markovmodel / pyemma_tutorials

How to analyze molecular dynamics data with PyEMMA
Creative Commons Attribution 4.0 International
71 stars 34 forks source link

install fails #57

Closed franknoe closed 6 years ago

franknoe commented 6 years ago

python setup.py install fails with the err msg below. I understand that I should try to install nglview myself, but we cannot expect the typical user to get this idea from the message below. Please explicitly tell the user what they should do.

I have then installed nglview with conda, but even after that re-running python setup.py install tries to install it again, leading to the same error. So I don't know at this point if the setup was otherwise successful.

Installed /Users/noe/anaconda/lib/python3.5/site-packages/jupyter_contrib_nbextensions-0.5.0-py3.5.egg
Searching for nglview
Reading https://pypi.python.org/simple/nglview/
Downloading https://files.pythonhosted.org/packages/b3/58/1d9bf6f955a2f6a238edd0440b93077ebdcf9bdd6c510646b8368a7644d5/nglview-1.1.3.tar.gz#sha256=7923009420dd6876b5f6d5c9cf13012e7840d187254668ddaf3b63692a6b85d1
Best match: nglview 1.1.3
Processing nglview-1.1.3.tar.gz
Writing /var/folders/ls/ph740md171l053d2dpylf6ym0000gn/T/easy_install-m79_7uoo/nglview-1.1.3/setup.cfg
Running nglview-1.1.3/setup.py -q bdist_egg --dist-dir /var/folders/ls/ph740md171l053d2dpylf6ym0000gn/T/easy_install-m79_7uoo/nglview-1.1.3/egg-dist-tmp-o5w2ce8v
setup.py entered
$PATH=/Users/noe/anaconda/bin:/Users/noe/anaconda/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/texbin
package init file 'nglview/tests/__init__.py' not found (or not a regular file)
package init file 'nglview/static/__init__.py' not found (or not a regular file)
warning: no files found matching 'nglview/js/*'
warning: no files found matching '*.*' under directory 'nglview/staticlab'
warning: no files found matching 'DEVELOPMENT.md'
warning: no previously-included files matching '*.pycinclude' found anywhere in distribution
warning: no previously-included files matching '*.ipynb' found anywhere in distribution
warning: no previously-included files matching '*.gif' found anywhere in distribution
warning: no previously-included files matching '*tests/notebooks/*' found anywhere in distribution
UPDATING build/lib/nglview/_version.py
set build/lib/nglview/_version.py to '1.1.3'
Trying to enable extensions
error: SandboxViolation: mkdir('/Users/noe/anaconda/etc/jupyter/nbconfig', 493) {}

The package setup script has attempted to modify files on your system
that are not within the EasyInstall build area, and has been aborted.

This package cannot be safely installed by EasyInstall, and may not
support alternate installation locations even if you run its setup
script by hand.  Please inform the package's author and the EasyInstall
maintainers to find out if a fix or workaround is available.
franknoe commented 6 years ago

continuing, I end up with 'ImportError: No module named 'mdshare'', so I assume the install script never got there. I am stopping now until the package is easily installable.

marscher commented 6 years ago

As the readme states, direct invocations of setup.py (or via pip) are not supported, but for people who know what they are doing/eg. are able to solve technical problems their self.

This also resolved issues with nglview / mdshare.