Hi, it does not mean anything, but for me its working locally on a Fedora (stable) machine.
If I can anything do to fix that, please let me know. Bjoern > 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. 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