[Bug 620385] Review Request: BEDTools - A flexible suite of utilities for comparing genomic features

Wed Sep 1 15:02:05 UTC 2010

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https://bugzilla.redhat.com/show_bug.cgi?id=620385

Martin Gieseking <martin.gieseking at uos.de> changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |ASSIGNED
         AssignedTo|nobody at fedoraproject.org    |martin.gieseking at uos.de
               Flag|                            |fedora-review?

--- Comment #11 from Martin Gieseking <martin.gieseking at uos.de> 2010-09-01 11:02:03 EDT ---
Here's the formal review. The package looks good now. Just one thing:
Since upstream said the pdf file is licensed under GPLv2, you should reflect
that in a License field of the -docs package. Alternatively, ask the developer
if he really meant GPLv2, or if GPLv2+ is also OK. In the latter case, you
don't need a separate License tag. Maybe he can add a corresponding notice in
the pdf file, too.

$ rpmlint /var/lib/mock/fedora-13-i386/result/*.rpm
BEDTools.i686: W: no-manual-page-for-binary complementBed
BEDTools.i686: W: no-manual-page-for-binary genomeCoverageBed
BEDTools.i686: W: no-manual-page-for-binary mergeBed
BEDTools.i686: W: no-manual-page-for-binary pairToPair
BEDTools.i686: W: no-manual-page-for-binary groupBy
BEDTools.i686: W: no-manual-page-for-binary fastaFromBed
BEDTools.i686: W: no-manual-page-for-binary slopBed
BEDTools.i686: W: no-manual-page-for-binary bedToIgv
BEDTools.i686: W: no-manual-page-for-binary overlap
BEDTools.i686: W: no-manual-page-for-binary subtractBed
BEDTools.i686: W: no-manual-page-for-binary bamToBed
BEDTools.i686: W: no-manual-page-for-binary intersectBed
BEDTools.i686: W: no-manual-page-for-binary maskFastaFromBed
BEDTools.i686: W: no-manual-page-for-binary bed12ToBed6
BEDTools.i686: W: no-manual-page-for-binary bedToBam
BEDTools.i686: W: no-manual-page-for-binary unionBedGraphs
BEDTools.i686: W: no-manual-page-for-binary sortBed
BEDTools.i686: W: no-manual-page-for-binary windowBed
BEDTools.i686: W: no-manual-page-for-binary closestBed
BEDTools.i686: W: no-manual-page-for-binary linksBed
BEDTools.i686: W: no-manual-page-for-binary shuffleBed
BEDTools.i686: W: no-manual-page-for-binary coverageBed
BEDTools.i686: W: no-manual-page-for-binary pairToBed
BEDTools.src: W: invalid-url Source1:
http://bedtools.googlecode.com/files/BEDTools-User-Manual.v3.pdf HTTP Error
404: Not Found
BEDTools.src: W: invalid-url Source0:
http://bedtools.googlecode.com/files/BEDTools.v2.9.0.tar.gz HTTP Error 404: Not
Found
4 packages and 0 specfiles checked; 0 errors, 25 warnings.

All above warnings can be ignored:
- no manual pages available
- invalid URL warnings are false positive

---------------------------------
key:

[+] OK
[.] OK, not applicable
[X] needs work
---------------------------------

[+] MUST: The package must be named according to the Package Naming Guidelines.
[+] MUST: The spec file name must match the base package %{name}.
[+] MUST: The package must meet the Packaging Guidelines.
[+] MUST: The package must be licensed with a Fedora approved license.
[X] MUST: The License field in the package spec file must match the actual
license.
    - add License: GPLv2 to the -docs package

[+] MUST: The file containing the text of the license(s) for the package must
be included in %doc.
    - no separate license file available for pdf file
    => docs package doesn't require a license file

[+] MUST: The spec file must be written in American English.
[+] MUST: The spec file for the package MUST be legible.
[+] MUST: The sources used to build the package must match the upstream source.
    $ md5sum BEDTools*
    85e66413587f3f1cbb5e9530c20c6d1e  BEDTools-User-Manual.v3.pdf
    85e66413587f3f1cbb5e9530c20c6d1e  BEDTools-User-Manual.v3.pdf.1
    a0ac1e63fe4a7ae72e33fd91c24ac3da  BEDTools.v2.9.0.tar.gz
    a0ac1e63fe4a7ae72e33fd91c24ac3da  BEDTools.v2.9.0.tar.gz.1

[+] MUST: The package MUST successfully compile and build into binary rpms on
at least one primary architecture.
[.] MUST: If the package does not successfully compile, build or work ...
[+] MUST: All build dependencies must be listed in BuildRequires.
[.] MUST: The spec file MUST handle locales properly.
[.] MUST: Packages storing shared libraries must call ldconfig in %post and
%postun.
[+] MUST: Packages must NOT bundle copies of system libraries.
[.] MUST: If the package is designed to be relocatable, ...
[+] MUST: A package must own all directories that it creates. 
[+] MUST: A Fedora package must not list a file more than once in %files.
[+] MUST: Permissions on files must be set properly.
[+] MUST: Each package must consistently use macros.
[+] MUST: The package must contain code, or permissable content.
[+] MUST: Large documentation files must go in a -doc subpackage.
[+] MUST: Files in %doc must not affect the runtime of the application.
[.] MUST: Header files must be in a -devel package.
[.] MUST: Static libraries must be in a -static package.
[.] MUST: .so files must go in a -devel package.
[.] MUST: devel packages must require the base package.
[+] MUST: Packages must NOT contain any .la libtool archives.
[.] MUST: Packages containing GUI applications must include a %{name}.desktop
file.
[+] MUST: Packages must not own files or directories already owned by other
packages.
[+] MUST: All filenames in rpm packages must be valid UTF-8.

[.] SHOULD: If the source package does not include license text(s) ...
[+] SHOULD: The reviewer should test that the package builds in mock.
[+] SHOULD: The package should compile and build into binary rpms on all
supported architectures.
[+] SHOULD: The reviewer should test that the package functions as described.
[.] SHOULD: If scriptlets are used, those scriptlets must be sane.
[.] SHOULD: Usually, subpackages other than devel should require the base
package.
    - doc package doesn't require the base package

[.] SHOULD: pkgconfig(.pc) files should be placed in a -devel pkg.
[.] SHOULD: If the package has file dependencies outside of /etc, /bin, /sbin,
/usr/bin, or /usr/sbin...
[X] SHOULD: your package should contain man pages for binaries/scripts. 
    - would be great if upstream could add manual pages for the utilities, 
      but that's optional, of course

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