Bug 481508

OK source files match upstream: 6da4d203440470d2709f3894e648b4aa
OK package meets naming and versioning guidelines.
FAIL specfile is properly named, is cleanly written and uses macros 
consistently.
- RPM_BUILD_ROOT vs. buildroot - use only one of these macros
OK dist tag is present.
OK build root is correct.
FAIL license field matches the actual license.
- You can find GPLv3+ in COPYING and PKG-INFO
OK license is open source-compatible. License text not included upstream.
OK latest version is being packaged.
OK BuildRequires are proper.
OK %clean is present.
OK package builds in mock (Rawhide/x86_64).
OK debuginfo package isn't need.
OK rpmlint is silent.
OK final provides and requires look sane.
OK no shared libraries are added to the regular linker search paths.
OK owns the directories it creates.
OK no duplicates in %files.
OK file permissions are appropriate.
OK no scriptlets present.
OK code, not content.
OK documentation is small, so no -docs subpackage is necessary.
OK %docs are not necessary for the proper functioning of the package.
OK no headers.
OK no pkgconfig files.
OK no libtool .la droppings.

Marcela, thanks for the review.

(In reply to comment #1)
> FAIL specfile is properly named, is cleanly written and uses macros 
> consistently.
> - RPM_BUILD_ROOT vs. buildroot - use only one of these macros

a stupid copy-and-paste-error, fixed

> FAIL license field matches the actual license.
> - You can find GPLv3+ in COPYING and PKG-INFO

fixed

Updated files:

Spec URL: http://fab.fedorapeople.org/packages/SRPMS/pipviewer.spec
SRPM URL:
http://fab.fedorapeople.org/packages/SRPMS/pipviewer-0.3.9-2.fc10.src.rpm

ACCEPTED

New Package CVS Request
=======================
Package Name: pipviewer
Short Description: Visualizer for multiple alignments of genomic sequences
Owners: fab
Branches: F-9 F-10
InitialCC:

cvs done.

pipviewer-0.3.9-2.fc9 has been pushed to the Fedora 9 testing repository.  If problems still persist, please make note of it in this bug report.
 If you want to test the update, you can install it with 
 su -c 'yum --enablerepo=updates-testing-newkey update pipviewer'.  You can provide feedback for this update here: http://admin.fedoraproject.org/updates/F9/FEDORA-2009-1394

pipviewer-0.3.9-2.fc10 has been pushed to the Fedora 10 testing repository.  If problems still persist, please make note of it in this bug report.
 If you want to test the update, you can install it with 
 su -c 'yum --enablerepo=updates-testing update pipviewer'.  You can provide feedback for this update here: http://admin.fedoraproject.org/updates/F10/FEDORA-2009-1405

There are serious problems with the Requires.  Although vhybridize is found at build-time as you have:

BuildRequires: vhybridize

this is not sufficient as the autodeps searcher in RPM does not search the resulting package and automatically add the dependent packages (unlike for Perl) and all dependent Python packages must be added *explicitly* in the .spec file, otherwise it fails on install:

$ pipviewer 
Traceback (most recent call last):
  File "/usr/bin/pipviewer", line 5, in <module>
    from pkg_resources import load_entry_point
  File "/usr/lib/python2.5/site-packages/pkg_resources.py", line 2562, in <module>
    working_set.require(__requires__)
  File "/usr/lib/python2.5/site-packages/pkg_resources.py", line 626, in require
    needed = self.resolve(parse_requirements(requirements))
  File "/usr/lib/python2.5/site-packages/pkg_resources.py", line 524, in resolve
    raise DistributionNotFound(req)  # XXX put more info here
pkg_resources.DistributionNotFound: vhybridize>=0.5.9

Ditto for  PyQt pygtk2 PyOpenGL, and you need the runtime versions of these (add any minimum version Requires as well):

Requires: PyQt, pygtk, PyOpenGL >= 2.0, vhybridize >= 0.5.9

Also it seems that PyOpenGL isn't sufficient to get this to work, as I have this installed

$ rpm -q PyOpenGL
PyOpenGL-3.0.0-0.9.b8.fc10.noarch

but it still fails at runtime.

