[Bug 1224385] Review Request: percolator - Software for postprocessing of shotgun proteomics data

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https://bugzilla.redhat.com/show_bug.cgi?id=1224385

David Tardon <dtardon@xxxxxxxxxx> changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
              Flags|                            |fedora-review+



--- Comment #14 from David Tardon <dtardon@xxxxxxxxxx> ---
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 RAMP_license_lgpl-2.1.txt in rpm(s)
  See:
  http://fedoraproject.org/wiki/Packaging/LicensingGuidelines#License_Text


===== 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:
     "Apache (v2.0)", "LGPL (v2.1 or later) (with incorrect FSF address)",
     "Unknown or generated". 84 files have unknown license. Detailed output of
     licensecheck in
     /home/dachjo/packaging/fedora/new/1224385-percolator/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.
[x]: Package requires other packages for directories it uses.
     Note: No known owner of /usr/share/licenses
[x]: Package must own all directories that it creates.
     Note: Directories without known owners: /usr/share/licenses
[x]: Package does not own files or directories owned by other packages.
     Note: Dirs in package are owned also by: /usr/share/xml(xml-common)

Maybe it would be better to require xml-common?

[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.
[-]: 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 10240 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]: 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

===== 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).
[-]: Fully versioned dependency in subpackages if applicable.
     Note: No Requires: %{name}%{?_isa} = %{version}-%{release} in percolator-
     data
[?]: Package functions as described.
[x]: Latest version is packaged.
[x]: Package does not include license text files separate from upstream.
[-]: 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.
[?]: 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:
[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: percolator-2.09.0-3.fc20.x86_64.rpm
          percolator-data-2.09.0-3.fc20.noarch.rpm
          percolator-2.09.0-3.fc20.src.rpm
percolator.x86_64: W: spelling-error Summary(en_US) postprocessing -> post
processing, post-processing, teleprocessing
percolator.x86_64: W: spelling-error Summary(en_US) proteomics -> Proterozoic
percolator.x86_64: W: spelling-error %description -l en_US spectrometry ->
spectrometer, spectroscopy, spectroscope
percolator.x86_64: W: spelling-error %description -l en_US peptide -> pep tide,
pep-tide, peptic
percolator.x86_64: W: invalid-url URL: http://per-colator.com/ [Errno 104]
Connection reset by peer
percolator.x86_64: W: no-documentation
percolator.x86_64: W: no-manual-page-for-binary tandem2pin
percolator.x86_64: W: no-manual-page-for-binary msgf2pin
percolator.x86_64: W: no-manual-page-for-binary percolator
percolator.x86_64: W: no-manual-page-for-binary elude
percolator.x86_64: W: no-manual-page-for-binary qvality
percolator.x86_64: W: no-manual-page-for-binary sqt2pin
percolator-data.noarch: W: summary-not-capitalized C percolator data files
percolator.src: W: spelling-error Summary(en_US) postprocessing -> post
processing, post-processing, teleprocessing
percolator.src: W: spelling-error Summary(en_US) proteomics -> Proterozoic
percolator.src: W: spelling-error %description -l en_US spectrometry ->
spectrometer, spectroscopy, spectroscope
percolator.src: W: spelling-error %description -l en_US peptide -> pep tide,
pep-tide, peptic
3 packages and 0 specfiles checked; 0 errors, 17 warnings.




Rpmlint (installed packages)
----------------------------
Cannot parse rpmlint output:


Requires
--------
percolator-data (rpmlib, GLIBC filtered):

percolator (rpmlib, GLIBC filtered):
    libbz2.so.1()(64bit)
    libc.so.6()(64bit)
    libdl.so.2()(64bit)
    libgcc_s.so.1()(64bit)
    libgcc_s.so.1(GCC_3.0)(64bit)
    libgcc_s.so.1(GCC_4.0.0)(64bit)
    libgomp.so.1()(64bit)
    libgomp.so.1(GOMP_1.0)(64bit)
    libm.so.6()(64bit)
    libpthread.so.0()(64bit)
    libsqlite3.so.0()(64bit)
    libstdc++.so.6()(64bit)
    libstdc++.so.6(CXXABI_1.3)(64bit)
    libstdc++.so.6(CXXABI_1.3.1)(64bit)
    libtokyocabinet.so.9()(64bit)
    libxerces-c-3.1.so()(64bit)
    libz.so.1()(64bit)
    libz.so.1(ZLIB_1.2.0)(64bit)
    percolator-data
    rtld(GNU_HASH)



Provides
--------
percolator-data:
    percolator-data

percolator:
    percolator
    percolator(x86-64)



Source checksums
----------------
https://github.com/percolator/percolator/tarball/master#/percolator-percolator-rel-2-09-0-g4e0d58a.tar.gz
:
  CHECKSUM(SHA256) this package     :
cbbbcf768c02f8c72501f24238780caae3b1f93c46fe76ab5764ab8db94669e9
  CHECKSUM(SHA256) upstream package :
cbbbcf768c02f8c72501f24238780caae3b1f93c46fe76ab5764ab8db94669e9
http://noble.gs.washington.edu/proj/percolator/data/yeast-01.sqt.tar.gz :
  CHECKSUM(SHA256) this package     :
6704da443434a1c6f15a24cccd4dbb5caeef5bc62e836a47f6fee351f911bf02
  CHECKSUM(SHA256) upstream package :
6704da443434a1c6f15a24cccd4dbb5caeef5bc62e836a47f6fee351f911bf02


Generated by fedora-review 0.5.2 (63c24cb) last change: 2014-07-14
Command line :/usr/bin/fedora-review -b 1224385
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