Yes this tar is broken at least on OSX. Other people have the same issue: http://code.google.com/p/libarchive/issues/detail?id=299 On Sep 20, 2013, at 10:41 AM, Bjoern Gruening <bjoern.gruening@gmail.com> wrote: > Hi Carlos, > >>> Hi Peter and Carlos, >>> >>>> On Mon, Sep 16, 2013 at 8:57 PM, Carlos Borroto >>>> <carlos.borroto@gmail.com> wrote: >>>>> I did an extra test. Started with a clean 'galaxy-dist'. This time >>>>> both repositories fail with the same error. I guess before something >>>>> was cached for the repository with version 0.1.4. >>>>> >>>>> I used biopython repository as a guide to write my tool dependency definition: >>>>> http://testtoolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61 >>>>> >>>>> I can confirm biopython repository is failing to install for me with >>>>> exactly the same error. I wonder if a recently addition in the test >>>>> toolshed broke the treatment of "prior_installation_required". >>>>> >>>>> Thanks, >>>>> Carlos >>>> >>>> Could be - note that currently Biopython isn't currently >>>> installing properly on the Test Tool Shed due to ALTAS >>>> failing (a requirement of NumPy which is a requirement >>>> of Biopython). Dave and Bjoern are I think looking at this >>>> already... >>> >>> I can't do much I tested it again and for me its working fine on my >>> computers I have at hand ... sorry. >>> >> >> In case it helps, this is how the INSTALLATION.log file ends on OS X 10.8.4: >> $ tail -n 3 ~/src/shed_tools_dependencies.central/atlas/3.10.1/iuc/package_atlas_3_10/3508de0ebae1/INSTALLATION.log >> x ATLAS/tune/lapack/lanbsrch.c >> tar: Error exit delayed from previous errors. >> ############################################# >> >> This is the relevant part I can find in Galaxy's log: >> [localhost] local: tar xfvj atlas3.10.1.tar.bz2 >> >> Warning: local() encountered an error (return code 1) while executing >> 'tar xfvj atlas3.10.1.tar.bz2' >> >> After noticing this I got what I'm guessing is the original file from >> sourceforge: >> http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.1/atlas3.10.1.tar.bz2 >> >> I can confirm that trying to untar this file fails with the exact same >> error. However, on Ubuntu 13.04 untaring this file works just fine. > > That is new to me. How can that happen? Anyone with an OS-X can confirm > that? > >> On Ubuntu 13.04 the error I see is: >> STDERR >> It appears you have cpu throttling enabled, which makes timings >> unreliable and an ATLAS install nonsensical. Aborting. >> See ATLAS/INSTALL.txt for further information >> ############################################# >> >> Björn, you said cpu throttling can be easily disable on Ubuntu. Can >> you comment how? Do I need to disable it completely, or should the >> install script do it when installing? > > ATLAS (once untared ;-)) needs cpu-throttling to be disabled to > optimizes its library. If it is not disabled ATLAS compilation will > fail. For OS-X I found that: > > http://apple.stackexchange.com/questions/41045/how-can-i-disable-cpu-throttling-and-cpu-disabling > > Sorry, I never touched a OS-X. Nevertheless, If its not disabled, it is > supposed to fail silently and downstream packages will not be affected. > But if its crashing during untarring, I can't do much. What I can do is > to repack the tarball and host it elsewhere. What brings me to: > > http://gmod.827538.n3.nabble.com/RFC-Storing-of-tarballs-and-patches-for-tool-dependencies-to-enable-reproducibility-td4036591.html > > Bad news for a Friday morning, sorry :( > Bjoern > > >> Thanks, >> Carlos >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/