Stringdb bug

[dvornyk@…]

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.

[Conrad Huang]

Hi, Dr. Dvornyk.

Are you installing StringDB from the toolshed interface? If so, when it ask whether to install for everyone or just yourself, which option did you select? Thanks.

Conrad

[dvornyk@…]

For everyone, because I have only one account on my laptop.

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.

-----Original Message-----
From: ChimeraX [mailto:ChimeraX-bugs-admin@cgl.ucsf.edu] 
Sent: Wednesday, November 8, 2017 20:27
Cc: conrad@cgl.ucsf.edu; dvornyk <dvornyk@hku.hk>; scooter@cgl.ucsf.edu
Subject: Re: [ChimeraX] #908: Stringdb bug

#908: Stringdb bug
--------------------------------+--------------------------
          Reporter:  dvornyk@…  |      Owner:  conrad
              Type:  defect     |     Status:  assigned
          Priority:  normal     |  Milestone:  Beta Release
         Component:  Tool Shed  |    Version:
        Resolution:             |   Keywords:
        Blocked By:             |   Blocking:
Notify when closed:             |   Platform:  all
           Project:  ChimeraX   |
--------------------------------+--------------------------

Comment (by conrad):

 Hi, Dr. Dvornyk.

 Are you installing StringDB from the toolshed interface?  If so, when it  ask whether to install for everyone or just yourself, which option did you  select?  Thanks.

 Conrad

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/908#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Conrad Huang]

Can you try installing "just for you" as a workaround? The difference between the two options is that "for everyone" installs into c:\Program Files\, whereas "just for you" installs into c:\Users\account\AppData\... which should be writable without extra permission. Alternatively, you can try running ChimeraX as administrator and see if that gives enough permission to write into c:\Program Files.

Conrad

[Eric Pettersen]

Milestone renamed

[Conrad Huang]

Generate a better error message, instead of a Python traceback, when user does not have permission to install/update tool.