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

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