Opened 7 years ago

Closed 6 years ago

#1642 closed defect (fixed)

Bundles from other builds being used

Reported by: goddard@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Tool Shed Version:
Keywords: Cc: Greg Couch
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.17763
ChimeraX Version: 0.9 (2019-01-25)
Description
Starting today's ChimeraX daily build and opening 6bb5 gives an error apparently because it is trying to use bundles from my development build (/cygwin/var/tmp/chimerax_build) on this machine.  It shouldn't be using bundles from other builds.

Log:
UCSF ChimeraX version: 0.9 (2019-01-25)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6bb5 format mmCIF fromDatabase pdb

6bb5 title:  
Human Oxy-Hemoglobin [more info...]  
  
Chain information for 6bb5 #1  
---  
Chain | Description  
A | Hemoglobin subunit α  
B | Hemoglobin subunit β  
  
Non-standard residues in 6bb5 #1  
---  
HEM — protoporphyrin IX containing Fe (HEME)  
OXY — oxygen molecule  
  
6bb5 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"c:\cygwin64\var\tmp\chimerax_build\develop\chimerax\chimerax.app\bin\lib\site-
packages\chimerax\map_series_gui\tool.py", line 223, in <lambda>  
ADD_MODELS, lambda name, m, s=session: models_added_cb(m, s))  
File
"c:\cygwin64\var\tmp\chimerax_build\develop\chimerax\chimerax.app\bin\lib\site-
packages\chimerax\map_series_gui\tool.py", line 237, in models_added_cb  
from chimerax.core.map.series.series import Map_Series  
ModuleNotFoundError: No module named 'chimerax.core.map'  
  
Error processing trigger "add models": No module named 'chimerax.core.map':  
ModuleNotFoundError: No module named 'chimerax.core.map'  
  
File
"c:\cygwin64\var\tmp\chimerax_build\develop\chimerax\chimerax.app\bin\lib\site-
packages\chimerax\map_series_gui\tool.py", line 237, in models_added_cb  
from chimerax.core.map.series.series import Map_Series  
  
See log for complete Python traceback.  
  
  




OpenGL version: 3.3.0 NVIDIA 391.58
OpenGL renderer: Quadro P6000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (14)

comment:1 by pett, 7 years ago

Cc: Greg Couch added
Component: Unassigned → Tool Shed
Owner: set to Conrad Huang
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Bundes from other builds being used

in reply to:  2 ; comment:2 by goddard@…, 7 years ago 

Doing “toolshed reload” and restarting ChimeraX daily does not fix the problem.

Deleting the toolshed cache directory reported by “toolshed cache” and restarting does not fix the problem.

comment:3 by Conrad Huang, 7 years ago

Weird. Somehow {{{C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\site-
packages}}} must have made it on to sys.path. Just to make sure, can you fire up Shell and print the value of sys.path?

comment:4 by Tom Goddard, 7 years ago

This error is running the ChimeraX-Jan-25-2019 and it is finding bundles in the /cygwin64/var/tmp/... build on the same machine (vizvault.cgl.ucsf.edu). Here is sys.path which does include the /var/tmp ChimeraX

Jupyter QtConsole 4.4.3

Current ChimeraX session available as 'session'.

Python 3.7.2 (tags/v3.7.2:9a3ffc0492, Dec 23 2018, 23:09:28) [MSC v.1916 64 bit (AMD64)]
Type 'copyright', 'credits' or 'license' for more information
IPython 6.5.0 -- An enhanced Interactive Python. Type '?' for help.

import sys

sys.path
Out[2]: 
['C:\\Program Files\\ChimeraX-Jan-25-2019\\bin\\python37.zip',
 'C:\\Program Files\\ChimeraX-Jan-25-2019\\bin\\DLLs',
 'C:\\Program Files\\ChimeraX-Jan-25-2019\\bin\\lib',
 'C:\\Program Files\\ChimeraX-Jan-25-2019\\bin',
 'C:\\Program Files\\ChimeraX-Jan-25-2019\\bin\\lib\\site-packages',
 'C:\\Program Files\\ChimeraX-Jan-25-2019\\bin\\lib\\site-packages\\line_profiler-2.1.2-py3.7-win-amd64.egg',
 'c:\\cygwin64\\var\\tmp\\chimerax_build\\develop\\chimerax\\chimerax.app\\bin\\lib\\site-packages',
 'C:\\Users\\goddard\\AppData\\Local\\UCSF\\ChimeraX\\0.9\\site-packages',
 'C:\\Program Files\\ChimeraX-Jan-25-2019\\bin\\lib\\site-packages\\IPython\\extensions']
Last edited 7 years ago by Conrad Huang (previous) (diff)

comment:5 by Conrad Huang, 7 years ago

Which machine is this happening on? Also, if you run python.exe from ChimeraX-Jan-25-2019 and print sys.path, does it still have the /var/tmp entry?

comment:6 by Tom Goddard, 7 years ago

This is vizvault.cgl.ucsf.edu, the machine connected to the vizvault projector.

