Björn, Peter,
In the course of my investigation, I've discovered a possible improvement to the lapack build recipe. If you change the cmake command from:
cmake .. -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/lapack
to:
cmake .. -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/lapack -DCMAKE_Fortran_FLAGS='-O2 -fPIC'
the need for the earlier sed command is eliminated, which may reduce the likelihood of environment-specific failures. Specifically, I attempted to install get_orfs_or_cdss on a local (linux) system, and the numpy installation's error message informed me that lapack was built without the -fPIC flag.
--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.cock@googlemail.com wrote:
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...
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