Peter,

I've made some changes to the way the test VM handles tool dependencies, which should reduce the frequency of this type of error, and will be running further tests today to see how I can improve the framework's handling of these situations.

   --Dave B.

On 10/11/2013 04:51 AM, Peter Cock wrote:
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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