Yes, the standalone ChimeraX python.exe run from a cygwin shell has the /var/tmp path.

$ cd /cygdrive/c/Program\ Files/ChimeraX-Jan-25-2019/bin/
$ ls
__pycache__     libarrays.dll     OpenMMDrude.dll  remove_pycache.py
ChimeraX.exe    liblogger.dll     OpenMMDrude.lib  Scripts
concrt140.dll   libs              OpenMMRPMD.dll   share
DLLs            msvcp140.dll      OpenMMRPMD.lib   structcomp
ffmpeg.exe      OpenMM.dll        plugins          vccorlib140.dll
include         OpenMM.lib        python.exe       vcruntime140.dll
Lib             OpenMMAmoeba.dll  python3.dll
libappdirs.dll  OpenMMAmoeba.lib  python37.dll
$ ./python.exe

$ ./python.exe -i
Python 3.7.2 (tags/v3.7.2:9a3ffc0492, Dec 23 2018, 23:09:28) [MSC v.1916 64 bit                                    (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> sys.path
['', 'C:\\Program Files\\ChimeraX-Jan-25-2019\\bin\\python37.zip', 'C:\\Program Files\\ChimeraX-Jan-25-2019\\bin\\DLLs', 'C:\\Program Files\\ChimeraX-Jan-25-2019\\bin\\lib', 'C:\\Program Files\\ChimeraX-Jan-25-2019\\bin', 'C:\\Program Files\\ChimeraX-Jan-25-2019\\bin\\lib\\site-packages', 'C:\\Program Files\\ChimeraX-Jan-25-2019\\bin\\lib\\site-packages\\line_profiler-2.1.2-py3.7-win-amd64.egg', 'c:\\cygwin64\\var\\tmp\\chimerax_build\\develop\\chimerax\\chimerax.app\\bin\\lib\\site-packages']
>>>
Last edited 7 years ago by Conrad Huang (previous) (diff)

comment:7 by Conrad Huang, 7 years ago

Can you run two more commands for me? (I can't ssh into vizvault.)

./python.exe -i -v
./python.exe -i -E -v

For both, run import sys; print(sys.path) just to see if there are differences. Thanks.

in reply to:  8 ; comment:8 by goddard@…, 7 years ago 

$ /cygdrive/c/Program\ Files/ChimeraX-Jan-25-2019/bin/python.exe -i
Python 3.7.2 (tags/v3.7.2:9a3ffc0492, Dec 23 2018, 23:09:28) [MSC v.1916
64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
['', 'C:\\Program Files\\ChimeraX-Jan-25-2019\\bin\\python37.zip',
'C:\\Program Files\\ChimeraX-Jan-25-2019\\bin\\DLLs', 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib', 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin', 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\site-packages', 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\site-packages\\line_profiler-2.1.2-py3.7-win-amd64.egg',
'c:\\cygwin64\\var\\tmp\\chimerax_build\\develop\\chimerax\\chimerax.app\\bin\\lib\\site-packages']
$ exit 

