AnIndex
> R-COPASI.i686: E: zero-length /usr/lib/R/library/COPASI/help/COPASI.rdb
> COPASI-sharp.i686: W: unstripped-binary-or-object
> /usr/lib/mono/copasicsP/libcopasics.so
> COPASI-sharp.i686: W: no-documentation
> COPASI-doc.noarch: W: no-documentation
> COPASI.src: W: spelling-error %description -l en_US customizable ->
> customization
> COPASI.src:489: E: hardcoded-library-path in %{_prefix}/lib/mono/copasicsP/
> 11 packages and 0 specfiles checked; 3 errors, 23 warnings.
> 
> Only issue of concern seems to be the unstripped files, but I'm guessing
> that that's related to the -debuginfo not working.
> 
> 
> Rpmlint (installed packages)
> ----------------------------
> perl-COPASI.i686: W: unstripped-binary-or-object
> /usr/lib/perl5/vendor_perl/auto/COPASI/COPASI.so
> perl-COPASI.i686: W: no-documentation
> java-COPASI.i686: W: unstripped-binary-or-object
> /usr/lib/copasi/libCopasiJava.so
> java-COPASI.i686: W: no-documentation
> COPASI-gui.i686: W: unstripped-binary-or-object /usr/bin/CopasiUI
> COPASI-gui.i686: W: no-documentation
> COPASI-gui.i686: W: no-manual-page-for-binary CopasiUI
> R-COPASI.i686: W: unstripped-binary-or-object
> /usr/lib/R/library/COPASI/libs/COPASI.so
> R-COPASI.i686: W: no-documentation
> R-COPASI.i686: E: zero-length /usr/lib/R/library/COPASI/help/AnIndex
> R-COPASI.i686: E: zero-length /usr/lib/R/library/COPASI/help/COPASI.rdb
> COPASI-sharp.i686: W: unstripped-binary-or-object
> /usr/lib/mono/copasicsP/libcopasics.so
> COPASI-sharp.i686: W: no-documentation
> COPASI-doc.noarch: W: no-documentation
> python-COPASI.i686: W: unstripped-binary-or-object
> /usr/lib/python2.7/site-packages/copasi/_COPASI.so
> python-COPASI.i686: W: no-documentation
> python3-COPASI.i686: W: unstripped-binary-or-object
> /usr/lib/python3.4/site-packages/copasi/_COPASI.so
> python3-COPASI.i686: W: no-documentation
> COPASI.i686: W: unstripped-binary-or-object /usr/bin/CopasiSE
> COPASI.i686: W: no-documentation
> COPASI.i686: W: no-manual-page-for-binary CopasiSE
> COPASI-data.noarch: W: no-documentation
> 10 packages and 0 specfiles checked; 2 errors, 20 warnings.
> 
> Same comment as above.

SPEC: https://sagitter.fedorapeople.org/COPASI/COPASI.spec
SRPM:
https://sagitter.fedorapeople.org/COPASI/COPASI-4.16.101-11.20150725git435d61.fc22.src.rpm

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