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 > ********************************** > > > ___________________________________________________________ > 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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