OBItools installation error (macOS Mojave)
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3.3 years ago

I have installed OBItools on my MacBook-Pro Mojave 10.14.5 using the instructions from the OBItools website (i.e., using $ python get-obitools.py). On my laptop the analyses were kind of slow and so I decided to instal it also on my iMac which is a bit more powerful and hopefully will handle better the workload. The iMac is running Mojave 10.14.5 as well. This is what I did

$ python get-obitools.py

and this is the error I get:

/var/folders/rt/_gx9q8vs4t77ftcp0c80hvj80000gn/T/tmp9A7e8R/obitools.zip
Downloading/unpacking OBITools
  Downloading OBITools-1.2.13.tar.gz (1.0MB): 1.0MB downloaded
  Saved /var/folders/rt/_gx9q8vs4t77ftcp0c80hvj80000gn/T/tmp9A7e8R/OBITools-1.2.13.tar.gz
  Running setup.py (path:/private/var/folders/rt/_gx9q8vs4t77ftcp0c80hvj80000gn/T/pip_build_giuliano/OBITools/setup.py) egg_info for package OBITools
    Downloading/unpacking Sphinx<2.0
    Downloading/unpacking babel>=1.3,!=2.0 (from Sphinx<2.0)
    Downloading/unpacking sphinxcontrib-websupport (from Sphinx<2.0)
      Downloading sphinxcontrib_websupport-1.1.2-py2.py3-none-any.whl
    Downloading/unpacking Jinja2>=2.3 (from Sphinx<2.0)
    Downloading/unpacking alabaster>=0.7,<0.8 (from Sphinx<2.0)
      Downloading alabaster-0.7.12-py2.py3-none-any.whl
    Downloading/unpacking imagesize (from Sphinx<2.0)
      Downloading imagesize-1.1.0-py2.py3-none-any.whl
    Downloading/unpacking six>=1.5 (from Sphinx<2.0)
      Downloading six-1.12.0-py2.py3-none-any.whl
    Requirement already satisfied (use --upgrade to upgrade): setuptools in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from Sphinx<2.0)
    Downloading/unpacking requests>=2.0.0 (from Sphinx<2.0)
    Downloading/unpacking Pygments>=2.0 (from Sphinx<2.0)
    Downloading/unpacking snowballstemmer>=1.1 (from Sphinx<2.0)
    Downloading/unpacking docutils>=0.11 (from Sphinx<2.0)
    Downloading/unpacking packaging (from Sphinx<2.0)
      Downloading packaging-19.0-py2.py3-none-any.whl
    Downloading/unpacking typing (from Sphinx<2.0)
      Downloading typing-3.7.4-py2-none-any.whl
    Downloading/unpacking pytz>=2015.7 (from babel>=1.3,!=2.0->Sphinx<2.0)
    Downloading/unpacking MarkupSafe>=0.23 (from Jinja2>=2.3->Sphinx<2.0)
      Downloading MarkupSafe-1.1.1.tar.gz
      Running setup.py (path:/private/var/folders/rt/_gx9q8vs4t77ftcp0c80hvj80000gn/T/pip_build_giuliano/MarkupSafe/setup.py) egg_info for package MarkupSafe
        /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'project_urls'
          warnings.warn(msg)
        /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'python_requires'
          warnings.warn(msg)

        no previously-included directories found matching 'docs/_build'
        warning: no previously-included files matching '*.py[co]' found anywhere in distribution
    Downloading/unpacking idna>=2.5,<2.9 (from requests>=2.0.0->Sphinx<2.0)
    Downloading/unpacking certifi>=2017.4.17 (from requests>=2.0.0->Sphinx<2.0)
    Downloading/unpacking chardet>=3.0.2,<3.1.0 (from requests>=2.0.0->Sphinx<2.0)
    Downloading/unpacking urllib3>=1.21.1,!=1.25.0,!=1.25.1,<1.26 (from requests>=2.0.0->Sphinx<2.0)
    Downloading/unpacking pyparsing>=2.0.2 (from packaging->Sphinx<2.0)
    Installing collected packages: Sphinx, babel, sphinxcontrib-websupport, Jinja2, alabaster, imagesize, six, requests, Pygments, snowballstemmer, docutils, packaging, typing, pytz, MarkupSafe, idna, certifi, chardet, urllib3, pyparsing
    Cleaning up...
    Exception:
    Traceback (most recent call last):
      File "distutils.ext/obidistutils/serenity/pip/basecommand.py", line 122, in main
      File "distutils.ext/obidistutils/serenity/pip/commands/install.py", line 283, in run
      File "distutils.ext/obidistutils/serenity/pip/req.py", line 1435, in install
      File "distutils.ext/obidistutils/serenity/pip/req.py", line 671, in install
      File "distutils.ext/obidistutils/serenity/pip/req.py", line 901, in move_wheel_files
      File "distutils.ext/obidistutils/serenity/pip/wheel.py", line 215, in move_wheel_files
      File "distutils.ext/obidistutils/serenity/pip/wheel.py", line 205, in clobber
      File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/os.py", line 157, in makedirs
        mkdir(name, mode)
    OSError: [Errno 13] Permission denied: '/Library/Python/2.7/site-packages/Sphinx-1.8.5.dist-info'

