Opened 5 years ago

Last modified 5 years ago

#4102 assigned defect

Excessive logging of already satisfied dependencies

Reported by: goddard@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Tool Shed Version:
Keywords: Cc:
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: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
Toolshed install of StrudelScore spews excessive logging info about dozens of ChimeraX bundles meeting a requirement.  The StrudelScore bundle only lists the following dependencies.

Requires-Dist: ChimeraX-Core (>=0.1)
Requires-Dist: ChimeraX-Clipper (~=0.15.0)
Requires-Dist: pandas (>=0.24)
Requires-Dist: mrcfile (>=1.1)
Requires-Dist: biopython (>=1.77)
Requires-Dist: recordtype (>=1.3)
Requires-Dist: threed-strudel (>=0.3)

I think the output should be much less verbose.


Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

Downloading bundle ChimeraX_StrudelScore-0.1-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
WARNING: The scripts mrcfile-header and mrcfile-validate are installed in
'/Users/goddard/Library/Application Support/ChimeraX/bin' which is not on
PATH.  
Consider adding this directory to PATH or, if you prefer to suppress this
warning, use --no-warn-script-location.  
WARNING: You are using pip version 20.2.2; however, version 20.3.3 is
available.  
You should consider upgrading via the
'/Users/goddard/Desktop/ChimeraX-1.1.1.app/Contents/MacOS/ChimeraX -m pip
install --upgrade pip' command.  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing /Users/goddard/Downloads/ChimeraX_StrudelScore-0.1-py3-none-any.whl  
Requirement already satisfied: ChimeraX-Core>=0.1 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
StrudelScore==0.1) (1.1.1)  
Requirement already satisfied: ChimeraX-Clipper~=0.15.0 in
/Users/goddard/Library/Application Support/ChimeraX/1.1/site-packages (from
ChimeraX-StrudelScore==0.1) (0.15.0)  
Requirement already satisfied: biopython>=1.77 in
/Users/goddard/Library/Application Support/ChimeraX/1.1/site-packages (from
ChimeraX-StrudelScore==0.1) (1.78)  
Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.0)  
Requirement already satisfied: ChimeraX-Atomic~=1.6.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.6.1)  
Requirement already satisfied: ChimeraX-Core>=0.1 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
StrudelScore==0.1) (1.1.1)  
Collecting threed-strudel>=0.3  
Downloading threed_strudel-0.3-py3-none-any.whl (405 kB)  
Requirement already satisfied: scipy in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from threed-
strudel>=0.3->ChimeraX-StrudelScore==0.1) (1.4.1)  
Requirement already satisfied: biopython>=1.77 in
/Users/goddard/Library/Application Support/ChimeraX/1.1/site-packages (from
ChimeraX-StrudelScore==0.1) (1.78)  
Requirement already satisfied: numpy in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from threed-
strudel>=0.3->ChimeraX-StrudelScore==0.1) (1.18.5)  
Requirement already satisfied: psutil in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from threed-
strudel>=0.3->ChimeraX-StrudelScore==0.1) (5.7.0)  
Collecting recordtype>=1.3  
Downloading recordtype-1.3-py2.py3-none-any.whl (9.0 kB)  
Requirement already satisfied: six in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from
recordtype>=1.3->ChimeraX-StrudelScore==0.1) (1.15.0)  
Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.0)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.1)  
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (2.2)  
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (2.0)  
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (2.0)  
Requirement already satisfied: ChimeraX-PDB~=2.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (2.1)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.0)  
Requirement already satisfied: ChimeraX-Core>=0.1 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
StrudelScore==0.1) (1.1.1)  
Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.0)  
Requirement already satisfied: ChimeraX-Core>=0.1 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
StrudelScore==0.1) (1.1.1)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
mmCIF~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-
StrudelScore==0.1) (1.2.1)  
Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.0)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
mmCIF~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-
StrudelScore==0.1) (1.0)  
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
mmCIF~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-
StrudelScore==0.1) (1.2)  
Requirement already satisfied: ChimeraX-PDB~=2.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (2.1)  
Requirement already satisfied: ChimeraX-Core>=0.1 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
StrudelScore==0.1) (1.1.1)  
Requirement already satisfied: ChimeraX-Atomic~=1.6.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.6.1)  
Requirement already satisfied: ChimeraX-AtomSearch~=2.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
ConnectStructure~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (2.0)  
Requirement already satisfied: ChimeraX-Core>=0.1 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
StrudelScore==0.1) (1.1.1)  
Requirement already satisfied: ChimeraX-Atomic~=1.6.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.6.1)  
Requirement already satisfied: ChimeraX-Surface~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-
StrudelScore==0.1) (1.0)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.1)  
Requirement already satisfied: ChimeraX-UI~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-
StrudelScore==0.1) (1.2.3)  
Requirement already satisfied: ChimeraX-Core>=0.1 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
StrudelScore==0.1) (1.1.1)  
Requirement already satisfied: ChimeraX-Atomic~=1.6.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.6.1)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
mmCIF~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-
StrudelScore==0.1) (1.2.1)  
Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.0)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
mmCIF~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-
StrudelScore==0.1) (1.0)  
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
mmCIF~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-
StrudelScore==0.1) (1.2)  
Requirement already satisfied: ChimeraX-Core>=0.1 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
StrudelScore==0.1) (1.1.1)  
Requirement already satisfied: ChimeraX-Atomic~=1.6.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.6.1)  
Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.0)  
Requirement already satisfied: ChimeraX-Core>=0.1 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
StrudelScore==0.1) (1.1.1)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.1)  
Requirement already satisfied: ChimeraX-Core>=0.1 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
StrudelScore==0.1) (1.1.1)  
Requirement already satisfied: ChimeraX-UI~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-
StrudelScore==0.1) (1.2.3)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
mmCIF~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-
StrudelScore==0.1) (1.0)  
Requirement already satisfied: ChimeraX-IO~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
OpenCommand~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.0)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
mmCIF~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-
StrudelScore==0.1) (1.2.1)  
Requirement already satisfied: ChimeraX-Core>=0.1 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
StrudelScore==0.1) (1.1.1)  
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
mmCIF~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-
StrudelScore==0.1) (1.2)  
Requirement already satisfied: ChimeraX-IO~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
OpenCommand~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.0)  
Requirement already satisfied: ChimeraX-Core>=0.1 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
StrudelScore==0.1) (1.1.1)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
mmCIF~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-
StrudelScore==0.1) (1.0)  
Requirement already satisfied: ChimeraX-IO~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
OpenCommand~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.0)  
