pysam samtools pysam-0.15.4-py2.7 read permissions problem

[radeksz]

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/*

[reneeotten (Renee Otten)]

In 7eabd81af9530839d7cae05e5f81e3b9fbcd6cd7/macports-ports (master):

py-pysam: fix permissions

• use python.rootname and default livecheck
• update homepage
• remove replaced_by code for old subports

Closes: #60238