Installation to non-system path triggers SandboxViolation about pyfits

[embray]

I've seen this before. This is caused by an upstream bug in setuptools. You should upgrade your setuptools version to the most recent--0.6c11 is very old.

[dkirkby]

I have updated to the latest setuptools 1.4.2 and still see the same problem using either the --prefix or --user options, e.g.:

$ easy_install --user pyfits
Searching for pyfits
Reading https://pypi.python.org/simple/pyfits/
Best match: pyfits 3.2
Downloading https://pypi.python.org/packages/source/p/pyfits/pyfits-3.2.tar.gz#md5=23fe76429fcd229f0abbd21535d1c41a
Processing pyfits-3.2.tar.gz
Writing /tmp/easy_install-di4fNj/pyfits-3.2/setup.cfg
Running pyfits-3.2/setup.py -q bdist_egg --dist-dir /tmp/easy_install-di4fNj/pyfits-3.2/egg-dist-tmp-kjgxgx
error: SandboxViolation: open('./test-easy-install-34053.write-test', 'w') {}

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.

[embray]

What does python -c 'import site; site._script()' output?

[dkirkby]

sys.path = [
    '',
    '/data/users/dkirkby/.local/lib/python2.7/site-packages/setuptools-1.4.1-py2.7.egg',
    '/data/apps/python/2.7.2/lib/python2.7/site-packages/PyYAML-3.10-py2.7-linux-x86_64.egg',
    '/data/apps/python/2.7.2/lib/python2.7/site-packages/pysam-0.6-py2.7-linux-x86_64.egg',
    '/data/apps/python/2.7.2/lib/python2.7/site-packages/Cython-0.17-py2.7-linux-x86_64.egg',
    '/data/apps/python/2.7.2/lib/python2.7/site-packages/screed-0.7-py2.7.egg',
    '/data/apps/python/2.7.2/lib/python2.7/site-packages/khmer-0.4-py2.7-linux-x86_64.egg',
    '/data/apps/python/2.7.2/lib/python2.7/site-packages/nose-1.3.0-py2.7.egg',
    '/data/apps/python/2.7.2/lib/python2.7/site-packages/pyDNase-0.1.0-py2.7-linux-x86_64.egg',
    '/data/apps/python/2.7.2/lib/python2.7/site-packages/clint-0.3.0p-py2.7.egg',
    '/data/apps/python/2.7.2/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg',
    '/data/apps/python/2.7.2/lib/python2.7/site-packages/pyparsing-2.0.1-py2.7.egg',
    '/data/apps/python/2.7.2/lib/python2.7/site-packages/tornado-3.1.1-py2.7.egg',
    '/data/apps/python/2.7.2/lib/python2.7/site-packages/python_dateutil-2.1-py2.7.egg',
    '/data/apps/python/2.7.2/lib/python2.7/site-packages/six-1.4.1-py2.7.egg',
    '/data/apps/python/2.7.2/lib/python2.7/site-packages/HTSeq-0.5.4p5-py2.7-linux-x86_64.egg',
    '/data/apps/python/2.7.2/lib/python2.7/site-packages/setuptools-1.4.2-py2.7.egg',
    '/data/apps/python/2.7.2',
    '/data/apps/python/2.7.2/lib/python2.7',
    '/data/users/dkirkby/local/lib/python2.7/site-packages',
    '/data/apps/python/2.7.2/lib/python27.zip',
    '/data/apps/python/2.7.2/lib/python2.7/plat-linux2',
    '/data/apps/python/2.7.2/lib/python2.7/lib-tk',
    '/data/apps/python/2.7.2/lib/python2.7/lib-old',
    '/data/apps/python/2.7.2/lib/python2.7/lib-dynload',
    '/data/users/dkirkby/.local/lib/python2.7/site-packages',
    '/data/apps/python/2.7.2/lib/python2.7/site-packages',
]
USER_BASE: '/data/users/dkirkby/.local' (exists)
USER_SITE: '/data/users/dkirkby/.local/lib/python2.7/site-packages' (exists)
ENABLE_USER_SITE: True

[tedgoddard]

First running

python distribute_setup.py --user

in the pyfits-3.2.2 directory allowed the install to proceed for me.