Peter, It looks like there may be a version conflict between package_numpy and either a system numpy or the Galaxy numpy egg. I'll investigate and keep you updated on my progress. --Dave B. On 09/30/2013 05:08 AM, Peter Cock wrote:
On Sun, Sep 29, 2013 at 1:17 PM, Björn Grüning wrote:
I updated R, numpy, scipy, scikit and removed the atlas dependency. It seems to work fine for the ChemicalToolBox. I do not remove the lapack dependency, because I did not get any complains until now.
I'm seeing problems on the Test Tool Shed with NumPy :(
The updated no-ATLAS numpy is revision f0490401cfff http://testtoolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7
My tools using NumPy via Biopython 1.62 do seem to be picking up this new NumPy package, which is good.
However, the install of NumPy seems to be failing in strange and *different* ways - which I suspect points to a Tool Shed test framework bug, perhaps in sharing the dependencies between tools?
----------------------
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id /9e9e3b860aa0 Looks like partial NumPy install?
Installation errors - no functional tests were run for any tools in this changeset revision Tool dependencies TypeNameVersion biopython package 1.62 Error Traceback (most recent call last): File "setup.py", line 463, in <module> setup(**setup_args) File "/usr/lib/python2.7/distutils/core.py", line 152, in setup dist.run_commands() File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands self.run_command(cmd) File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "setup.py", line 216, in run if check_dependencies_once(): File "setup.py", line 123, in check_dependencies_once _CHECKED = check_dependencies() File "setup.py", line 163, in check_dependencies if is_Numpy_installed(): File "setup.py", line 282, in is_Numpy_installed return bool(can_import("numpy")) File "setup.py", line 274, in can_import return __import__(module_name) File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/__init__.py", line 137, in <module> import add_newdocs File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/add_newdocs.py", line 9, in <module> from numpy.lib import add_newdoc File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/lib/__init__.py", line 13, in <module> from polynomial import * File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/lib/polynomial.py", line 11, in <module> import numpy.core.numeric as NX AttributeError: 'module' object has no attribute 'core'
----------------------
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id/9e9e3b860aa0 Apparently the same error:
Installation errors - no functional tests were run for any tools in this changeset revision Tool dependencies TypeNameVersion biopython package 1.62 Error Traceback (most recent call last): File "setup.py", line 463, in <module> setup(**setup_args) File "/usr/lib/python2.7/distutils/core.py", line 152, in setup dist.run_commands() File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands self.run_command(cmd) File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "setup.py", line 216, in run if check_dependencies_once(): File "setup.py", line 123, in check_dependencies_once _CHECKED = check_dependencies() File "setup.py", line 163, in check_dependencies if is_Numpy_installed(): File "setup.py", line 282, in is_Numpy_installed return bool(can_import("numpy")) File "setup.py", line 274, in can_import return __import__(module_name) File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/__init__.py", line 137, in <module> import add_newdocs File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/add_newdocs.py", line 9, in <module> from numpy.lib import add_newdoc File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/lib/__init__.py", line 13, in <module> from polynomial import * File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/lib/polynomial.py", line 11, in <module> import numpy.core.numeric as NX AttributeError: 'module' object has no attribute 'core'
----------------------
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/d08767ae73ce Looks like a different partial NumPy install?
Installation errors - no functional tests were run for any tools in this changeset revision Tool dependencies TypeNameVersion biopython package 1.62 Error Traceback (most recent call last): File "setup.py", line 393, in <module> if is_Numpy_installed(): File "setup.py", line 282, in is_Numpy_installed return bool(can_import("numpy")) File "setup.py", line 274, in can_import return __import__(module_name) File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/__init__.py", line 137, in <module> import add_newdocs File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/add_newdocs.py", line 9, in <module> from numpy.lib import add_newdoc File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/lib/__init__.py", line 4, in <module> from type_check import * File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/lib/type_check.py", line 8, in <module> import numpy.core.numeric as _nx File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/core/__init__.py", line 42, in <module> __all__ += shape_base.__all__ AttributeError: 'module' object has no attribute '__all__'
----------------------
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/834cf6618a14 Looks like yet another different partial NumPy install?
Installation errors - no functional tests were run for any tools in this changeset revision Tool dependencies TypeNameVersion biopython package 1.62 Error Bio/Cluster/clustermodule.c: In function ‘py_median’: Bio/Cluster/clustermodule.c:2164:31: error: ‘PyArray_NOTYPE’ undeclared (first use in this function) Bio/Cluster/clustermodule.c:2164:31: note: each undeclared identifier is reported only once for each function it appears in Bio/Cluster/clustermodule.c: In function ‘py_mean’: Bio/Cluster/clustermodule.c:2230:31: error: ‘PyArray_NOTYPE’ undeclared (first use in this function) error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
----------------------
http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/308ec20faefb My old favourite, listed under "Latest revision: failing tool tests" but with no visible test results or install failure - but as this also depends on Biopython and NumPy so it probably failed installation too.
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/