Hi Nate,
Thanks for the fast response. You were right, python2-6-dev wasn’t installed. I’m all for using 2.7 and that’s what’s installed on the system but I don’t
know how to do that in the virtual environment. Can you tell me how to switch that? Sorry if that’s a ridiculously basic question!
Thanks,
Dori
From: Nate Coraor [mailto:nate@bx.psu.edu]
Sent: Tuesday, August 12, 2014 10:08 AM
To: Sajdak, Doris
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] can't install numpy from toolshed
On Aug 12, 2014, at 9:59 AM, Sajdak, Doris <djm29@buffalo.edu> wrote:
I’m running Galaxy in a virtual environment as described here (OS is Debian 3.2.54-2):
When I go to install package_numpy_1_7 from the tool shed, I get the following errors:
Running from numpy source directory.
/ifs/projects/galaxy/database/tmp/tmp-toolshed-mtdaP2Rhs/numpy-1.7.1/numpy/distutils/command/config.py:413: DeprecationWarning:
+++++++++++++++++++++++++++++++++++++++++++++++++
Usage of get_output is deprecated: please do not
use it anymore, and avoid configuration checks
involving running executable on the target machine.
+++++++++++++++++++++++++++++++++++++++++++++++++
DeprecationWarning)
Traceback (most recent call last):
File "setup.py", line 214, in <module>
setup_package()
File "setup.py", line 207, in setup_package
configuration=configuration )
File "/ifs/projects/galaxy/database/tmp/tmp-toolshed-mtdaP2Rhs/numpy-1.7.1/numpy/distutils/core.py", line 186, in setup
return old_setup(**new_attr)
File "/usr/lib/python2.6/distutils/core.py", line 152, in setup
dist.run_commands()
File "/usr/lib/python2.6/distutils/dist.py", line 975, in run_commands
self.run_command(cmd)
File "/usr/lib/python2.6/distutils/dist.py", line 995, in run_command
cmd_obj.run()
File "/ifs/projects/galaxy/database/tmp/tmp-toolshed-mtdaP2Rhs/numpy-1.7.1/numpy/distutils/command/install.py", line 55, in run
r = old_install.run(self)
File "/usr/lib/python2.6/distutils/command/install.py", line 615, in run
self.run_command('build')
File "/usr/lib/python2.6/distutils/cmd.py", line 333, in run_command
self.distribution.run_command(command)
File "/usr/lib/python2.6/distutils/dist.py", line 995, in run_command
cmd_obj.run()
File "/ifs/projects/galaxy/database/tmp/tmp-toolshed-mtdaP2Rhs/numpy-1.7.1/numpy/distutils/command/build.py", line 37, in run
old_build.run(self)
File "/usr/lib/python2.6/distutils/command/build.py", line 135, in run
self.run_command(cmd_name)
File "/usr/lib/python2.6/distutils/cmd.py", line 333, in run_command
self.distribution.run_command(command)
File "/usr/lib/python2.6/distutils/dist.py", line 995, in run_command
cmd_obj.run()
File "/ifs/projects/galaxy/database/tmp/tmp-toolshed-mtdaP2Rhs/numpy-1.7.1/numpy/distutils/command/build_src.py", line 152, in run
self.build_sources()
File "/ifs/projects/galaxy/database/tmp/tmp-toolshed-mtdaP2Rhs/numpy-1.7.1/numpy/distutils/command/build_src.py", line 169, in build_sources
self.build_extension_sources(ext)
File "/ifs/projects/galaxy/database/tmp/tmp-toolshed-mtdaP2Rhs/numpy-1.7.1/numpy/distutils/command/build_src.py", line 328, in build_extension_sources
sources = self.generate_sources(sources, ext)
File "/ifs/projects/galaxy/database/tmp/tmp-toolshed-mtdaP2Rhs/numpy-1.7.1/numpy/distutils/command/build_src.py", line 385, in generate_sources
source = func(extension, build_dir)
File "numpy/core/setup.py", line 410, in generate_config_h
moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir)
File "numpy/core/setup.py", line 41, in check_types
out = check_types(*a, **kw)
File "numpy/core/setup.py", line 271, in check_types
"Cannot compile 'Python.h'. Perhaps you need to "\
SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.
python-dev is installed on the machine, though I don’t know if that matters in the virtual environment. Any idea what’s causing this?
Hi Dori,
Can you check that python2.6-dev is also installed? On Debian Wheezy, python-dev installs the development files for Python 2.7, but your default python appears to be Python 2.6.
That said, unless you are using 2.6 intentionally, I would suggest switching to 2.7. Although the Galaxy server and most Galaxy tools written in Python will run in 2.6, some tools now require Python 2.7.
--nate
THANKS!
Dori
**********************************
Dori Sajdak
Senior Systems Administrator
State University of NY at Buffalo
Center for Computational Research
701 Ellicott St
Buffalo, NY 14203
Phone: (716) 881-8934
Fax: (716) 849-6656
**********************************
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