[Bug 462251] Review Request: PyMOL - python molecular graphics

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https://bugzilla.redhat.com/show_bug.cgi?id=462251





--- Comment #10 from Tim Fenn <fenn at stanford.edu>  2008-10-06 14:57:46 EDT ---
(In reply to comment #8)
>   - The license tag should be "MIT and BSD and ZPLv2.0 and
>     Bitstream Vera and OFL".
> 

Done.

> * Source0
>   - Please add revision number of svn also to the name of
>     Source0 tarball (i.e. pymol-1.1-20080912svn3419.tar.gz)
> 

Done.

> * python modules dependency
>   - Please check if all python modules related rpms are correctly
>     added to Requires.
>     * For example chempy/fast/__init__.py contains:
> ------------------------------------------------
>      6  from Numeric import *
>      7  from Precision import *
> ------------------------------------------------
>       I guess pymol should have "Requires: python-numeric" (maybe even
>       more)
> 

I did my best to double-check all the python imports, everything should be
covered now.

> 
> * optflags
>   - build.log shows:
> ------------------------------------------------
>    226  creating build/temp.linux-i686-2.5/layer5
>    227  gcc -pthread -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
> -mtune=generic -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -O2 -g -pipe
> -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
> -fasynchronous-unwind-tables -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE
> -D_PYMOL_FREETYPE -D_HAVE_LIBPNG -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3
> -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -I/usr/include/python2.5 -c
> ov/src/OVContext.c -o build/temp.linux-i686-2.5/ov/src/OVContext.o -ffast-math
> -funroll-loops -O3
> ------------------------------------------------
>     Please remove "-ffast-math -funroll-loops -O3". These flags makes
>     debugging difficult, or changes calculation precision.
> 

Done - I set up the optflags as just "-O2" - is this sufficient?

> * Document
>   - Please also add the following file(s) to %doc
> -------------------------------------------------
> AUTHORS
> -------------------------------------------------
> 

Done.

> * generic rpmlint issue
> -------------------------------------------------
> pymol.i386: W: incoherent-version-in-changelog 1.1-3 1.1-3.20080912svn3419.fc10
> pymol-debuginfo.i386: W: spurious-executable-perm
> /usr/src/debug/pymol-1.1/contrib/champ/feedback2.c
> pymol-debuginfo.i386: W: spurious-executable-perm
> /usr/src/debug/pymol-1.1/contrib/champ/feedback2.h
> pymol-debuginfo.i386: W: spurious-executable-perm
> /usr/src/debug/pymol-1.1/contrib/champ/err2.c

Fixed.

> -------------------------------------------------
>   - Change the %changelog entry like below:
> -------------------------------------------------
> * Thu Oct 02 2008 Tim Fenn <fenn at stanford.edu> - 1.1-3-20080912svn3419
> - fix release tag, add egg-info, minor fixes

done.

> * segv
>   - By the way for pymol causes segv with
> -------------------------------------------------
> pymol-1.1-3.20080912svn3419.fc10.i386
> mesa-libGL-7.1-0.37.fc10.i386
> python-2.5.2-1.fc10.i386
> -------------------------------------------------
>     when just launching pymol.
>     gdb log attached.

I can't reproduce this on my F8 machine, I'll try to find a machine for F10
testing.  I'll also get in touch with upstream and see if there are any
suggestions there.

spec url: http://www.stanford.edu/~fenn/packs/pymol.spec
srpm url:
http://www.stanford.edu/~fenn/packs/pymol-1.1-4.20080912svn3419.f8.src.rpm

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