Process shell exited abnormally with code 130
$ /cygdrive/c/Program\ Files/ChimeraX-Jan-25-2019/bin/python.exe -i -v
import _frozen_importlib # frozen
import _imp # builtin
import '_thread' # <class '_frozen_importlib.BuiltinImporter'>
import '_warnings' # <class '_frozen_importlib.BuiltinImporter'>
import '_weakref' # <class '_frozen_importlib.BuiltinImporter'>
# installing zipimport hook
import 'zipimport' # <class '_frozen_importlib.BuiltinImporter'>
# installed zipimport hook
import '_frozen_importlib_external' # <class
'_frozen_importlib.FrozenImporter'>
import '_io' # <class '_frozen_importlib.BuiltinImporter'>
import 'marshal' # <class '_frozen_importlib.BuiltinImporter'>
import 'nt' # <class '_frozen_importlib.BuiltinImporter'>
import _thread # previously loaded ('_thread')
import '_thread' # <class '_frozen_importlib.BuiltinImporter'>
import _weakref # previously loaded ('_weakref')
import '_weakref' # <class '_frozen_importlib.BuiltinImporter'>
import 'winreg' # <class '_frozen_importlib.BuiltinImporter'>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\encodings\__pycache__\__init__.cpython-37.pyc
matches C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\encodings\__init__.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\encodings\\__pycache__\\__init__.cpython-37.pyc'
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\codecs.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\codecs.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\codecs.cpython-37.pyc'
import '_codecs' # <class '_frozen_importlib.BuiltinImporter'>
import 'codecs' # <_frozen_importlib_external.SourceFileLoader object at
0x00000214AF2954E0>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\encodings\__pycache__\aliases.cpython-37.pyc
matches C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\encodings\aliases.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\encodings\\__pycache__\\aliases.cpython-37.pyc'
import 'encodings.aliases' #
<_frozen_importlib_external.SourceFileLoader object at
0x00000214AF2A9FD0>
import 'encodings' # <_frozen_importlib_external.SourceFileLoader object
at 0x00000214AF2898D0>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\encodings\__pycache__\utf_8.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\encodings\utf_8.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\encodings\\__pycache__\\utf_8.cpython-37.pyc'
import 'encodings.utf_8' # <_frozen_importlib_external.SourceFileLoader
object at 0x00000214AF2BD080>
import '_signal' # <class '_frozen_importlib.BuiltinImporter'>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\encodings\__pycache__\latin_1.cpython-37.pyc
matches C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\encodings\latin_1.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\encodings\\__pycache__\\latin_1.cpython-37.pyc'
import 'encodings.latin_1' #
<_frozen_importlib_external.SourceFileLoader object at
0x00000214AF2BD4A8>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\io.cpython-37.pyc matches
C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\io.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\io.cpython-37.pyc'
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\abc.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\abc.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\abc.cpython-37.pyc'
import '_abc' # <class '_frozen_importlib.BuiltinImporter'>
import 'abc' # <_frozen_importlib_external.SourceFileLoader object at
0x00000214AF2BDA20>
import 'io' # <_frozen_importlib_external.SourceFileLoader object at
0x00000214AF2BD668>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\_bootlocale.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\_bootlocale.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\_bootlocale.cpython-37.pyc'
import '_locale' # <class '_frozen_importlib.BuiltinImporter'>
import '_bootlocale' # <_frozen_importlib_external.SourceFileLoader
object at 0x00000214AF2BD8D0>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\encodings\__pycache__\cp1252.cpython-37.pyc
matches C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\encodings\cp1252.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\encodings\\__pycache__\\cp1252.cpython-37.pyc'
import 'encodings.cp1252' # <_frozen_importlib_external.SourceFileLoader
object at 0x00000214AF2C47B8>
Python 3.7.2 (tags/v3.7.2:9a3ffc0492, Dec 23 2018, 23:09:28) [MSC v.1916
64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\site.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\site.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\site.cpython-37.pyc'
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\os.cpython-37.pyc matches
C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\os.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\os.cpython-37.pyc'
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\stat.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\stat.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\stat.cpython-37.pyc'
import '_stat' # <class '_frozen_importlib.BuiltinImporter'>
import 'stat' # <_frozen_importlib_external.SourceFileLoader object at
0x00000214AF421438>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\ntpath.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\ntpath.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\ntpath.cpython-37.pyc'
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\genericpath.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\genericpath.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\genericpath.cpython-37.pyc'
import 'genericpath' # <_frozen_importlib_external.SourceFileLoader
object at 0x00000214AF42C2E8>
import 'ntpath' # <_frozen_importlib_external.SourceFileLoader object at
0x00000214AF421AC8>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\_collections_abc.cpython-37.pyc
matches C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\_collections_abc.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\_collections_abc.cpython-37.pyc'
