[Bug 1167467] Review Request: bionetgen - Software for rule-based modeling of biochemical systems

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https://bugzilla.redhat.com/show_bug.cgi?id=1167467



--- Comment #3 from Mukundan Ragavan <nonamedotc@xxxxxxxxx> ---

Hi, here is the detailed review.


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

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


Issues:
=======
- 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 %doc.
  Note: Cannot find LICENSE.txt in rpm(s)
  See:
  http://fedoraproject.org/wiki/Packaging/LicensingGuidelines#License_Text

---> Bogus warning. License is installed using %license macro and hence no
shown under %doc.


===== 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]: 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:
     "MIT/X11 (BSD like)", "BSD (2 clause)", "GPL (v2 or later)", "GPL (v3 or
     later)", "Unknown or generated". 349 files have unknown license. Detailed
     output of licensecheck in
     /home/mukundan/ownCloud/pkg_reviews/1167467-bionetgen/licensecheck.txt


---> This looks fine.

[x]: License file installed when any subpackage combination is installed.
[x]: Package must own all directories that it creates.
     Note: Directories without known owners: /usr/share/licenses

---> Bogus warning. Directory provided by filesystem package in rawhide.

[x]: %build honors applicable compiler flags or justifies otherwise.
[x]: Package contains no bundled libraries without FPC exception.

---> depends on sundials, bundled items removed in prep.

[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
[-]: 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 30720 bytes in 3 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]: 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 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 do not use a name that already exist
[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

Perl:
[x]: Package contains the mandatory BuildRequires and Requires:.

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

Generic:
[x]: 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 bionetgen-
     perl
[x]: Package functions as described.
[x]: Latest version is packaged.
[x]: Package does not include license text files separate from upstream.
[x]: 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.
[x]: %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]: 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]: Dist tag is present (not strictly required in GL).
[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:
[!]: Package should not use obsolete m4 macros
     Note: Some obsoleted macros found, see the attachment.
     See: https://fedorahosted.org/FedoraReview/wiki/AutoTools

---> Changing this to [x]. As far as I can tell from the configure.ac file and
auto{conf/make} docs, all else seems fine.

Spec file correctly changes some of the obsolete macros. From the spec,

sed -i 's/AC_PROG_LIBTOOL/AM_PROG_AR\nLT_INIT/' configure.ac
sed -i 's/cvode-2\.6\.0//; s/muparser_v2_2_3//' configure.ac Makefile.am

The error mentioned here,

AutoTools: Obsoleted m4s found
------------------------------
  AC_PROG_LIBTOOL found in:
  BioNetGen-2.2.5-stable/Network3/cvode-2.6.0/configure.ac:91

is bogus since the entire directory is removed in %prep (bundled stuff).


[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: bionetgen-2.2.5-1.fc22.x86_64.rpm
          bionetgen-perl-2.2.5-1.fc22.noarch.rpm
          bionetgen-2.2.5-1.fc22.src.rpm
bionetgen.x86_64: W: spelling-error %description -l en_US transduction ->
transaction, introductions, transducer
bionetgen.x86_64: W: no-manual-page-for-binary run_network
bionetgen-perl.noarch: W: no-documentation
bionetgen.src: W: spelling-error %description -l en_US transduction ->
transaction, introductions, transducer
bionetgen.src: W: invalid-url Source0:
https://bionetgen.googlecode.com/files/BioNetGen-2.2.5-stable.zip HTTP Error
404: Not Found

---> Bogus. Perhaps, the network was down temporarily.

3 packages and 0 specfiles checked; 0 errors, 5 warnings.




Rpmlint (installed packages)
----------------------------
]0;<mock-chroot><mock-chroot>[root@imladris /]# rpmlint bionetgen-perl
bionetgen
bionetgen-perl.noarch: W: no-documentation
bionetgen.x86_64: W: spelling-error %description -l en_US transduction ->
transaction, introductions, transducer
bionetgen.x86_64: W: no-manual-page-for-binary run_network
2 packages and 0 specfiles checked; 0 errors, 3 warnings.
]0;<mock-chroot><mock-chroot>[root@imladris /]# echo 'rpmlint-done:'



Requires
--------
bionetgen-perl (rpmlib, GLIBC filtered):
    /usr/bin/perl
    bionetgen
    perl(Carp)
    perl(Class::Struct)
    perl(Config)
    perl(Cwd)
    perl(Data::Dumper)
    perl(Exporter)
    perl(File::Basename)
    perl(File::Path)
    perl(File::Spec)
    perl(FindBin)
    perl(Getopt::Long)
    perl(IO::Handle)
    perl(IO::Select)
    perl(IPC::Open3)
    perl(List::Util)
    perl(Math::Trig)
    perl(POSIX)
    perl(Scalar::Util)
    perl(Symbol)
    perl(constant)
    perl(lib)
    perl(strict)
    perl(vars)
    perl(warnings)

bionetgen (rpmlib, GLIBC filtered):
    bionetgen-perl
    libc.so.6()(64bit)
    libgcc_s.so.1()(64bit)
    libgcc_s.so.1(GCC_3.0)(64bit)
    libm.so.6()(64bit)
    libmuparser.so.2()(64bit)
    libstdc++.so.6()(64bit)
    libstdc++.so.6(CXXABI_1.3)(64bit)
    libsundials_cvode.so.1()(64bit)
    libsundials_nvecserial.so.0()(64bit)
    perl(:MODULE_COMPAT_5.20.1)
    rtld(GNU_HASH)



Provides
--------
bionetgen-perl:
    bionetgen-perl

bionetgen:
    bionetgen
    bionetgen(x86-64)



Source checksums
----------------
https://bionetgen.googlecode.com/files/BioNetGen-2.2.5-stable.zip :
  CHECKSUM(SHA256) this package     :
4186ae1b8990e192775ead0bb7ae40170802d859bb9396047deb8cedaa02ad03
  CHECKSUM(SHA256) upstream package :
4186ae1b8990e192775ead0bb7ae40170802d859bb9396047deb8cedaa02ad03





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