installation error

[sterding]

hi,

I got the following error when upgrading to the latest version of kPal. I'm a newbie of python. It seems related with cython. Could you please help?

[xd010@eris1n2 ~]$ pip install --install-option="--install-dir=/PHShome/xd010/lib/python2.7/site-packages/" --upgrade kPal
Requirement already up-to-date: kPal in ./lib/python2.7/site-packages
Requirement already up-to-date: numpy in ./lib/python2.7/site-packages (from kPal)
Requirement already up-to-date: h5py>=2.1 in ./lib/python2.7/site-packages (from kPal)
Requirement already up-to-date: biopython in ./lib/python2.7/site-packages (from kPal)
Requirement already up-to-date: semantic-version in ./lib/python2.7/site-packages (from kPal)
Requirement already up-to-date: future in ./lib/python2.7/site-packages (from kPal)
Downloading/unpacking Cython>=0.17 from https://pypi.python.org/packages/source/C/Cython/Cython-0.23.4.tar.gz#md5=157df1f69bcec6b56fd97e0f2e057f6e (from h5py>=2.1->kPal)
Downloading Cython-0.23.4.tar.gz (1.6MB): 1.6MB downloaded
Running setup.py (path:/tmp/pip_build_xd010/Cython/setup.py) egg_info for package Cython
Unable to find pgen, not compiling formal grammar.

warning: no files found matching '*.pyx' under directory 'Cython/Debugger/Tests'
warning: no files found matching '*.pxd' under directory 'Cython/Debugger/Tests'
warning: no files found matching '*.h' under directory 'Cython/Debugger/Tests'
warning: no files found matching '*.pxd' under directory 'Cython/Utility'

Requirement already up-to-date: six in ./lib/python2.7/site-packages (from h5py>=2.1->kPal)
Installing collected packages: Cython
Found existing installation: Cython 0.21
Uninstalling Cython:
Cleaning up...
Exception:
Traceback (most recent call last):
File "/PHShome/xd010/lib/python2.7/site-packages/pip/basecommand.py", line 122, in main
status = self.run(options, args)
File "/PHShome/xd010/lib/python2.7/site-packages/pip/commands/install.py", line 283, in run
requirement_set.install(install_options, global_options, root=options.root_path)
File "/PHShome/xd010/lib/python2.7/site-packages/pip/req.py", line 1431, in install
requirement.uninstall(auto_confirm=True)
File "/PHShome/xd010/lib/python2.7/site-packages/pip/req.py", line 598, in uninstall
paths_to_remove.remove(auto_confirm)
File "/PHShome/xd010/lib/python2.7/site-packages/pip/req.py", line 1836, in remove
renames(path, new_path)
File "/PHShome/xd010/lib/python2.7/site-packages/pip/util.py", line 295, in renames
shutil.move(old, new)
File "/PHShome/xd010/lib/python2.7/shutil.py", line 300, in move
rmtree(src)
File "/PHShome/xd010/lib/python2.7/shutil.py", line 247, in rmtree
rmtree(fullname, ignore_errors, onerror)
File "/PHShome/xd010/lib/python2.7/shutil.py", line 247, in rmtree
rmtree(fullname, ignore_errors, onerror)
File "/PHShome/xd010/lib/python2.7/shutil.py", line 247, in rmtree
rmtree(fullname, ignore_errors, onerror)
File "/PHShome/xd010/lib/python2.7/shutil.py", line 252, in rmtree
onerror(os.remove, fullname, sys.exc_info())
File "/PHShome/xd010/lib/python2.7/shutil.py", line 250, in rmtree
os.remove(fullname)
OSError: [Errno 13] Permission denied: '/apps/source/python-lib/python2.7/cython/0.21/lib/python2.7/site-packages/Cython-0.21-py2.7-linux-x86_64.egg/Cython/Build/Tests/TestInline.py'

Storing debug log for failure in /PHShome/xd010/.pip/pip.log

-Xianjun

[martijnvermaat]

Hi @sterding,

I'm not sure what's going on here, but it looks like something specific to
your Python setup.

Although you're trying to install packages in your homedir, apparently Cython
is already system-wide
(/apps/source/python-lib/python2.7/cython/0.21/lib/python2.7/site-packages). Since
one of our dependencies needs a newer Cython version, it tries to uninstall
that one but you don't have permissions to touch the system-wide Cython
package.

As an alternative, you could try installing in a
Virtual Environment,
isolated from the system Python packages. E.g,:

virtualenv kpal
source kpal/bin/activate
pip install kpal