import '_collections_abc' # <_frozen_importlib_external.SourceFileLoader
object at 0x00000214AF42C8D0>
import 'os' # <_frozen_importlib_external.SourceFileLoader object at
0x00000214AF413048>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\_sitebuiltins.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\_sitebuiltins.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\_sitebuiltins.cpython-37.pyc'
import '_sitebuiltins' # <_frozen_importlib_external.SourceFileLoader
object at 0x00000214AF4133C8>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\types.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\types.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\types.cpython-37.pyc'
import 'types' # <_frozen_importlib_external.SourceFileLoader object at
0x00000214AF4197B8>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\importlib\__pycache__\__init__.cpython-37.pyc
matches C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\importlib\__init__.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\importlib\\__pycache__\\__init__.cpython-37.pyc'
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\warnings.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\warnings.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\warnings.cpython-37.pyc'
import 'warnings' # <_frozen_importlib_external.SourceFileLoader object
at 0x00000214AF569588>
import 'importlib' # <_frozen_importlib_external.SourceFileLoader object
at 0x00000214AF569198>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\importlib\__pycache__\util.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\importlib\util.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\importlib\\__pycache__\\util.cpython-37.pyc'
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\importlib\__pycache__\abc.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\importlib\abc.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\importlib\\__pycache__\\abc.cpython-37.pyc'
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\importlib\__pycache__\machinery.cpython-37.pyc
matches C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\importlib\machinery.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\importlib\\__pycache__\\machinery.cpython-37.pyc'
import 'importlib.machinery' #
<_frozen_importlib_external.SourceFileLoader object at
0x00000214AF57E208>
import 'importlib.abc' # <_frozen_importlib_external.SourceFileLoader
object at 0x00000214AF570978>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\contextlib.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\contextlib.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\contextlib.cpython-37.pyc'
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\collections\__pycache__\__init__.cpython-37.pyc
matches C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\collections\__init__.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\collections\\__pycache__\\__init__.cpython-37.pyc'
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\operator.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\operator.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\operator.cpython-37.pyc'
import '_operator' # <class '_frozen_importlib.BuiltinImporter'>
import 'operator' # <_frozen_importlib_external.SourceFileLoader object
at 0x00000214AF5AF780>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\keyword.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\keyword.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\keyword.cpython-37.pyc'
import 'keyword' # <_frozen_importlib_external.SourceFileLoader object
at 0x00000214AF5B6978>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\heapq.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\heapq.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\heapq.cpython-37.pyc'
import '_heapq' # <class '_frozen_importlib.BuiltinImporter'>
import 'heapq' # <_frozen_importlib_external.SourceFileLoader object at
0x00000214AF5B1358>
import 'itertools' # <class '_frozen_importlib.BuiltinImporter'>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\reprlib.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\reprlib.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\reprlib.cpython-37.pyc'
import 'reprlib' # <_frozen_importlib_external.SourceFileLoader object
at 0x00000214AF5B1940>
import '_collections' # <class '_frozen_importlib.BuiltinImporter'>
import 'collections' # <_frozen_importlib_external.SourceFileLoader
object at 0x00000214AF5909B0>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\functools.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\functools.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\functools.cpython-37.pyc'
import '_functools' # <class '_frozen_importlib.BuiltinImporter'>
import 'functools' # <_frozen_importlib_external.SourceFileLoader object
at 0x00000214AF590DA0>
import 'contextlib' # <_frozen_importlib_external.SourceFileLoader
object at 0x00000214AF57E048>
import 'importlib.util' # <_frozen_importlib_external.SourceFileLoader
object at 0x00000214AF5699B0>
# possible namespace for C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\site-packages\mpl_toolkits
# possible namespace for C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\site-packages\sphinxcontrib
# destroy sphinxcontrib
import 'site' # <_frozen_importlib_external.SourceFileLoader object at
0x00000214AF2C4BE0>
import 'atexit' # <class '_frozen_importlib.BuiltinImporter'>
['', 'C:\\Program Files\\ChimeraX-Jan-25-2019\\bin\\python37.zip',
'C:\\Program Files\\ChimeraX-Jan-25-2019\\bin\\DLLs', 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib', 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin', 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\site-packages', 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\site-packages\\line_profiler-2.1.2-py3.7-win-amd64.egg',
'c:\\cygwin64\\var\\tmp\\chimerax_build\\develop\\chimerax\\chimerax.app\\bin\\lib\\site-packages']
$ exit 

