On Wed, Oct 9, 2013 at 10:01 PM, Björn Grüning
<bjoern.gruen...@pharmazie.uni-freiburg.de> wrote:
> Am Mittwoch, den 09.10.2013, 19:15 +0100 schrieb Peter Cock:
>> On Tue, Oct 8, 2013 at 9:57 PM, Dave Bouvier <d...@bx.psu.edu> wrote:
>> > Peter, Björn,
>> >
>> > I have restored gfortran to the repository test host. I believe it was
>> > inadvertently removed, possibly as a side effect of updating packages or
>> > removing packages that were causing conflicts with the Galaxy eggs. Numpy
>> > and biopython should now install successfully, as they do in my local
>> > environment.
>> >
>> >    --Dave B.
>>
>> Thanks Dave, fingers crossed for tonight's test run :)
>>
>> Bjoern - it looks like we can leave the NumPy definition as is...
>
> Ah sorry, totally forgot about it :(
>

Progress, Fortran is working and lapack seems to have installed, but:
e.g. http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename

Installation errors - no functional tests were run for any tools in
this changeset revision
Tool dependencies
TypeNameVersion
biopython package 1.62
Error
running install Numerical Python (NumPy) is not installed. This
package is required for many Biopython features. Please install it
before you install Biopython. You can install Biopython anyway, but
anything dependent on NumPy will not work. If you do this, and later
install NumPy, you should then re-install Biopython. You can find
NumPy at http://numpy.scipy.org
TypeNameVersion
numpy package 1.7.1
Error
Running from numpy source directory.
/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmp3kNwuR/tmp-toolshed-mtdGJ0d5H/numpy-1.7.1/numpy/distutils/system_info.py:1494:
UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not
found. Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting the
ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__)
/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmp3kNwuR/tmp-toolshed-mtdGJ0d5H/numpy-1.7.1/numpy/distutils/system_info.py:1408:
UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not
found. Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting the
ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__)
error: Command "/usr/bin/gfortran -Wall -Wall -shared
build/temp.linux-x86_64-2.7/numpy/linalg/lapack_litemodule.o
build/temp.linux-x86_64-2.7/numpy/linalg/python_xerbla.o
-L/ToolDependencies/lapack/3.4.2/iuc/package_lapack_3_4/60957bd68fe2/lapack/lib
-Lbuild/temp.linux-x86_64-2.7 -llapack -lblas -lgfortran -o
build/lib.linux-x86_64-2.7/numpy/linalg/lapack_lite.so" failed with
exit status 1


Most of that is warnings about not using ATLAS (which we
expect) but I'm not quite sure why it fails...

Peter

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