On Tue, Oct 1, 2013 at 9:18 PM, Dave Bouvier <d...@bx.psu.edu> wrote:
> I've done some investigating, and it looks like there is an irregularity
> with the installation of package_numpy_1_7, and somehow
> package_biopython_1_62 is not finding the (successfully) installed numpy
> dependency. I duplicated the dependency chain for seq_select_by_id on my
> local tool shed, and got the following error for biopython's tool dependency
> record when installing seq_select_by_id into my local Galaxy instance:
>
>                     export
> PYTHONPATH=$PYTHONPATH:/var/galaxy/tool_dependencies/biopython/1.62/devteam/package_biopython_1_62/c3c8665cb0af/lib/python
> &&
>                     export PATH=$PATH:$PATH_NUMPY &&
>                     export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &&
>                     python setup.py install --install-lib
> /var/galaxy/tool_dependencies/biopython/1.62/devteam/package_biopython_1_62/c3c8665cb0af/lib/python
>
> STDOUT
> 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
>
> Note that when I installed seq_select_by_id, numpy installed correctly, and
> PYTHONPATH was populated with the right values.
>
>    --Dave B.

Hi Dave, Bjeorn,

Right now NumPy isn't installing at all on the Test Tool Shed.

Dave - is is possible that the system was updated and the
Fortran compiler removed? e.g.

http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/834cf6618a14
reports:

Installation errors - no functional tests were run for any tools in
this changeset revision
Tool dependencies
TypeNameVersion
lapack package 3.4.2
Error
CMake Error: your Fortran compiler: "CMAKE_Fortran_COMPILER-NOTFOUND"
was not found. Please set CMAKE_Fortran_COMPILER to a valid compiler
path or name. CMake Error at
/usr/share/cmake-2.8/Modules/CMakeFortranInformation.cmake:27
(get_filename_component): get_filename_component called with incorrect
number of arguments Call Stack (most recent call first):
CMakeLists.txt:2 (project) CMake Error: CMAKE_Fortran_COMPILER not
set, after EnableLanguage CMake Error: Internal CMake error,
TryCompile configure of cmake failed CMake Error at
/usr/share/cmake-2.8/Modules/CMakeFortranInformation.cmake:27
(get_filename_component): get_filename_component called with incorrect
number of arguments Call Stack (most recent call first):
CMakeLists.txt:2 (project) CMake Error: CMAKE_Fortran_COMPILER not
set, after EnableLanguage CMake Error: Internal CMake error,
TryCompile configure of cmake failed CMake Error at
/usr/share/cmake-2.8/Modules/CMakeFortranInformation.cmake:27
(get_filename_component): get_filename_component called with incorrect
number of arguments Call Stack (most recent call first):
CMakeLists.txt:2 (project) CMake Error: CMAKE_Fortran_COMPILER not
set, after EnableLanguage CMake Error: Internal CMake error,
TryCompile configure of cmake failed CMake Error at
/usr/share/cmake-2.8/Modules/CMakeFortranInformation.cmake:27
(get_filename_component): get_filename_component called with incorrect
number of arguments Call Stack (most recent call first):
CMakeLists.txt:2 (project) CMake Error: CMAKE_Fortran_COMPILER not
set, after EnableLanguage CMake Error: Internal CMake error,
TryCompile configure of cmake failed CMake Error at
/usr/share/cmake-2.8/Modules/CMakeFortranInformation.cmake:27
(get_filename_component): get_filename_component called with incorrect
number of arguments Call Stack (most recent call first):
CMakeLists.txt:2 (project) CMake Error: CMAKE_Fortran_COMPILER not
set, after EnableLanguage CMake Error: Internal CMake error,
TryCompile configure of cmake failed

Since this seems to be breaking lapack, perhaps we should
further simplify package_numpy_1_7 not to use lapack or
ATLAS? What do you think Bjoern?

http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7
http://testtoolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7

Regards,

Peter
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