Process shell exited abnormally with code 130
$ /cygdrive/c/Program\ Files/ChimeraX-Jan-25-2019/bin/python.exe -i -E
-v
import _frozen_importlib # frozen
import _imp # builtin
import '_thread' # <class '_frozen_importlib.BuiltinImporter'>
import '_warnings' # <class '_frozen_importlib.BuiltinImporter'>
import '_weakref' # <class '_frozen_importlib.BuiltinImporter'>
# installing zipimport hook
import 'zipimport' # <class '_frozen_importlib.BuiltinImporter'>
# installed zipimport hook
import '_frozen_importlib_external' # <class
'_frozen_importlib.FrozenImporter'>
import '_io' # <class '_frozen_importlib.BuiltinImporter'>
import 'marshal' # <class '_frozen_importlib.BuiltinImporter'>
import 'nt' # <class '_frozen_importlib.BuiltinImporter'>
import _thread # previously loaded ('_thread')
import '_thread' # <class '_frozen_importlib.BuiltinImporter'>
import _weakref # previously loaded ('_weakref')
import '_weakref' # <class '_frozen_importlib.BuiltinImporter'>
import 'winreg' # <class '_frozen_importlib.BuiltinImporter'>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\encodings\__pycache__\__init__.cpython-37.pyc
matches C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\encodings\__init__.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\encodings\\__pycache__\\__init__.cpython-37.pyc'
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\codecs.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\codecs.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\codecs.cpython-37.pyc'
import '_codecs' # <class '_frozen_importlib.BuiltinImporter'>
import 'codecs' # <_frozen_importlib_external.SourceFileLoader object at
0x0000012F1E4754E0>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\encodings\__pycache__\aliases.cpython-37.pyc
matches C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\encodings\aliases.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\encodings\\__pycache__\\aliases.cpython-37.pyc'
import 'encodings.aliases' #
<_frozen_importlib_external.SourceFileLoader object at
0x0000012F1E489FD0>
import 'encodings' # <_frozen_importlib_external.SourceFileLoader object
at 0x0000012F1E4698D0>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\encodings\__pycache__\utf_8.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\encodings\utf_8.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\encodings\\__pycache__\\utf_8.cpython-37.pyc'
import 'encodings.utf_8' # <_frozen_importlib_external.SourceFileLoader
object at 0x0000012F1E49D080>
import '_signal' # <class '_frozen_importlib.BuiltinImporter'>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\encodings\__pycache__\latin_1.cpython-37.pyc
matches C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\encodings\latin_1.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\encodings\\__pycache__\\latin_1.cpython-37.pyc'
import 'encodings.latin_1' #
<_frozen_importlib_external.SourceFileLoader object at
0x0000012F1E49D4A8>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\io.cpython-37.pyc matches
C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\io.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\io.cpython-37.pyc'
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\abc.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\abc.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\abc.cpython-37.pyc'
import '_abc' # <class '_frozen_importlib.BuiltinImporter'>
import 'abc' # <_frozen_importlib_external.SourceFileLoader object at
0x0000012F1E49DA20>
import 'io' # <_frozen_importlib_external.SourceFileLoader object at
0x0000012F1E49D668>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\_bootlocale.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\_bootlocale.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\_bootlocale.cpython-37.pyc'
import '_locale' # <class '_frozen_importlib.BuiltinImporter'>
import '_bootlocale' # <_frozen_importlib_external.SourceFileLoader
object at 0x0000012F1E49D8D0>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\encodings\__pycache__\cp1252.cpython-37.pyc
matches C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\encodings\cp1252.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\encodings\\__pycache__\\cp1252.cpython-37.pyc'
import 'encodings.cp1252' # <_frozen_importlib_external.SourceFileLoader
object at 0x0000012F1E4A47B8>
Python 3.7.2 (tags/v3.7.2:9a3ffc0492, Dec 23 2018, 23:09:28) [MSC v.1916
64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\site.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\site.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\site.cpython-37.pyc'
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\os.cpython-37.pyc matches
C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\os.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\os.cpython-37.pyc'
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\stat.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\stat.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\stat.cpython-37.pyc'
import '_stat' # <class '_frozen_importlib.BuiltinImporter'>
import 'stat' # <_frozen_importlib_external.SourceFileLoader object at
0x0000012F1E601438>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\ntpath.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\ntpath.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\ntpath.cpython-37.pyc'
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\genericpath.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\genericpath.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\genericpath.cpython-37.pyc'
import 'genericpath' # <_frozen_importlib_external.SourceFileLoader
object at 0x0000012F1E60C2E8>
import 'ntpath' # <_frozen_importlib_external.SourceFileLoader object at
0x0000012F1E601AC8>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\_collections_abc.cpython-37.pyc
matches C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\_collections_abc.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\_collections_abc.cpython-37.pyc'
