Hi, I tried to things to solve it.
1: I uploaded a new version to: http://testtoolshed.g2.bx.psu.edu/view/iuc/package_atlas_3_10 this time with target_filename="ATLAS.tar.bz2". That is a rather new feature, so you will need a recent Galaxy version. The prosite is that we do not need to call 'tar', we are using the python tarfile module. Hopefully that will work, also on OS-X 2: I have created: http://testtoolshed.g2.bx.psu.edu/view/iuc/package_atlas_3_11 Peter was able to install it on OS-X, at least on commandline, so I have hope that this one is working, well. The downside is, that it is a unstable version and will disappear from the server. Would be great if you can give both a try. For me its working. That means on ubuntu its installed and on Fedora its failing silently with 'It appears you have cpu throttling enabled, which makes timings unreliable and an ATLAS install nonsensical. Aborting. See ATLAS/INSTALL.txt for further information'. Thanks for your help! Bjoern > On Thu, Sep 19, 2013 at 5:15 PM, Björn Grüning > <bjoern.gruen...@pharmazie.uni-freiburg.de> wrote: > > 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. > > 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? > > 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/
