[khmer] normalize-by-median.py - IOError: [Errno 30] Read-only file system:

[C. Titus Brown]

Is your virtualenv really at '/'?  If it's under

	/user/efraim/foo/env

then you would want to do

	ln /user/efraim/foo/env/bin/pip /user/efraim/foo/env/bin/pip2

You might also need to do a

	deactivate
	. /user/efraim/foo/env/bin/activate

but this is getting into uncharted territory for me fast... a maybe easier
alternative would be to edit Makefile and replace 'pip2' with 'pip'.

cheers,
--ttius

On Sun, Jul 06, 2014 at 10:22:30PM -0500, Efraim Rodrigues wrote:
> I did it. Now, this is the response I get
> 
>  make test
> pip2 install --user nose || pip2 install nose
> /virtualenv/khmerEnv/bin/python2.7: error while loading shared libraries:
> libpython2.7.so.1.0: cannot open shared object file: No such file or
> directory
> /virtualenv/khmerEnv/bin/python2.7: error while loading shared libraries:
> libpython2.7.so.1.0: cannot open shared object file: No such file or
> directory
> make: *** [test] Error 127
> 
> 
> It tries to open this folder ( /virtualenv/khmerEnv/bin/python2.7 ) but in
> fact it does not exist.
> 
> 
> On Sun, Jul 6, 2014 at 10:11 PM, C. Titus Brown <ctb at msu.edu> wrote:
> 
> > On Sun, Jul 06, 2014 at 10:09:20PM -0500, Efraim Rodrigues wrote:
> > > When I try to run 'make test'. It looks like it calls a script which runs
> > > pip2. I guess I cannot change it.
> > >
> > > Oh, do not feel sorry. You guys are willing to help and that's all that
> > > matters.
> >
> > well, thanks ;)
> >
> > You can do:
> >
> >         ln <virtualenv>/bin/pip <virtualenv>/bin/pip2
> >
> > where you replace <virtualenv> with the path to your virtualenv directory.
> >
> > cheers,
> > --titus
> >
> > > On Sun, Jul 6, 2014 at 10:01 PM, C. Titus Brown <ctb at msu.edu> wrote:
> > >
> > > > Just try pip (not pip2). Sorry for all the mess :(
> > > >
> > > > On Jul 6, 2014, at 7:53 PM, Efraim Rodrigues <efraimnaassom at gmail.com>
> > > > wrote:
> > > >
> > > > Hi. Thanks for your response.
> > > >
> > > > It looks like the we are supposed to choose the version of the
> > virtualenv.
> > > > I found all the versions here
> > > > https://pypi.python.org/packages/source/v/virtualenv/ so I am followed
> > > > these steps using the newest version of the virtualen, in this case, I
> > > > believe that is,
> > > >
> > https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.9.tar.gz
> > > >
> > > > Anyway, I ran all the tests and it still returns the same problem.
> > > >
> > > >  make test
> > > > pip2 install --user nose || pip2 install nose
> > > > /bin/sh: pip2: command not found
> > > > /bin/sh: pip2: command not found
> > > > make: *** [test] Error 127
> > > >
> > > > In fact, there is no pip2 inside khmerEnv. I can just see these files:
> > > >
> > > > activate      activate.fish     easy_install      pip      python
> > > > python2.7
> > > > activate.csh  activate_this.py  easy_install-2.7  pip-2.7  python2
> > > >
> > > > Should I try another version of virutalenv or perhaps another similar
> > tool?
> > > >
> > > > Thank y'all for trying to help me.
> > > >
> > > >
> > > > On Sun, Jul 6, 2014 at 5:25 PM, C. Titus Brown <ctb at msu.edu> wrote:
> > > >
> > > >> On Sat, Jul 05, 2014 at 03:01:47PM -0500, Efraim Rodrigues wrote:
> > > >> > Hi everyone,
> > > >> >
> > > >> > Actually, when I tried to install by running 'make test', it
> > returned
> > > >> the
> > > >> > following message:
> > > >> >
> > > >> > pip2 install --user nose || pip2 install nose
> > > >> > /bin/sh: pip2: command not found
> > > >> > /bin/sh: pip2: command not found
> > > >> >
> > > >> >
> > > >> > Even though we have python/2.7 installed, It looks like my system
> > has
> > > >> > python/2.6 as default. Hence, in order to install 'khmer', I
> > followed
> > > >> these
> > > >> > steps:
> > > >> >
> > > >> > module load python/2.7
> > > >> >
> > > >> > python setup.py install --user
> > > >> >
> > > >> > Apparently, it worked to install it locally, however I'm not sure
> > about
> > > >> any
> > > >> > additional file or module.
> > > >>
> > > >> OK, I would suggest running the tests inside of virtualenv.  try:
> > > >>
> > > >> curl -O
> > > >>
> > https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.x.y.tar.gz
> > > >> tar xzf virtualenv*
> > > >> cd virtualenv-*; python2.7 virtualenv.py ../khmerEnv; cd ..
> > > >> source khmerEnv/bin/activate
> > > >>
> > > >> and then 'make test'.
> > > >>
> > > >> thanks!
> > > >> --titus
> > > >>
> > > >>
> > > >
> >
> > --
> > C. Titus Brown, ctb at msu.edu
> >

-- 
C. Titus Brown, ctb at msu.edu