$ pipviewer 
Traceback (most recent call last):
  File "/usr/bin/pipviewer", line 5, in <module>
    from pkg_resources import load_entry_point
  File "/usr/lib/python2.5/site-packages/pkg_resources.py", line 2562, in <module>
    working_set.require(__requires__)
  File "/usr/lib/python2.5/site-packages/pkg_resources.py", line 626, in require
    needed = self.resolve(parse_requirements(requirements))
  File "/usr/lib/python2.5/site-packages/pkg_resources.py", line 524, in resolve
    raise DistributionNotFound(req)  # XXX put more info here
pkg_resources.DistributionNotFound: OpenGL>=2.0

The last OpenGL problem appears to be a problem with the information in the egg file:

/usr/lib/python2.5/site-packages/pipviewer-0.3.9-py2.5.egg-info/requires.txt

it contains

OpenGL>=2.0
vhybridize>=0.5.9

but the package is called PyOpenGL not OpenGL, if you change OpenGL -> PyOpenGL it starts.

Note to reviewer: you should ensure you test the package at run-time on at least one release before approving a package.

Also the summary has multiple typos:

Pipviewer is a visualizer for multiple 
alignements 
^^^ alignments

of genomic sequences.  It highlights conserved regions and allows basic
anotations.
^^^ annotations

Its main goal is to find conserved probes for the
construction of gene order data sets.  Selected regions marked as
'probes' can be expoxted to fasta format.  It can also 
retreive 
^^^ retrieve

gene annotations 
form 
^^^ from

the NBCI and display this information along the
alignement.
^^^ alignment

Thanks for testing this application.

(In reply to comment #9)
> The last OpenGL problem appears to be a problem with the information in the egg
> file:
> 
> /usr/lib/python2.5/site-packages/pipviewer-0.3.9-py2.5.egg-info/requires.txt
> 
> it contains
> 
> OpenGL>=2.0
> vhybridize>=0.5.9
> 
> but the package is called PyOpenGL not OpenGL, if you change OpenGL -> PyOpenGL
> it starts.

Patch0 should fix this

(In reply to comment #11)
> Also the summary has multiple typos:

thanks, fixed

Updated files
Spec URL: http://fab.fedorapeople.org/packages/SRPMS/pipviewer.spec
SRPM URL:
http://fab.fedorapeople.org/packages/SRPMS/pipviewer-0.3.9-3.fc10.src.rpm

It works from the command line but unfortunately it still does not work from the menu.

pipviewer-0.3.9-5.fc10 has been submitted as an update for Fedora 10.
http://admin.fedoraproject.org/updates/pipviewer-0.3.9-5.fc10

pipviewer-0.3.9-5.fc9 has been submitted as an update for Fedora 9.
http://admin.fedoraproject.org/updates/pipviewer-0.3.9-5.fc9

pipviewer-0.3.9-5.fc9 has been pushed to the Fedora 9 testing repository.  If problems still persist, please make note of it in this bug report.
 If you want to test the update, you can install it with 
 su -c 'yum --enablerepo=updates-testing-newkey update pipviewer'.  You can provide feedback for this update here: http://admin.fedoraproject.org/updates/F9/FEDORA-2009-2344

pipviewer-0.3.9-5.fc10 has been pushed to the Fedora 10 testing repository.  If problems still persist, please make note of it in this bug report.
 If you want to test the update, you can install it with 
 su -c 'yum --enablerepo=updates-testing update pipviewer'.  You can provide feedback for this update here: http://admin.fedoraproject.org/updates/F10/FEDORA-2009-2345

pipviewer-0.3.9-5.fc10 has been pushed to the Fedora 10 stable repository.  If problems still persist, please make note of it in this bug report.

pipviewer-0.3.9-5.fc9 has been pushed to the Fedora 9 stable repository.  If problems still persist, please make note of it in this bug report.