Re: [galaxy-dev] can't install numpy from toolshed

12 Aug 2014

      On Aug 12, 2014, at 10:15 AM, Sajdak, Doris <djm29@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-a...

--nate
...
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):
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Use...
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
**********************************
___________________________________________________________
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/