id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
908	Stringdb bug	dvornyk@…	Conrad Huang	"{{{
Hello,

When trying to install the above module, see the following:
RuntimeError: Processing c:\users\v_dvo_000\downloads\chimerax_stringdb-0.1-py3-none-any.whl
Requirement not upgraded as not directly required: ChimeraX-Core>=0.1 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Stringdb==0.1)
Collecting ChimeraX-Cytoscape>=0.1 (from ChimeraX-Stringdb==0.1)
Downloading https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxcytoscape/releases/0.1/ChimeraX_Cytoscape-0.1-py3-none-any.whl
Requirement not upgraded as not directly required: grako==3.16.5 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Core>=0.1->ChimeraX-Stringdb==0.1)
Requirement not upgraded as not directly required: Pillow==4.2.1 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Core>=0.1->ChimeraX-Stringdb==0.1)
Requirement not upgraded as not directly required: setuptools==34.4.1 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Core>=0.1->ChimeraX-Stringdb==0.1)
Requirement not upgraded as not directly required: suds-jurko==0.6 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Core>=0.1->ChimeraX-Stringdb==0.1)
Requirement not upgraded as not directly required: colorama==0.3.7 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Core>=0.1->ChimeraX-Stringdb==0.1)
Requirement not upgraded as not directly required: sortedcontainers==1.5.7 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Core>=0.1->ChimeraX-Stringdb==0.1)
Requirement not upgraded as not directly required: beautifulsoup4==4.5.3 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Core>=0.1->ChimeraX-Stringdb==0.1)
Requirement not upgraded as not directly required: msgpack-python>=0.5 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Core>=0.1->ChimeraX-Stringdb==0.1)
Requirement not upgraded as not directly required: olefile in c:\program files\chimerax\bin\lib\site-packages (from Pillow==4.2.1->ChimeraX-Core>=0.1->ChimeraX-Stringdb==0.1)
Requirement not upgraded as not directly required: six>=1.6.0 in c:\program files\chimerax\bin\lib\site-packages (from setuptools==34.4.1->ChimeraX-Core>=0.1->ChimeraX-Stringdb==0.1)
Requirement not upgraded as not directly required: packaging>=16.8 in c:\program files\chimerax\bin\lib\site-packages (from setuptools==34.4.1->ChimeraX-Core>=0.1->ChimeraX-Stringdb==0.1)
Requirement not upgraded as not directly required: appdirs>=1.4.0 in c:\program files\chimerax\bin\lib\site-packages (from setuptools==34.4.1->ChimeraX-Core>=0.1->ChimeraX-Stringdb==0.1)
Requirement not upgraded as not directly required: pyparsing in c:\program files\chimerax\bin\lib\site-packages (from packaging>=16.8->setuptools==34.4.1->ChimeraX-Core>=0.1->ChimeraX-Stringdb==0.1)
Installing collected packages: ChimeraX-Cytoscape, ChimeraX-Stringdb
Exception:
Traceback (most recent call last):
File ""C:\Program Files\ChimeraX\bin\lib\site-packages\pip\basecommand.py"", line 215, in main
status = self.run(options, args)
File ""C:\Program Files\ChimeraX\bin\lib\site-packages\pip\commands\install.py"", line 342, in run
prefix=options.prefix_path,
File ""C:\Program Files\ChimeraX\bin\lib\site-packages\pip\req\req_set.py"", line 784, in install
**kwargs
File ""C:\Program Files\ChimeraX\bin\lib\site-packages\pip\req\req_install.py"", line 851, in install
self.move_wheel_files(self.source_dir, root=root, prefix=prefix)
File ""C:\Program Files\ChimeraX\bin\lib\site-packages\pip\req\req_install.py"", line 1064, in move_wheel_files
isolated=self.isolated,
File ""C:\Program Files\ChimeraX\bin\lib\site-packages\pip\wheel.py"", line 345, in move_wheel_files
clobber(source, lib_dir, True)
File ""C:\Program Files\ChimeraX\bin\lib\site-packages\pip\wheel.py"", line 316, in clobber
ensure_dir(destdir)
File ""C:\Program Files\ChimeraX\bin\lib\site-packages\pip\utils\__init__.py"", line 83, in ensure_dir
os.makedirs(path)
File ""C:\Program Files\ChimeraX\bin\lib\os.py"", line 220, in makedirs
mkdir(name, mode)
PermissionError: [WinError 5] Access is denied: 'C:\\Program Files\\ChimeraX\\bin\\Lib\\site-packages\\chimerax\\cytoscape'


File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\toolshed\__init__.py"", line 708, in _run_pip
raise RuntimeError(output + error)

See log for complete Python traceback.

If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and describe what you were doing and include a copy of the contents of the log.

Sincerely,


Dr. Volodymyr Dvornyk
Honorary Associate Professor
School of Biological Sciences
University of Hong Kong
Pokfulam
Hong Kong

Associate Professor of Genetics
Department of Life Sciences
College of Science and General Studies
Alfaisal University
P.O. Box 50927
Riyadh, 11533
Saudi Arabia
Tel.: +966 11 2157656

""It can't be ever, because it can be never!"" (A.P. Chekhov)

The information contained in this email message is strictly confidential. If you are not the intended recipient, any use, interference with, disclosure or copying of this material is unauthorized and prohibited. If you have received this communication in error, please notify me immediately, and delete the original message.


}}}
"	defect	closed	normal	0.6	Tool Shed		fixed		Scooter Morris				all	ChimeraX