Requirement already satisfied: ChimeraX-Core>=0.1 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
StrudelScore==0.1) (1.1.1)  
Requirement already satisfied: ChimeraX-Atomic~=1.6.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.6.1)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
mmCIF~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-
StrudelScore==0.1) (1.2.1)  
Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.0)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.1)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
mmCIF~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-
StrudelScore==0.1) (1.0)  
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.0.4)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (2.0)  
Requirement already satisfied: ChimeraX-Map~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.0.1)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.0)  
Requirement already satisfied: ChimeraX-Core>=0.1 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
StrudelScore==0.1) (1.1.1)  
Requirement already satisfied: ChimeraX-Core>=0.1 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
StrudelScore==0.1) (1.1.1)  
Requirement already satisfied: ChimeraX-Core>=0.1 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
StrudelScore==0.1) (1.1.1)  
Requirement already satisfied: ChimeraX-Dssp~=2.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (2.0)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.1)  
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (2.2)  
Requirement already satisfied: ChimeraX-MapFit~=2.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (2.0)  
Requirement already satisfied: ChimeraX-Atomic~=1.6.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.6.1)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.0)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
mmCIF~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-
StrudelScore==0.1) (1.0)  
Requirement already satisfied: ChimeraX-Core>=0.1 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
StrudelScore==0.1) (1.1.1)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.1)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
mmCIF~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-
StrudelScore==0.1) (1.2.1)  
Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.0)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
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Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.1)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.0)  
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (2.0)  
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
mmCIF~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-
StrudelScore==0.1) (1.2)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (2.0)  
Requirement already satisfied: ChimeraX-UI~=1.0 in
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Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-
StrudelScore==0.1) (1.2.3)  
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (2.0)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
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Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.0)  
Requirement already satisfied: ChimeraX-Core>=0.1 in
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StrudelScore==0.1) (1.1.1)  
Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in
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Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.0)  
Requirement already satisfied: ChimeraX-Core>=0.1 in
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StrudelScore==0.1) (1.1.1)  
Requirement already satisfied: ChimeraX-Atomic~=1.6.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.6.1)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in
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Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (2.0)  
Requirement already satisfied: ChimeraX-Core>=0.1 in
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StrudelScore==0.1) (1.1.1)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
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Requirement already satisfied: ChimeraX-Map~=1.0 in
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Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.0.1)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
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Requirement already satisfied: ChimeraX-Core>=0.1 in
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StrudelScore==0.1) (1.1.1)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
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Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.1)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in
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Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (2.0)  
Requirement already satisfied: ChimeraX-Core>=0.1 in
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StrudelScore==0.1) (1.1.1)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
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Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.1)  
Requirement already satisfied: ChimeraX-Map~=1.0 in
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Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.0.1)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
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Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.1)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in
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Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (2.0)  
Requirement already satisfied: ChimeraX-UI~=1.0 in
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Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-
StrudelScore==0.1) (1.2.3)  
Requirement already satisfied: ChimeraX-MapFit~=2.0 in
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StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (2.0)  
Requirement already satisfied: ChimeraX-Map~=1.0 in
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Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-
Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.0.1)  
Requirement already satisfied: ChimeraX-Core>=0.1 in
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StrudelScore==0.1) (1.1.1)  
Requirement already satisfied: numpy in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from threed-
strudel>=0.3->ChimeraX-StrudelScore==0.1) (1.18.5)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.0)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
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Atomic~=1.6.0->ChimeraX-Clipper~=0.15.0->ChimeraX-StrudelScore==0.1) (1.0)  
Requirement already satisfied: ChimeraX-Core>=0.1 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from ChimeraX-
StrudelScore==0.1) (1.1.1)  
Collecting mrcfile>=1.1  
Downloading mrcfile-1.2.0-py2.py3-none-any.whl (43 kB)  
Requirement already satisfied: numpy in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from threed-
strudel>=0.3->ChimeraX-StrudelScore==0.1) (1.18.5)  
Collecting pandas>=0.24  
Downloading pandas-1.2.0-cp37-cp37m-macosx_10_9_x86_64.whl (10.3 MB)  
Requirement already satisfied: numpy in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from threed-
strudel>=0.3->ChimeraX-StrudelScore==0.1) (1.18.5)  
Requirement already satisfied: python-dateutil>=2.7.3 in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from
pandas>=0.24->ChimeraX-StrudelScore==0.1) (2.8.1)  
Requirement already satisfied: pytz>=2017.3 in
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pandas>=0.24->ChimeraX-StrudelScore==0.1) (2020.1)  
Requirement already satisfied: six in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from
recordtype>=1.3->ChimeraX-StrudelScore==0.1) (1.15.0)  
Requirement already satisfied: numpy in
./ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages (from threed-
strudel>=0.3->ChimeraX-StrudelScore==0.1) (1.18.5)  
Installing collected packages: mrcfile, threed-strudel, recordtype, pandas,
ChimeraX-StrudelScore  
Successfully installed ChimeraX-StrudelScore-0.1 mrcfile-1.2.0 pandas-1.2.0
recordtype-1.3 threed-strudel-0.3  
Lock 4797724816 acquired on
/Users/goddard/Library/Caches/ChimeraX/1.1/toolshed/bundle_info.cache.lock  
Lock 4797724816 released on
/Users/goddard/Library/Caches/ChimeraX/1.1/toolshed/bundle_info.cache.lock  
\---  

