Ubuntu
pymol package

pymol can't start, missing file from init script (merge pymol from Debian unstable)

Bug #448594 reported by Asker Brejnrod
14
This bug affects 1 person
Affects Status Importance Assigned to Milestone
pymol (Debian)
Fix Released
Unknown
pymol (Ubuntu)
Fix Released
Medium
Unassigned

Bug Description

Binary package hint: pymol

Pymol fails to start due to the init script being wrong:
$ pymol
python2.6: can't open file '/var/lib/python-support/python2.6/pymol//__init__.py': [Errno 2] No such file or directory

This is the same bug as http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=529417 and the patch works fine.

lsb_release -rd
Description: Ubuntu karmic (development branch)
Release: 9.10

$ apt-cache policy pymol
pymol:
  Installed: 1.1-1ubuntu2
  Candidate: 1.1-1ubuntu2
  Version table:
 *** 1.1-1ubuntu2 0
        500 http://dk.archive.ubuntu.com karmic/universe Packages
        100 /var/lib/dpkg/status

Revision history for this message
Daniel Leidert (dleidert-deactivatedaccount) wrote :

Syncing pymol (1.2r1-2) should fix this issue and several others and update pymol to the latest release.

Revision history for this message
Scott Howard (showard314) wrote :
Download full text (3.2 KiB)

I'm going to check if we can just sync with debian.
Here's the debian changelog:

 pymol (1.2r1-2) unstable; urgency=low

   * debian/control (Build-Depends): Added python for python.mk.
   * debian/pymol.launch.in: Replace $* with $@ and add a construct to replace
     the test (closes: #549268).
   * debian/rules: Include python.mk.
     (install): Use --install-layout=deb via py_setup_install_args (closes:
     #547871).
   * debian/patches/02_test-suite.dpatch: Adjusted.
     - test/pymol-test: Include /usr/lib/pythonX.Y/dist-packages too.
   * debian/patches/20_output_license_terms.dpatch: Added.
     - Show the Debian package copyright file when using 'Output License
       Terms', which fully reproduces the LICENSE file.
   * debian/patches/00list: Adjusted.

 -- Daniel Leidert (dale) <email address hidden> Sat, 03 Oct 2009 01:04:21 +0200
pymol (1.2r1-1) unstable; urgency=low

   * New upstream release.

   [ Michael Banck ]
   * debian/patches/06_remove_shebang.dpatch: Removed, applied upstream.
   * debian/patches/13_activate_vmd_plugin.dpatch: Updated.
   * debian/patches/14_script_not_executable.dpatch: Removed, applied upstream.
   * debian/patches/16_pymem_del.dpatch: Likewise.
   * debian/patches/17_cmyk_png_data_path.dpatch: Updated.
   * debian/pymol.launch.in: Add quotes around $* to not fail on filenames with
     whitespace in them (closes: #506967).
   * debian/rules (clean): Removed bashism (closes: #535410).
   * debian/control (Homepage): Updated.
   * debian/control (Uploaders): Removed Li Daobing.
   * debian/patches/18_enable_gl_shaders.dpatch: New patch, enable OpenGL
     shaders, taken from upstream.
   * debian/pymol.launch.in: Do not add $* to command line if empty, avoiding a
     traceback on startup.
   * debian/rules (GCC43_ICES_HERE): Removed.
   * debian/control (Build-Depends): Removed g++-4.2 on arm and armel
     (closes: #533794).
   * debian/control (Build-Depends): Replaced glutg3-dev with freeglut3-dev
     (closes: #543702).

   [ Daniel Leidert ]
   * debian/control: Added DM-Upload-Allowed field.
     (Standards-Version): Bumped to 3.8.3.
     (Vcs-Svn): Fixed vcs-field-uses-not-recommended-uri-format.
     (Description): Fixed typo (thanks to lintian).
   * debian/pymol-32.xpm: Renamed to debian/pymol.xpm.
   * debian/pymol.applications,
     debian/gnome-pymol.keys,
     debian/gnome-pymol.mime: Dropped. This is for GNOME<=2.4.
   * debian/pymol.dirs,
     debian/pymol.install: Added for debhelper-based build system.
   * debian/pymol.doc-base: Added to register reference card.
   * debian/pymol.menu (icon): Fixed after rename.
   * debian/pymol.launch.in: Fixed PYMOL_PATH (closes: #529417). Make this
     self-detecting (closes: #516040).
   * debian/rules: Reworked to be more debhelper-like and clean. Permission
     fixes have been dropped (fixed upstream).
   * debian/README.source: Added to comply to policy.
   * debian/patches/04_Rules.make.dpatch: Dropped.
   * debian/patches/05_examples_data_path.dpatch: Adjusted to use PYMOL_DATA.
   * debian/patches/19_blosum_matrix_path.dpatch: Added.
     - modules/pymol/fitting.py: Search for the matrices in the correct path
       (closes: #...

Read more...

