can't install numpy from toolshed

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can't install numpy from toolshed

bflogalaxy

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

**********************************

 

 


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Re: can't install numpy from toolshed

Nate Coraor (nate@bx.psu.edu)
On Aug 12, 2014, at 9:59 AM, Sajdak, Doris <[hidden email]> 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
**********************************
 
 
___________________________________________________________
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/


___________________________________________________________
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/
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Re: can't install numpy from toolshed

bflogalaxy

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:[hidden email]]
Sent: Tuesday, August 12, 2014 10:08 AM
To: Sajdak, Doris
Cc: [hidden email]
Subject: Re: [galaxy-dev] can't install numpy from toolshed

 

On Aug 12, 2014, at 9:59 AM, Sajdak, Doris <[hidden email]> 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

**********************************

 

 

___________________________________________________________
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/

 


___________________________________________________________
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/
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Re: can't install numpy from toolshed

Nate Coraor (nate@bx.psu.edu)
On Aug 12, 2014, at 10:15 AM, Sajdak, Doris <[hidden email]> 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:


--nate

 
Thanks,
Dori
 
 
From: Nate Coraor [[hidden email]] 
Sent: Tuesday, August 12, 2014 10:08 AM
To: Sajdak, Doris
Cc: [hidden email]
Subject: Re: [galaxy-dev] can't install numpy from toolshed
 
On Aug 12, 2014, at 9:59 AM, Sajdak, Doris <[hidden email]> 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
**********************************
 
 
___________________________________________________________
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/


___________________________________________________________
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/