tar xvfj atlas3.11.11.tar.bz2 shows no errors on OSX and creates one ATLAS folder.
best, ido On Sep 20, 2013, at 11:17 AM, Bjoern Gruening <bjoern.gruen...@gmail.com> wrote: > Hi Ido and Carlos, > > can you check if that tarball is working? > > http://downloads.sourceforge.net/project/math-atlas/Developer%20%28unstable%29/3.11.11/atlas3.11.11.tar.bz2 > > The chance is low, but if its working for you I will consider to create a new > version for it. > Thanks, > Bjoern > >> 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.gruen...@gmail.com >> > wrote: >> >> >> > Hi Carlos, >> > >> >>> Hi Peter and Carlos, >> >>> >> >>>> On Mon, Sep 16, 2013 at 8:57 PM, Carlos Borroto >> >>>> <carlos.borr...@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. 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