Am Montag, den 07.10.2013, 14:07 +0100 schrieb Peter Cock:
On Tue, Oct 1, 2013 at 9:18 PM, Dave Bouvier <dave@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?
I'm a little bit sceptic to remove features only because the Test Utility can not handle it. On the other hand I understand that numpy should just work and that your test failing since month because of my dependencies. I will get rid of it tomorrow. As a result we can setup_virtualenv and install numpy from pip directly I think. Is that ok for you? Cheers, 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