Opened 5 years ago

Last modified 5 years ago

#3710 assigned defect

Problem installing ISOLDE into 1.0

Reported by: yonca.ural-blimke@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Tool Shed Version:
Keywords: Cc: Tristan Croll
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
Hi,

I wanted to instal ISOLDE but get an error in the process

Shortly: I clicked on the Tools/More Tools... (toolshed) tab and selected ISOLDE install. In the Log panel of chimeraX the following error appeared (posted below) and the installation was not successful (I could not find ISEOLDE in Tools/General/). I have MacOS, version 10.15.6 and installed chimeraX, version 1.0 from 2020-06-04.

How can I instal and run ISOLDE from ChimeraX?

Many Thanks,
Yonca

--
Log:

Downloading bundle ChimeraX_ISOLDE-1.0.1-cp37-cp37m-macosx_10_13_x86_64.whl:
Traceback (most recent call last): 
  File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py",
line 193, in _run_module_as_main 
    "__main__", mod_spec) 
  File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py",
line 85, in _run_code 
    exec(code, run_globals) 
  File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/ChimeraX_main.py", line 895, in <module> 
    exit_code = init(sys.argv) 
  File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/ChimeraX_main.py", line 693, in init 
    run_name='__main__', alter_sys=True) 
  File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py",
line 205, in run_module 
    return _run_module_code(code, init_globals, run_name, mod_spec) 
  File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py",
line 96, in _run_module_code 
    mod_name, mod_spec, pkg_name, script_name) 
  File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py",
line 85, in _run_code 
    exec(code, run_globals) 
  File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/pip/__main__.py", line 10, in <module> 
    if sys.path[0] in ('', os.getcwd()): 
FileNotFoundError: [Errno 2] No such file or directory 

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

Downloading bundle ChimeraX_ISOLDE-1.0.1-cp37-cp37m-macosx_10_13_x86_64.whl  
ERROR:  
Traceback (most recent call last):  
File  
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py",  
line 193, in _run_module_as_main  
"__main__", mod_spec)  
File  
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py",  
line 85, in _run_code  
exec(code, run_globals)  
File  
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-  
packages/ChimeraX_main.py", line 895, in <module>  
exit_code = init(sys.argv)  
File  
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-  
packages/ChimeraX_main.py", line 693, in init  
run_name='__main__', alter_sys=True)  
File  
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py",  
line 205, in run_module  
return _run_module_code(code, init_globals, run_name, mod_spec)  
File  
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py",  
line 96, in _run_module_code  
mod_name, mod_spec, pkg_name, script_name)  
File  
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py",  
line 85, in _run_code  
exec(code, run_globals)  
File  
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-  
packages/pip/__main__.py", line 10, in <module>  
if sys.path[0] in ('', os.getcwd()):  
FileNotFoundError: [Errno 2] No such file or directory  
  
  
  

> toolshed show

Downloading bundle ChimeraX_ISOLDE-1.0.1-cp37-cp37m-macosx_10_13_x86_64.whl  
ERROR:  
Traceback (most recent call last):  
File  
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py",  
line 193, in _run_module_as_main  
"__main__", mod_spec)  
File  
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py",  
line 85, in _run_code  
exec(code, run_globals)  
File  
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-  
packages/ChimeraX_main.py", line 895, in <module>  
exit_code = init(sys.argv)  
File  
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-  
packages/ChimeraX_main.py", line 693, in init  
run_name='__main__', alter_sys=True)  
File  
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py",  
line 205, in run_module  
return _run_module_code(code, init_globals, run_name, mod_spec)  
File  
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py",  
line 96, in _run_module_code  
mod_name, mod_spec, pkg_name, script_name)  
File  
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py",  
line 85, in _run_code  
exec(code, run_globals)  
File  
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-  
packages/pip/__main__.py", line 10, in <module>  
if sys.path[0] in ('', os.getcwd()):  
FileNotFoundError: [Errno 2] No such file or directory  
  
  
  

> ui tool show Toolbar

> toolshed show

Downloading bundle ChimeraX_Clipper-0.14.0-cp37-cp37m-macosx_10_13_x86_64.whl  
ERROR:  
Traceback (most recent call last):  
File  
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py",  
line 193, in _run_module_as_main  
"__main__", mod_spec)  
File  
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py",  
line 85, in _run_code  
exec(code, run_globals)  
File  
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-  
packages/ChimeraX_main.py", line 895, in <module>  
exit_code = init(sys.argv)  
File  
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-  
packages/ChimeraX_main.py", line 693, in init  
run_name='__main__', alter_sys=True)  
File  
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py",  
line 205, in run_module  
return _run_module_code(code, init_globals, run_name, mod_spec)  
File  
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py",  
line 96, in _run_module_code  
mod_name, mod_spec, pkg_name, script_name)  
File  
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py",  
line 85, in _run_code  
exec(code, run_globals)  
File  
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-  
packages/pip/__main__.py", line 10, in <module>  
if sys.path[0] in ('', os.getcwd()):  
FileNotFoundError: [Errno 2] No such file or directory  
  
  
  

> help help:contact.html

> toolshed show




OpenGL version: 4.1 INTEL-14.7.8
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 512 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 1037.147.4.0.0 (iBridge: 17.16.16610.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.6 (19G2021)
      Kernel Version: Darwin 19.6.0
      Time since boot: 2:51

Graphics/Displays:

    Intel Iris Plus Graphics:

      Chipset Model: Intel Iris Plus Graphics
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x8a53
      Revision ID: 0x0007
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        DELL U2715H:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 59 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: GH85D62F00FL
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: Thunderbolt/DisplayPort

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

Change History (5)

comment:1 by pett, 5 years ago

Cc: Tristan Croll added
Component: Unassigned → Tool Shed
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Problem installing ISOLDE into 1.0

comment:2 by Tristan Croll, 5 years ago

I've seen errors looking like this when I've started ChimeraX from a bash shell in a directory that no longer existed (i.e. I'd deleted it from another shell instance). Could that be what happened here?

comment:3 by Tristan Croll, 5 years ago

The same error was just reported to me by Billy Poon on the ChimeraX team (in MacOS 10.14). Install failed when ChimeraX was launched from the GUI, but succeeded when it was launched from a terminal window.

comment:4 by Tristan Croll, 5 years ago

Great to hear that it's working for you now! But the fact that it's not working from the GUI is still a rather odd bug - the error is being thrown by os.getcwd(), which as far as I'm aware can only happen if the process's current working directory is deleted while it's still running. What makes it further confusing is, why does this seemingly only happen for a subset of cases? If it was happening for everyone, I'd expect a flood of bug reports.

in reply to:  5 ; comment:5 by yonca.ural-blimke@…, 5 years ago 

Dear Tristan,


many thanks for the solution. As in the case of Billy Poon, I had the 
issue while starting ChimeraX from GUI. Indeed, when I started chimeraX 
from terminal now, I was able to install Isolde and run it without 
problems. For me, the issue is solved as now I know that I should start 
chimeraX from terminal.


Best regards,

Yonca


On 14.09.20 20:11, ChimeraX wrote:
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