Opened 7 years ago

Closed 7 years ago

#1379 closed defect (not a bug)

Failure on OSX 10.11

Reported by: chimerax-bug-report@… Owned by:
Priority: normal Milestone:
Component: Platform Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-15.6.0-x86_64-i386-64bit
ChimeraX Version: 0.7 (2018-08-07)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.7 (2018-08-07)  
OpenGL version: 4.1 INTEL-10.14.74  
OpenGL renderer: Intel(R) HD Graphics 6000  
OpenGL vendor: Intel Inc.  
How to cite UCSF ChimeraX  

open "/Users/leslieleepedraza/Downloads/5yx2 (1).pdb"

Opened PDB data containing 8380 atoms and 8616 bonds  
Chain information for 5yx2 (1).pdb #1  
---  
Chain | Description  
A D | DNA (cytosine-5)-methyltransferase 3A  
B C | DNA (cytosine-5)-methyltransferase 3-like  
E F | DNA (25-mer)  
  
Error processing trigger "frame drawn"  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/triggerset.py", line 126, in invoke  
return self._func(self._name, data)  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/filehistory.py", line 69, in <lambda>  
t.add_handler('frame drawn', lambda *args, s=self: s.capture_thumbnails_cb())  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/filehistory.py", line 81, in capture_thumbnails_cb  
fs.capture_image(models, ses)  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/filehistory.py", line 152, in capture_image  
self.image = models_image(session, models, size)  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/filehistory.py", line 209, in models_image  
image = v.image(width, height, camera = c, drawings = models)  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 397, in image  
from PIL import Image  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/Image.py", line 60, in <module>  
from . import _imaging as core  
ImportError:
dlopen(/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/_imaging.cpython-36m-darwin.so, 2): Symbol not found:
_clock_gettime  
Referenced from:
/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/.dylibs/liblzma.5.dylib (which was built for Mac OS X 10.12)  
Expected in: /usr/lib/libSystem.B.dylib  
in
/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/.dylibs/liblzma.5.dylib  

save image "/Users/leslieleepedraza/Desktop/CORE Papers L13 onward/5YX2.png"
width 345 height 457

Traceback (most recent call last):  
  File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/gui.py", line 744, in <lambda>  
    save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))  
  File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/gui.py", line 532, in file_save_cb  
    self.save_dialog.display(self, session)  
  File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/save_dialog.py", line 141, in display  
    fmt.save(session, filename)  
  File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/save_dialog.py", line 40, in save  
    return self._save(session, filename)  
  File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/save_dialog.py", line 269, in save  
    run(session, cmd)  
  File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/run.py", line 31, in run  
    results = command.run(text, log=log)  
  File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2561, in run  
    result = ci.function(session, **kw_args)  
  File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/save.py", line 61, in save  
    fmt.export(session, filename, fmt.nicknames[0], **kw)  
  File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/io.py", line 198, in export  
    result = self.export_func(session, path, **kw)  
  File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/image.py", line 97, in save_image  
    from PIL import PngImagePlugin  
  File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/PngImagePlugin.py", line 39, in <module>  
    from . import Image, ImageFile, ImagePalette  
  File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/Image.py", line 60, in <module>  
    from . import _imaging as core  
ImportError:
dlopen(/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/_imaging.cpython-36m-darwin.so, 2): Symbol not found:
_clock_gettime  
  Referenced from:
/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/.dylibs/liblzma.5.dylib (which was built for Mac OS X 10.12)  
  Expected in: /usr/lib/libSystem.B.dylib  
 in
/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/.dylibs/liblzma.5.dylib  
  

ImportError:
dlopen(/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/_imaging.cpython-36m-darwin.so, 2): Symbol not found:
_clock_gettime  
Referenced from:
/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/.dylibs/liblzma.5.dylib (which was built for Mac OS X 10.12)  
Expected in: /usr/lib/libSystem.B.dylib  
in
/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/.dylibs/liblzma.5.dylib  
  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/Image.py", line 60, in  
from . import _imaging as core  
  
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.
Don't include any data you wish to remain private since a publicly viewable
bug report will be created.  

save image "/Users/leslieleepedraza/Desktop/CORE Papers L13 onward/5YX2.png"
width 345 height 457

Traceback (most recent call last):  
  File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/gui.py", line 744, in <lambda>  
    save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))  
  File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/gui.py", line 532, in file_save_cb  
    self.save_dialog.display(self, session)  
  File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/save_dialog.py", line 141, in display  
    fmt.save(session, filename)  
  File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/save_dialog.py", line 40, in save  
    return self._save(session, filename)  
  File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/save_dialog.py", line 269, in save  
    run(session, cmd)  
  File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/run.py", line 31, in run  
    results = command.run(text, log=log)  
  File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2561, in run  
    result = ci.function(session, **kw_args)  
  File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/save.py", line 61, in save  
    fmt.export(session, filename, fmt.nicknames[0], **kw)  
  File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/io.py", line 198, in export  
    result = self.export_func(session, path, **kw)  
  File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/image.py", line 97, in save_image  
    from PIL import PngImagePlugin  
  File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/PngImagePlugin.py", line 39, in <module>  
    from . import Image, ImageFile, ImagePalette  
  File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/Image.py", line 60, in <module>  
    from . import _imaging as core  
ImportError:
dlopen(/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/_imaging.cpython-36m-darwin.so, 2): Symbol not found:
_clock_gettime  
  Referenced from:
/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/.dylibs/liblzma.5.dylib (which was built for Mac OS X 10.12)  
  Expected in: /usr/lib/libSystem.B.dylib  
 in
/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/.dylibs/liblzma.5.dylib  
  

ImportError:
dlopen(/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/_imaging.cpython-36m-darwin.so, 2): Symbol not found:
_clock_gettime  
Referenced from:
/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/.dylibs/liblzma.5.dylib (which was built for Mac OS X 10.12)  
Expected in: /usr/lib/libSystem.B.dylib  
in
/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/.dylibs/liblzma.5.dylib  
  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/Image.py", line 60, in  
from . import _imaging as core  
  
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.
Don't include any data you wish to remain private since a publicly viewable
bug report will be created.  




OpenGL version: 4.1 INTEL-10.14.74
OpenGL renderer: Intel(R) HD Graphics 6000
OpenGL vendor: Intel Inc.

Change History (1)

comment:1 by Eric Pettersen, 7 years ago

Component: Unassigned → Platform
Platform: → all
Project: → ChimeraX
Resolution: → not a bug
Status: new → closed
Summary: ChimeraX bug report submission → Failure on OSX 10.11

Download page notes that it doesn't work on 10.11 or earlier

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