On Wed, Dec 18, 2013 at 02:33:22PM -0800, Alexander Hansen wrote:
> On 12/18/13 1:45 PM, Matthew Franklin wrote:
>> 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
>>
>>
Matt,
This issue is resolved now in both the the 10.6 and 10.7 trees of fink with
pymol-py-1.6.9-1 release.
Jack
>>
>
> The tarball got updated without a corresponding version change.
> Unfortunately the packaging for 10.6 wasn't updated correspondingly. How
> to handle that is up to the maintainer.
>
> Since _we_ generate those tarballs, I might advocate that we either
> include a revision number in the filename--maybe the first package
> revision for which the tarball is valid--or have the package use
> SourceRename so that we mirror valid past snapshots so that folks aren't
> left high and dry.
>
> --
> Alexander Hansen, Ph.D.
> Fink User Liaison
> My package updates: http://finkakh.wordpress.com/
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