[MacPorts] #60238: pysam samtools pysam-0.15.4-py2.7 read permissions problem

[MacPorts]

#60238: pysam samtools pysam-0.15.4-py2.7 read permissions problem
---------------------+----------------------
 Reporter:  radeksz  |      Owner:  (none)
     Type:  defect   |     Status:  new
 Priority:  Normal   |  Milestone:
Component:  ports    |    Version:
 Keywords:           |       Port:  py-pysam
---------------------+----------------------
 No read permissions for
 /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/pysam-0.15.4-py2.7.egg-info/*

 {{{
 [minis]$ ll
 /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/pysam-0.15.4-py2.7.egg-info
 total 0
 -rw-r-----  1 root  wheel   1.5K  9 Mar 15:07 PKG-INFO
 -rw-r-----  1 root  wheel   8.6K  9 Mar 15:07 SOURCES.txt
 -rw-r-----  1 root  wheel     1B  9 Mar 15:07 dependency_links.txt
 -rw-r-----  1 root  wheel     1B 19 Jan 21:52 not-zip-safe
 -rw-r-----  1 root  wheel     6B  9 Mar 15:07 top_level.txt
 }}}

 Crashes jupyter (maybe even python) on startup.

 {{{
 [~]$ notebook
 Traceback (most recent call last):
   File "/opt/local/bin/jupyter-2.7", line 6, in <module>
     from pkg_resources import load_entry_point
   File
 "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/pkg_resources/__init__.py", line 3251, in <module>
     @_call_aside
   File
 "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/pkg_resources/__init__.py", line 3235, in _call_aside
     f(*args, **kwargs)
   File
 "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/pkg_resources/__init__.py", line 3264, in
 _initialize_master_working_set
     working_set = WorkingSet._build_master()
   File
 "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/pkg_resources/__init__.py", line 574, in _build_master
     ws = cls()
   File
 "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/pkg_resources/__init__.py", line 567, in __init__
     self.add_entry(entry)
   File
 "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/pkg_resources/__init__.py", line 623, in add_entry
     for dist in find_distributions(entry, True):
   File
 "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/pkg_resources/__init__.py", line 2065, in find_on_path
     for dist in factory(fullpath):
   File
 "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/pkg_resources/__init__.py", line 2135, in
 distributions_from_metadata
     root, entry, metadata, precedence=DEVELOP_DIST,
   File
 "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/pkg_resources/__init__.py", line 2592, in from_location
     py_version=py_version, platform=platform, **kw
   File
 "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/pkg_resources/__init__.py", line 2994, in _reload_version
     md_version = self._get_version()
   File
 "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/pkg_resources/__init__.py", line 2772, in _get_version
     version = _version_from_file(lines)
   File
 "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/pkg_resources/__init__.py", line 2556, in
 _version_from_file
     line = next(iter(version_lines), '')
   File
 "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/pkg_resources/__init__.py", line 2767, in _get_metadata
     for line in self.get_metadata_lines(name):
   File
 "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/pkg_resources/__init__.py", line 1432, in
 get_metadata_lines
     return yield_lines(self.get_metadata(name))
   File
 "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/pkg_resources/__init__.py", line 1420, in get_metadata
     value = self._get(path)
   File
 "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/pkg_resources/__init__.py", line 1616, in _get
     with open(path, 'rb') as stream:
 IOError: [Errno 13] Permission denied:
 '/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/pysam-0.15.4-py2.7.egg-info/PKG-INFO'
 }}}

 Temporary remedy:
 {{{
 sudo chmod a+r
 /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
 /site-packages/pysam-0.15.4-py2.7.egg-info/*
 }}}

-- 
Ticket URL: <https://trac.macports.org/ticket/60238>
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