Question: Rpy2 And Mac Os X 10.6
0
gravatar for Science_Robot
8.7 years ago by
Science_Robot1.1k
Gainesville, FL
Science_Robot1.1k wrote:

I know there's already a question for 10.5 but I have 10.6 and a different error.

I have R 2.11.1 and Python 2.7 (Same error w/ 2.6):
R was installed with homebrew.

Any ideas?


Traceback (most recent call last):
  File "/usr/local/bin/easy_install", line 8, in <module>
    load_entry_point('setuptools==0.6c11', 'console_scripts', 'easy_install')()
  File "build/bdist.macosx-10.4-i386/egg/setuptools/command/easy_install.py", line 1712, in main
  File "build/bdist.macosx-10.4-i386/egg/setuptools/command/easy_install.py", line 1700, in with_ei_usage
  File "build/bdist.macosx-10.4-i386/egg/setuptools/command/easy_install.py", line 1716, in <lambda>
  File "/usr/local/lib/python2.7/distutils/core.py", line 152, in setup
    dist.run_commands()
  File "/usr/local/lib/python2.7/distutils/dist.py", line 953, in run_commands
    self.run_command(cmd)
  File "/usr/local/lib/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "build/bdist.macosx-10.4-i386/egg/setuptools/command/easy_install.py", line 211, in run
  File "build/bdist.macosx-10.4-i386/egg/setuptools/command/easy_install.py", line 446, in easy_install
  File "build/bdist.macosx-10.4-i386/egg/setuptools/command/easy_install.py", line 476, in install_item
  File "build/bdist.macosx-10.4-i386/egg/setuptools/command/easy_install.py", line 655, in install_eggs
  File "build/bdist.macosx-10.4-i386/egg/setuptools/command/easy_install.py", line 930, in build_and_install
  File "build/bdist.macosx-10.4-i386/egg/setuptools/command/easy_install.py", line 919, in run_setup
  File "build/bdist.macosx-10.4-i386/egg/setuptools/sandbox.py", line 62, in run_setup
  File "build/bdist.macosx-10.4-i386/egg/setuptools/sandbox.py", line 105, in run
  File "build/bdist.macosx-10.4-i386/egg/setuptools/sandbox.py", line 64, in <lambda>
  File "setup.py", line 372, in <module>
  File "/usr/local/lib/python2.7/distutils/core.py", line 152, in setup
    dist.run_commands()
  File "/usr/local/lib/python2.7/distutils/dist.py", line 953, in run_commands
    self.run_command(cmd)
  File "/usr/local/lib/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "build/bdist.macosx-10.4-i386/egg/setuptools/command/bdist_egg.py", line 167, in run
  File "/usr/local/lib/python2.7/distutils/cmd.py", line 326, in run_command
    self.distribution.run_command(command)
  File "/usr/local/lib/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "build/bdist.macosx-10.4-i386/egg/setuptools/command/egg_info.py", line 177, in run
  File "build/bdist.macosx-10.4-i386/egg/setuptools/command/egg_info.py", line 252, in find_sources
  File "build/bdist.macosx-10.4-i386/egg/setuptools/command/egg_info.py", line 306, in run
  File "build/bdist.macosx-10.4-i386/egg/setuptools/command/egg_info.py", line 330, in add_defaults
  File "build/bdist.macosx-10.4-i386/egg/setuptools/command/sdist.py", line 203, in add_defaults
  File "/usr/local/lib/python2.7/distutils/cmd.py", line 312, in get_finalized_command
    cmd_obj.ensure_finalized()
  File "/usr/local/lib/python2.7/distutils/cmd.py", line 109, in ensure_finalized
    self.finalize_options()
  File "setup.py", line 111, in finalize_options
  File "setup.py", line 264, in get_rconfig
  File "setup.py", line 252, in from_string
ValueError: Invalid substring

in string
R • 2.6k views
ADD COMMENTlink modified 8.5 years ago • written 8.7 years ago by Science_Robot1.1k
1
gravatar for Science_Robot
8.7 years ago by
Science_Robot1.1k
Gainesville, FL
Science_Robot1.1k wrote:

As usual, I asked a question on Biostar and then came back 5 minutes later to answer it.

I commented out the lines producing the error in setup.py: 251-253

        #if not ok:
        #    raise ValueError('Invalid substring\n' + substring 
        #                     + '\nin string\n' + string)

Installation works, I ran the tests in rpy/robjects/tests and everything came out OK.

import rpy2 works as well.

But I have the feeling that something somewhere is deeply wrong.

ADD COMMENTlink modified 8.7 years ago • written 8.7 years ago by Science_Robot1.1k

"import rpy" ? Is this about rpy or rpy2 ? If rpy2, what is the version you are trying out ?

Otherwise, you are commenting out a section that stops the install when something unexpected is happening. This seems to indicate that the homebrew R is built/installed not quite the way the script anticipates it.

ADD REPLYlink written 8.7 years ago by Laurent Gautier810
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