    Storing debug log for failure in /Users/giuliano/Library/Logs/pip.log
    Traceback (most recent call last):
      File "<string>", line 17, in <module>
      File "/private/var/folders/rt/_gx9q8vs4t77ftcp0c80hvj80000gn/T/pip_build_giuliano/OBITools/setup.py", line 39, in <module>
      File "distutils.ext/obidistutils/core.py", line 27, in <module>
      File "distutils.ext/obidistutils/command/build_sphinx.py", line 36, in <module>
      File "distutils.ext/obidistutils/serenity/checkpackage.py", line 95, in install_requirements
      File "distutils.ext/obidistutils/serenity/checkpackage.py", line 183, in pip_install_package
      File "distutils.ext/obidistutils/serenity/pip/__init__.py", line 177, in main
      File "distutils.ext/obidistutils/serenity/pip/__init__.py", line 129, in parseopts
      File "distutils.ext/obidistutils/serenity/pip/__init__.py", line 110, in create_main_parser
      File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/posixpath.py", line 364, in abspath
        cwd = os.getcwd()
    OSError: [Errno 2] No such file or directory
    Complete output from command python setup.py egg_info:
    Downloading/unpacking Sphinx<2.0

Downloading/unpacking babel>=1.3,!=2.0 (from Sphinx<2.0)

Downloading/unpacking sphinxcontrib-websupport (from Sphinx<2.0)

  Downloading sphinxcontrib_websupport-1.1.2-py2.py3-none-any.whl

Downloading/unpacking Jinja2>=2.3 (from Sphinx<2.0)

Downloading/unpacking alabaster>=0.7,<0.8 (from Sphinx<2.0)

  Downloading alabaster-0.7.12-py2.py3-none-any.whl

Downloading/unpacking imagesize (from Sphinx<2.0)

  Downloading imagesize-1.1.0-py2.py3-none-any.whl

Downloading/unpacking six>=1.5 (from Sphinx<2.0)

  Downloading six-1.12.0-py2.py3-none-any.whl

Requirement already satisfied (use --upgrade to upgrade): setuptools in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from Sphinx<2.0)

Downloading/unpacking requests>=2.0.0 (from Sphinx<2.0)

Downloading/unpacking Pygments>=2.0 (from Sphinx<2.0)

Downloading/unpacking snowballstemmer>=1.1 (from Sphinx<2.0)

Downloading/unpacking docutils>=0.11 (from Sphinx<2.0)

Downloading/unpacking packaging (from Sphinx<2.0)

  Downloading packaging-19.0-py2.py3-none-any.whl

Downloading/unpacking typing (from Sphinx<2.0)

  Downloading typing-3.7.4-py2-none-any.whl

Downloading/unpacking pytz>=2015.7 (from babel>=1.3,!=2.0->Sphinx<2.0)

Downloading/unpacking MarkupSafe>=0.23 (from Jinja2>=2.3->Sphinx<2.0)

  Downloading MarkupSafe-1.1.1.tar.gz

  Running setup.py (path:/private/var/folders/rt/_gx9q8vs4t77ftcp0c80hvj80000gn/T/pip_build_giuliano/MarkupSafe/setup.py) egg_info for package MarkupSafe

    /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'project_urls'

      warnings.warn(msg)

    /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'python_requires'

      warnings.warn(msg)



    no previously-included directories found matching 'docs/_build'

    warning: no previously-included files matching '*.py[co]' found anywhere in distribution

Downloading/unpacking idna>=2.5,<2.9 (from requests>=2.0.0->Sphinx<2.0)

Downloading/unpacking certifi>=2017.4.17 (from requests>=2.0.0->Sphinx<2.0)

