On Wed, Oct 9, 2013 at 10:01 PM, Björn Grüning <bjoern.gruening@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 <dave@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