Revision history for this message
Scott Howard (showard314) wrote :

Attached is the source changelog. There are dozens of fixes and few improvements to the program.

Bug Watch Updater (bug-watch-updater)
Changed in pymol (Debian):
status: Unknown → Fix Released
David Tomaschik (matir)
summary: - unable to start up
+ pymol can't start, missing file from init script.
Revision history for this message
Scott Howard (showard314) wrote : Re: pymol can't start, missing file from init script.

karmic pbuilder build log for the debian sync. I'm trying to get it up as a ppa for testing, but LP 's ftp keeps timing out. We're in beta, so I don't know how good our chances are of getting this synced. We may just have to wait until next month when Ubuntu auto-syncs with Debian.

Alessio Treglia (quadrispro)
Changed in pymol (Ubuntu):
importance: Undecided → Medium
Revision history for this message
Scott Howard (showard314) wrote :

Ubuntu needs a small change from Debian, so we can't sync.

debian/pymol.launch.in needs to run the command for pymol.__init__ not pymol. See http://bugs.python.org/issue4195.

I have it rebuilt with the change and it is working properly. Attached is the build log and screen shot.

Please test the PPA at:
https://edge.launchpad.net/~showard314/+archive/ppa
(There is a huge backlog, it may take a while). I'm adding a bzr branch for merge and subscribing sponsors.

Install log:
(Reading database ... 275223 files and directories currently installed.)
Preparing to replace pymol 1.2r1-2~ppa1 (using pymol_1.2r1-2ubuntu1~ppa1_amd64.deb) ...
Unpacking replacement pymol ...
Setting up pymol (1.2r1-2ubuntu1~ppa1) ...

Processing triggers for python-support ...
Processing triggers for desktop-file-utils ...
Processing triggers for doc-base ...
Processing 1 changed doc-base file(s)...
Registering documents with scrollkeeper...
Processing triggers for man-db ...

Revision history for this message
Scott Howard (showard314) wrote :
Scott Howard (showard314)
summary: - pymol can't start, missing file from init script.
+ pymol can't start, missing file from init script (merge pymol from
+ Debian unstable)
Revision history for this message
StefanPotyra (sistpoty) wrote :

ACK #1.

Revision history for this message
Iulian Udrea (iulian) wrote :

Ack #2. Approved.

Changed in pymol (Ubuntu):
status: New → Confirmed
Fabrice Coutadeur (fabricesp)
Changed in pymol (Ubuntu):
assignee: nobody → fabrice_sp (fabricesp)
status: Confirmed → In Progress
Revision history for this message
Fabrice Coutadeur (fabricesp) wrote :

Uploaded. Thanks for your contribution!

I had to fix the changelog, as entries are mixed up in your branch. I got the one from your ppa.
Also, next time, please also attach a debdiff: this would have made me the life a lot easier :-)

Thanks,
Fabrice

Changed in pymol (Ubuntu):
assignee: fabrice_sp (fabricesp) → nobody
status: In Progress → Fix Committed
Revision history for this message
Launchpad Janitor (janitor) wrote :

This bug was fixed in the package pymol - 1.2r1-2ubuntu1

---------------
pymol (1.2r1-2ubuntu1) karmic; urgency=low

  * Synced with Debian (LP: #448594)
  * debian/pymol.launch.in: changed pymol to pymol.__init__i to be able to run
    the application (see http://bugs.python.org/issue4195)

 -- Scott Howard <email address hidden> Sun, 11 Oct 2009 23:45:07 -0400

Changed in pymol (Ubuntu):
status: Fix Committed → Fix Released
Revision history for this message
Scott Howard (showard314) wrote : Re: [Bug 448594] Re: pymol can't start, missing file from init script (merge pymol from Debian unstable)

Thank you for your help and the comments Fabrice, I'm sorry it was
extra work! Next time I'll do a merge and a debdiff, they are easy
enough to make.

I saw it failed on ia64 here:

layer2/RepCylBond.c: In function 'RepCylinderBox':
layer2/RepCylBond.c:2154: internal compiler error: in
insert_in_history_vect, at sel-sched-ir.c:1514
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.4/README.Bugs> for instructions.
error: command 'gcc' failed with exit status 1
make: *** [build-stamp] Error 1
dpkg-buildpackage: error: debian/rules build gave error exit status 2

I don't know if this is something we just have to wait out and rebuild
ia64 later or something we should do.

Revision history for this message
Fabrice Coutadeur (fabricesp) wrote :

thanks to follow up on that issue :-)

IMHO, ftbfs on ia64 are not critical, especially if they are gcc bugs: the priority is on i386 and amd64.

Thanks,
Fabrice

Revision history for this message
Scott Kitterman (kitterman) wrote : Re: [Bug 448594] Re: pymol can't start, missing file from init script (merge pymol from Debian unstable)

That's an internal compiler error in gcc. Chances are slim to one it will
get fixed this release, but it should be investigated.

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