Hi all -
I'm trying to use Fink to install Pymol, and it doesn't appear to be
working. (See below for config information.) I've run fink selfupdate
and update-all.
When I execute "fink install pymol-py27" (or -py26) I successfully
installed a whole bunch of Python packages the first time I ran the
command. However, things run into trouble when I get to the actual
Pymol code.
The download of the Pymol tarball fails with a checksum error:
curl --connect-timeout 30 -f -L -A 'fink/0.36.1' -O
http://distfiles.master.finkmirrors.net/pymol-1.6.0-src.tar.bz2
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 8472k 100 8472k 0 0 706k 0 0:00:11 0:00:11 --:--:--
1044k
The checksum of the file is incorrect. The most likely cause for this is
a corrupted or incomplete download
Expected: bae7424af441978fd9939ac029fdc366
Actual: MD5(1706c013269d41125ebb3bb0573300fe)
SHA1(eece9a1624d2e84ea4da284ae639a79bca02c700)
Downloading the file "pymol-1.6.0-src.tar.bz2" failed.
I have gotten the same error, with exactly the same filesize and
checksum, every time I've tried, from multiple different mirrors.
Therefore, I think it's not a transmission error. It's possible our
firewall is messing things up, but no other fink download has had this
problem.
If I ignore the checksum problem, and tell fink to use the file anyway,
it unpacks it OK and begins the installation process. Things start to go
wrong at the file patching stage:
patching file contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c
patching file contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c
patching file layer4/Cmd.c
patching file contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp
patching file contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp
can't find file to patch at input line 173
Perhaps you used the wrong -p or --strip option?
The text leading up to this was:
--------------------------
|--- pymol-1.5/contrib/pyopengl/openglutil.c.orig 2013-06-07
20:11:42.000000000 -0400
|+++ pymol-1.5/contrib/pyopengl/openglutil.c 2013-06-07
20:12:18.000000000 -0400
--------------------------
Indeed, I can't find openglutil.c anywhere in the pymol directories (or
anywhere in /sw). If I skip this patch, things proceed for a little
longer before failing for good:
patching file layer2/RepSurface.c
patching file layer3/Selector.c
Hunk #1 succeeded at 8660 (offset 45 lines).
patching file layer2/ObjectMolecule2.c
patching file layer2/RepCylBond.c
### execution of /tmp/fink.SOSLL failed, exit code 1
### execution of /tmp/fink.kMmYU failed, exit code 1
Removing runtime build-lock...
Removing build-lock package...
/sw/bin/dpkg-lockwait -r fink-buildlock-pymol-py27-1.6.0-3
(Reading database ... 36268 files and directories currently installed.)
Removing fink-buildlock-pymol-py27-1.6.0-3 ...
Failed: phase patching: pymol-py27-1.6.0-3 failed
It looks to me like the fink installation script doesn't match the files
actually present in the tarball. I imagine this is related to the
checksum error. Could somebody please advise me on how to proceed? Is
the problem on my end, or something the package maintainer needs to address?
Thanks for any help you can provide,
Matt
Config information:
Package manager version: 0.36.1
Distribution version: selfupdate-rsync Wed Dec 18 11:37:21 2013, 10.6,
x86_64
Trees: local/main stable/main unstable/main unstable/crypto
Xcode.app: 3.2.6
Xcode command-line tools: 3.2.6
pymol-py27-1.6.0-3 is set to build with only one job.
Operating system is an Intel Mac Pro 5.1, running OS X 10.6.8. Fink is
being run in an X11 window, XQuartz 2.3.6.
--
Matthew Franklin, Ph. D.
Senior Scientist
New York Structural Biology Center
89 Convent Avenue, New York, NY 10027
(212) 939-0660 ext. 9374
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