import '_collections_abc' # <_frozen_importlib_external.SourceFileLoader
object at 0x0000012F1E60C8D0>
import 'os' # <_frozen_importlib_external.SourceFileLoader object at
0x0000012F1E5F3048>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\_sitebuiltins.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\_sitebuiltins.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\_sitebuiltins.cpython-37.pyc'
import '_sitebuiltins' # <_frozen_importlib_external.SourceFileLoader
object at 0x0000012F1E5F33C8>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\types.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\types.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\types.cpython-37.pyc'
import 'types' # <_frozen_importlib_external.SourceFileLoader object at
0x0000012F1E5F97B8>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\importlib\__pycache__\__init__.cpython-37.pyc
matches C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\importlib\__init__.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\importlib\\__pycache__\\__init__.cpython-37.pyc'
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\warnings.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\warnings.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\warnings.cpython-37.pyc'
import 'warnings' # <_frozen_importlib_external.SourceFileLoader object
at 0x0000012F1E749588>
import 'importlib' # <_frozen_importlib_external.SourceFileLoader object
at 0x0000012F1E749198>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\importlib\__pycache__\util.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\importlib\util.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\importlib\\__pycache__\\util.cpython-37.pyc'
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\importlib\__pycache__\abc.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\importlib\abc.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\importlib\\__pycache__\\abc.cpython-37.pyc'
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\importlib\__pycache__\machinery.cpython-37.pyc
matches C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\importlib\machinery.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\importlib\\__pycache__\\machinery.cpython-37.pyc'
import 'importlib.machinery' #
<_frozen_importlib_external.SourceFileLoader object at
0x0000012F1E75E208>
import 'importlib.abc' # <_frozen_importlib_external.SourceFileLoader
object at 0x0000012F1E750978>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\contextlib.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\contextlib.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\contextlib.cpython-37.pyc'
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\collections\__pycache__\__init__.cpython-37.pyc
matches C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\collections\__init__.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\collections\\__pycache__\\__init__.cpython-37.pyc'
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\operator.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\operator.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\operator.cpython-37.pyc'
import '_operator' # <class '_frozen_importlib.BuiltinImporter'>
import 'operator' # <_frozen_importlib_external.SourceFileLoader object
at 0x0000012F1E78F780>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\keyword.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\keyword.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\keyword.cpython-37.pyc'
import 'keyword' # <_frozen_importlib_external.SourceFileLoader object
at 0x0000012F1E796978>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\heapq.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\heapq.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\heapq.cpython-37.pyc'
import '_heapq' # <class '_frozen_importlib.BuiltinImporter'>
import 'heapq' # <_frozen_importlib_external.SourceFileLoader object at
0x0000012F1E791358>
import 'itertools' # <class '_frozen_importlib.BuiltinImporter'>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\reprlib.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\reprlib.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\reprlib.cpython-37.pyc'
import 'reprlib' # <_frozen_importlib_external.SourceFileLoader object
at 0x0000012F1E791940>
import '_collections' # <class '_frozen_importlib.BuiltinImporter'>
import 'collections' # <_frozen_importlib_external.SourceFileLoader
object at 0x0000012F1E7709B0>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\functools.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\functools.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\functools.cpython-37.pyc'
import '_functools' # <class '_frozen_importlib.BuiltinImporter'>
import 'functools' # <_frozen_importlib_external.SourceFileLoader object
at 0x0000012F1E770DA0>
import 'contextlib' # <_frozen_importlib_external.SourceFileLoader
object at 0x0000012F1E75E048>
import 'importlib.util' # <_frozen_importlib_external.SourceFileLoader
object at 0x0000012F1E7499B0>
# possible namespace for C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\site-packages\mpl_toolkits
# possible namespace for C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\site-packages\sphinxcontrib
# destroy sphinxcontrib
import 'site' # <_frozen_importlib_external.SourceFileLoader object at
0x0000012F1E4A4BE0>
import 'atexit' # <class '_frozen_importlib.BuiltinImporter'>
['', 'C:\\Program Files\\ChimeraX-Jan-25-2019\\bin\\python37.zip',
'C:\\Program Files\\ChimeraX-Jan-25-2019\\bin\\DLLs', 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib', 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin', 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\site-packages', 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\site-packages\\line_profiler-2.1.2-py3.7-win-amd64.egg',
'c:\\cygwin64\\var\\tmp\\chimerax_build\\develop\\chimerax\\chimerax.app\\bin\\lib\\site-packages']
$ exit 

