Hi Dave, thanks for the pointer.
I updated the testtoolshed package. For me installing fine. I will wait one more day and have a look at Peter's Testcases. I will than migrate it to the main toolshed. Changes are now also in github. Thanks, Björn > 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.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 > > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/