Downloading/unpacking chardet>=3.0.2,<3.1.0 (from requests>=2.0.0->Sphinx<2.0)

Downloading/unpacking urllib3>=1.21.1,!=1.25.0,!=1.25.1,<1.26 (from requests>=2.0.0->Sphinx<2.0)

Downloading/unpacking pyparsing>=2.0.2 (from packaging->Sphinx<2.0)

Installing collected packages: Sphinx, babel, sphinxcontrib-websupport, Jinja2, alabaster, imagesize, six, requests, Pygments, snowballstemmer, docutils, packaging, typing, pytz, MarkupSafe, idna, certifi, chardet, urllib3, pyparsing

Cleaning up...

Exception:

Traceback (most recent call last):

  File "distutils.ext/obidistutils/serenity/pip/basecommand.py", line 122, in main

  File "distutils.ext/obidistutils/serenity/pip/commands/install.py", line 283, in run

  File "distutils.ext/obidistutils/serenity/pip/req.py", line 1435, in install

  File "distutils.ext/obidistutils/serenity/pip/req.py", line 671, in install

  File "distutils.ext/obidistutils/serenity/pip/req.py", line 901, in move_wheel_files

  File "distutils.ext/obidistutils/serenity/pip/wheel.py", line 215, in move_wheel_files

  File "distutils.ext/obidistutils/serenity/pip/wheel.py", line 205, in clobber

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/os.py", line 157, in makedirs

    mkdir(name, mode)

OSError: [Errno 13] Permission denied: '/Library/Python/2.7/site-packages/Sphinx-1.8.5.dist-info'



Storing debug log for failure in /Users/giuliano/Library/Logs/pip.log

Traceback (most recent call last):

  File "<string>", line 17, in <module>

  File "/private/var/folders/rt/_gx9q8vs4t77ftcp0c80hvj80000gn/T/pip_build_giuliano/OBITools/setup.py", line 39, in <module>

  File "distutils.ext/obidistutils/core.py", line 27, in <module>

  File "distutils.ext/obidistutils/command/build_sphinx.py", line 36, in <module>

  File "distutils.ext/obidistutils/serenity/checkpackage.py", line 95, in install_requirements

  File "distutils.ext/obidistutils/serenity/checkpackage.py", line 183, in pip_install_package

  File "distutils.ext/obidistutils/serenity/pip/__init__.py", line 177, in main

  File "distutils.ext/obidistutils/serenity/pip/__init__.py", line 129, in parseopts

  File "distutils.ext/obidistutils/serenity/pip/__init__.py", line 110, in create_main_parser

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/posixpath.py", line 364, in abspath

    cwd = os.getcwd()

OSError: [Errno 2] No such file or directory

----------------------------------------
Cleaning up...
Command python setup.py egg_info failed with error code 1 in /private/var/folders/rt/_gx9q8vs4t77ftcp0c80hvj80000gn/T/pip_build_giuliano/OBITools
Storing debug log for failure in /Users/giuliano/Library/Logs/pip.log
Installing OBITools (1.2.13) in serenity mode


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You are running on a Mac platform
You are running on a Mac platform
You are running on a Mac platform
Traceback (most recent call last):
  File "setup.py", line 37, in <module>
    serenity=serenity_mode(PACKAGE,VERSION)
  File "distutils.ext/obidistutils/serenity/__init__.py", line 109, in serenity_mode
    serenity_snake(args.virtual,package,version)
  File "distutils.ext/obidistutils/serenity/__init__.py", line 56, in serenity_snake
    enforce_good_python()
  File "distutils.ext/obidistutils/serenity/rerun.py", line 50, in enforce_good_python
    raise DistutilsError,'No good python identified on your system'
distutils.errors.DistutilsError: No good python identified on your system
Traceback (most recent call last):
  File "get-obitools.py", line 45234, in <module>
    main()
  File "get-obitools.py", line 45196, in main
    envactivate = open(os.path.join(virtualenvname,'bin','activate')).readlines()
IOError: [Errno 2] No such file or directory: '/Applications/OBItools/OBITools-1.2.13/bin/activate'

Now...I have tried all sorts of possible solutions from the web (including pip and sudo install and other suggestions), but nothing really changed. Obviously, there is something that is not right, but I couldn't figure it out!!! And no, I do not want to use the docker solution suggested in some posts.

Any help would be much appreciated.

obitools python macOS • 1.3k views
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