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: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<mailto: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<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/
___________________________________________________________ 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/
