On Thu, Oct 10, 2013 at 10:00 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> 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...

Hi Guys,

Bjoern - good news for you, the installation of NumPy can
work on the current Test Tool Shed.

Dave - bad news for you, last night I had 3 NumPy install failures
(all different) and 2 successes - which to me suggests a possible
race condition in the nightly testing?

(1) Last night on the Test Tool Shed this failed as in email above:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/834cf6618a14

(2) This failed with the simpler message:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/308ec20faefb

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

(3) Here the installation seems to have failed silently, leading to a
test failure at the import stage:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id/9e9e3b860aa0

Tests that failed
Tool id: seq_select_by_id
Tool version: seq_select_by_id
Test: test_tool_000000
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/seq_select_by_id/seq_select_by_id/0.0.6)
Stderr:
Fatal error: Exit code 1 ()
Biopython 1.54 or later is required

(4, 5) However these also depend on Biopython 1.62 and worked:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/d08767ae73ce
(failed last night)

http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id/8a34c565a473

My guess is a race condition where multiple attempts are being made in
parallel to install NumPy (in the same place), and this causes some of
these attempts to fail. But that is without looking at the code at all
;)

Regards,

Peter

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