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

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





--- Comment #8 from Mamoru Tasaka <mtasaka at ioa.s.u-tokyo.ac.jp>  2008-10-04 15:11:53 EDT ---
Created an attachment (id=319472)
 --> (https://bugzilla.redhat.com/attachment.cgi?id=319472)
gdb log when pymol causes segv

Well, for 1.1-3svn:

* License
------------------------------------------------
Overall license : MIT

contrib/modules/ExtensionClass.LICENSE  ZPLv2.0
contrib/modules/ExtensionClass.c-py152  BSD
contrib/uiuc/plugins/LICENSE   BSD
contrib/uiuc/plugins/molfile_plugin/LICENSE BSD
layer1/FontTTF.h    Bitstream Vera
layer1/FontTTF2.h    OFL
ov/src/OVRandom.c    BSD
------------------------------------------------
  - The license tag should be "MIT and BSD and ZPLv2.0 and
    Bitstream Vera and OFL".

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

* 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)


* 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.

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

* 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
-------------------------------------------------
  - 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
-------------------------------------------------
  - Fix the permissions of C codes in the tarball to 0644 to suppress
    rpmlint warnings for debuginfo rpm.

* 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.

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