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 > > >
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/ ------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk _______________________________________________ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
