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?

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/

Reply via email to