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

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