Process shell exited abnormally with code 130

comment:9 by Conrad Huang, 7 years ago

Sorry about this. A few more commands:

./python.exe -I -c "import sys; print(sys.path)"
./python.exe -s -c "import sys; print(sys.path)"
./python.exe -S -c "import sys; print(sys.path)"

If any of these produce a sys.path that does not include /var/tmp, can you rerun it with the -v flag? Thanks.

in reply to:  10 ; comment:10 by goddard@…, 7 years ago 

The -S version did not have /var. 

$ /cygdrive/c/Program\ Files/ChimeraX-Jan-25-2019/bin/python.exe -I -c
"import sys; print(sys.path)"
['C:\\Program Files\\ChimeraX-Jan-25-2019\\bin\\python37.zip',
'C:\\Program Files\\ChimeraX-Jan-25-2019\\bin\\DLLs', 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib', 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin', 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\site-packages', 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\site-packages\\line_profiler-2.1.2-py3.7-win-amd64.egg',
'c:\\cygwin64\\var\\tmp\\chimerax_build\\develop\\chimerax\\chimerax.app\\bin\\lib\\site-packages']


$ /cygdrive/c/Program\ Files/ChimeraX-Jan-25-2019/bin/python.exe -s -c
"import sys; print(sys.path)"
['', 'C:\\Program Files\\ChimeraX-Jan-25-2019\\bin\\python37.zip',
'C:\\Program Files\\ChimeraX-Jan-25-2019\\bin\\DLLs', 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib', 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin', 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\site-packages', 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\site-packages\\line_profiler-2.1.2-py3.7-win-amd64.egg',
'c:\\cygwin64\\var\\tmp\\chimerax_build\\develop\\chimerax\\chimerax.app\\bin\\lib\\site-packages']


$ /cygdrive/c/Program\ Files/ChimeraX-Jan-25-2019/bin/python.exe -S -c
"import sys; print(sys.path)"
['', 'C:\\Program Files\\ChimeraX-Jan-25-2019\\bin\\python37.zip',
'C:\\Program Files\\ChimeraX-Jan-25-2019\\bin\\DLLs', 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib', 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin'] 