Successfully installed ChimeraX-StrudelScore-0.1 mrcfile-1.2.0 pandas-1.2.0
recordtype-1.3 threed-strudel-0.3  
Installed ChimeraX-StrudelScore (0.1)  
Downloading bundle ChimeraX_StrudelScore-0.1-py3-none-any.whl  
Bundle installation canceled  




OpenGL version: 4.1 ATI-3.10.18
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,3
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1037.147.4.0.0 (iBridge: 17.16.16610.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H2)
      Kernel Version: Darwin 19.6.0
      Time since boot: 20 days 10:16

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro Vega 20:

      Chipset Model: Radeon Pro Vega 20
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x69af
      Revision ID: 0x00c0
      ROM Revision: 113-D2060I-087
      VBIOS Version: 113-D20601MA0T-016
      Option ROM Version: 113-D20601MA0T-016
      EFI Driver Version: 01.01.087
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    biopython: 1.78
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-Clipper: 0.15.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-ISOLDE: 1.0.2
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RMF: 0.9
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StrudelScore: 0.1
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Tempy: 0.6.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    MolecularDynamicsViewer: 1.1
    mrcfile: 1.2.0
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    pandas: 1.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    recordtype: 1.3
    requests: 2.24.0
    scipy: 1.4.1
    Send2Trash: 1.5.0
    SEQCROW: 0.20
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    threed-strudel: 0.3
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Change History (1)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Tool Shed
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Excessive logging of already satisfied dependencies
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