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
> >



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