$ /cygdrive/c/Program\ Files/ChimeraX-Jan-25-2019/bin/python.exe -v -S
-c "import sys; print(sys.path)"
import _frozen_importlib # frozen
import _imp # builtin
import '_thread' # <class '_frozen_importlib.BuiltinImporter'>
import '_warnings' # <class '_frozen_importlib.BuiltinImporter'>
import '_weakref' # <class '_frozen_importlib.BuiltinImporter'>
# installing zipimport hook
import 'zipimport' # <class '_frozen_importlib.BuiltinImporter'>
# installed zipimport hook
import '_frozen_importlib_external' # <class
'_frozen_importlib.FrozenImporter'>
import '_io' # <class '_frozen_importlib.BuiltinImporter'>
import 'marshal' # <class '_frozen_importlib.BuiltinImporter'>
import 'nt' # <class '_frozen_importlib.BuiltinImporter'>
import _thread # previously loaded ('_thread')
import '_thread' # <class '_frozen_importlib.BuiltinImporter'>
import _weakref # previously loaded ('_weakref')
import '_weakref' # <class '_frozen_importlib.BuiltinImporter'>
import 'winreg' # <class '_frozen_importlib.BuiltinImporter'>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\encodings\__pycache__\__init__.cpython-37.pyc
matches C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\encodings\__init__.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\encodings\\__pycache__\\__init__.cpython-37.pyc'
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\codecs.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\codecs.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\codecs.cpython-37.pyc'
import '_codecs' # <class '_frozen_importlib.BuiltinImporter'>
import 'codecs' # <_frozen_importlib_external.SourceFileLoader object at
0x000001B046D15518>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\encodings\__pycache__\aliases.cpython-37.pyc
matches C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\encodings\aliases.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\encodings\\__pycache__\\aliases.cpython-37.pyc'
import 'encodings.aliases' #
<_frozen_importlib_external.SourceFileLoader object at
0x000001B046D29FD0>
import 'encodings' # <_frozen_importlib_external.SourceFileLoader object
at 0x000001B046D09908>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\encodings\__pycache__\utf_8.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\encodings\utf_8.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\encodings\\__pycache__\\utf_8.cpython-37.pyc'
import 'encodings.utf_8' # <_frozen_importlib_external.SourceFileLoader
object at 0x000001B046D3D0B8>
import '_signal' # <class '_frozen_importlib.BuiltinImporter'>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\encodings\__pycache__\latin_1.cpython-37.pyc
matches C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\encodings\latin_1.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\encodings\\__pycache__\\latin_1.cpython-37.pyc'
import 'encodings.latin_1' #
<_frozen_importlib_external.SourceFileLoader object at
0x000001B046D3D4E0>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\io.cpython-37.pyc matches
C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\io.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\io.cpython-37.pyc'
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\abc.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\abc.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\abc.cpython-37.pyc'
import '_abc' # <class '_frozen_importlib.BuiltinImporter'>
import 'abc' # <_frozen_importlib_external.SourceFileLoader object at
0x000001B046D3DA58>
import 'io' # <_frozen_importlib_external.SourceFileLoader object at
0x000001B046D3D6A0>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\__pycache__\_bootlocale.cpython-37.pyc
matches C:\Program Files\ChimeraX-Jan-25-2019\bin\lib\_bootlocale.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\__pycache__\\_bootlocale.cpython-37.pyc'
import '_locale' # <class '_frozen_importlib.BuiltinImporter'>
import '_bootlocale' # <_frozen_importlib_external.SourceFileLoader
object at 0x000001B046D3D908>
# C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\encodings\__pycache__\cp1252.cpython-37.pyc
matches C:\Program
Files\ChimeraX-Jan-25-2019\bin\lib\encodings\cp1252.py
# code object from 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib\\encodings\\__pycache__\\cp1252.cpython-37.pyc'
import 'encodings.cp1252' # <_frozen_importlib_external.SourceFileLoader
object at 0x000001B046D447F0>
Python 3.7.2 (tags/v3.7.2:9a3ffc0492, Dec 23 2018, 23:09:28) [MSC v.1916
64 bit (AMD64)] on win32
['', 'C:\\Program Files\\ChimeraX-Jan-25-2019\\bin\\python37.zip',
'C:\\Program Files\\ChimeraX-Jan-25-2019\\bin\\DLLs', 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin\\lib', 'C:\\Program
Files\\ChimeraX-Jan-25-2019\\bin']
# cleanup[3] wiping _codecs
# cleanup[3] wiping encodings.aliases
# cleanup[3] wiping encodings.utf_8
# cleanup[3] wiping encodings.latin_1
# cleanup[3] wiping encodings.cp1252
# cleanup[3] wiping sys
# clear builtins._
# clear sys.path
# clear sys.argv
# clear sys.ps1
# clear sys.ps2
# clear sys.last_type
# clear sys.last_value
# clear sys.last_traceback
# clear sys.path_hooks
# clear sys.path_importer_cache
# clear sys.meta_path
# clear sys.__interactivehook__
# clear sys.flags
# clear sys.float_info
# restore sys.stdin
# restore sys.stdout
# restore sys.stderr
# cleanup[2] removing sys
# cleanup[2] removing builtins
# cleanup[2] removing _frozen_importlib
# cleanup[2] removing _imp
# cleanup[2] removing _thread
# cleanup[2] removing _warnings
# cleanup[2] removing _weakref
# cleanup[2] removing zipimport
# cleanup[2] removing _frozen_importlib_external
# cleanup[2] removing _io
# cleanup[2] removing marshal
# cleanup[2] removing nt
# cleanup[2] removing winreg
# cleanup[2] removing encodings
# destroy encodings
# cleanup[2] removing codecs
# cleanup[2] removing _codecs
# cleanup[2] removing encodings.aliases
# cleanup[2] removing encodings.utf_8
# cleanup[2] removing _signal
# cleanup[2] removing __main__
# destroy __main__
# cleanup[2] removing encodings.latin_1
# cleanup[2] removing io
# destroy io
# cleanup[2] removing abc
# destroy abc
# cleanup[2] removing _abc
# cleanup[2] removing _bootlocale
# destroy _bootlocale
# cleanup[2] removing _locale
# cleanup[2] removing encodings.cp1252
# destroy zipimport
# destroy _signal
# destroy _abc
# destroy _locale
# cleanup[3] wiping _frozen_importlib
# destroy _frozen_importlib_external
# cleanup[3] wiping _imp
# cleanup[3] wiping _thread
# cleanup[3] wiping _warnings
# cleanup[3] wiping _weakref
# cleanup[3] wiping _io
# cleanup[3] wiping marshal
# cleanup[3] wiping nt
# cleanup[3] wiping winreg
# cleanup[3] wiping codecs
# cleanup[3] wiping builtins
$

comment:11 by pett, 7 years ago

Summary: Bundes from other builds being used → Bundles from other builds being used

comment:12 by Tom Goddard, 7 years ago

This error is on vive.cgl.ucsf.edu, not vizvault.cgl.ucsf.edu as I reported in comment 4. I told Greg who is trying to get sshd going on vive now.

comment:13 by Conrad Huang, 7 years ago

Owner: changed from Conrad Huang to Greg Couch

Fixed in b4a03dcf9.

line_profiler (currently) has to be rebuilt from source when we updated to Python 3.7. The "classic" way to do so is python setup.py build install, but that uses the old easy_install procedure, which ended up creating a setuptools.pth in site-packages. Worse, the content of that file is the absolute path to site-packages, which is how an independent installation of ChimeraX was still looking at its original build location for modules. Changing to building a whl and using pip to install it fixed the problem.

But now it doesn't install on Linux, which Greg will fix.

comment:14 by Greg Couch, 6 years ago

Resolution: → fixed
Status: assigned → closed

Got line profiler working with current version of Python. Need to build from source, by unpacking source, removing cython generated file, then building.

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