On Aug 12, 2014, at 10:15 AM, Sajdak, Doris <dj...@buffalo.edu> wrote:
> 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!
Hi Dori,
You can have virtualenv use a specified Python interpreter with the --python
argument to virtualenv(.py), by using the VIRTUALENV_PYTHON environment
varaible, or by calling virtualenv.py with the desired python interpreter (e.g.
`/usr/bin/python2.7 /path/to/virtualenv.py /path/to/venvdir`). See the
documentation for more:
https://virtualenv.pypa.io/en/latest/virtualenv.html#environment-variables-and-configuration-files
--nate
>
> Thanks,
> Dori
>
>
> From: Nate Coraor [mailto:n...@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 <dj...@buffalo.edu> wrote:
>
>
> I’m running Galaxy in a virtual environment as described here (OS is Debian
> 3.2.54-2):
> https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Use_a_clean_environment
>
> 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
> Web: http://ccr.buffalo.edu
> **********************************
>
>
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