Entering edit mode
4.8 years ago
gln.colosimo
•
0
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.
