Opened 7 years ago

Closed 7 years ago

#1255 closed defect (wontfix)

OS X 10.10 symbol (_clock_gettime) problem

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
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-14.5.0-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: 3.3 INTEL-10.0.35  
OpenGL renderer: Intel HD Graphics 3000 OpenGL Engine  
OpenGL vendor: Intel Inc.  
How to cite UCSF ChimeraX  

open
/Users/ucsf/Desktop/Chamba/RPRD1B/tetramer/average_structs/phosphoserine_acetyl_lysine_2_average.pdb

Opened PDB data containing 9092 atoms and 9216 bonds  
Chain information for phosphoserine_acetyl_lysine_2_average.pdb #1  
---  
Chain | Description  
| No description available  
  
Error processing trigger "frame drawn"  
Traceback (most recent call last):  
File
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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(/Applications/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:
/Applications/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
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/.dylibs/liblzma.5.dylib  

select up

296 atoms, 297 bonds selected  

select up

9092 atoms, 9216 bonds selected  

color green

open
/Users/ucsf/Desktop/Chamba/RPRD1B/tetramer/average_structs/phosphoserine_acetyl_lysine_2_9_average.pdb

Opened PDB data containing 9100 atoms and 9228 bonds  
Chain information for phosphoserine_acetyl_lysine_2_9_average.pdb #2  
---  
Chain | Description  
| No description available  
  
Error processing trigger "frame drawn"  
Traceback (most recent call last):  
File
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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(/Applications/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:
/Applications/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
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/.dylibs/liblzma.5.dylib  

select up

88 atoms, 88 bonds selected  

select up

9100 atoms, 9228 bonds selected  

color silver

select up

46 atoms, 46 bonds selected  

select up

9092 atoms, 9216 bonds selected  

color sel green

open
/Users/ucsf/Desktop/Chamba/RPRD1B/tetramer/average_structs/phosphoserine_acetyl_lysine_9_average.pdb

Opened PDB data containing 9092 atoms and 9213 bonds  
Chain information for phosphoserine_acetyl_lysine_9_average.pdb #3  
---  
Chain | Description  
| No description available  
  
Error processing trigger "frame drawn"  
Traceback (most recent call last):  
File
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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(/Applications/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:
/Applications/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
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/.dylibs/liblzma.5.dylib  

select up

88 atoms, 88 bonds selected  

select up

9092 atoms, 9213 bonds selected  

color sel black

color sel dark grey

color sel red

delete HC

matchmaker #0 to #1

No molecules/chains to match specified  

matchmaker #0: to #1:

Expected a keyword  

matchmaker #1 to #0 bring #2

No 'to' model specified  

matchmaker #1 to #0

No 'to' model specified  

matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker phosphoserine_acetyl_lysine_2_average.pdb, chain (blank) (#1) with
phosphoserine_acetyl_lysine_2_9_average.pdb, chain (blank) (#2), sequence
alignment score = 2799  
RMSD between 322 pruned atom pairs is 1.030 angstroms; (across all 549 pairs:
2.401)  
  

matchmaker #3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker phosphoserine_acetyl_lysine_2_average.pdb, chain (blank) (#1) with
phosphoserine_acetyl_lysine_9_average.pdb, chain (blank) (#3), sequence
alignment score = 2811.6  
RMSD between 356 pruned atom pairs is 1.117 angstroms; (across all 549 pairs:
2.450)  
  

select :262 -280

566 atoms, 623 bonds selected  

display sel

show sel

select sel z<5

Expected a keyword  

select sel .z<5

Expected a keyword  

select z<5

Expected an objects specifier or a keyword  

select :262-280 z<5

Expected a keyword  

select :262-280 Z<5

Expected a keyword  

select :262-280 z<5

Expected a keyword  

select :542-560

567 atoms, 620 bonds selected  

display sel

show sel

delete HC

save session /Users/ucsf/Desktop/Ps_acetylated_aligned.cxs

Session file format is not finalized, and thus might not be restorable in
other versions of ChimeraX.  

Traceback (most recent call last):  
  File
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/save_dialog.py", line 93, in _session_save  
    run(session, "save session %s" % quote_if_necessary(filename))  
  File
"/Applications/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
"/Applications/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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/session.py", line 905, in save_session  
    save(session, filename, **kw)  
  File
"/Applications/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
"/Applications/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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/session.py", line 717, in save  
    session.save(output, version=version)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/session.py", line 464, in save  
    from . import serialize  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/serialize.py", line 53, in <module>  
    from PIL import Image  
  File
"/Applications/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(/Applications/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:
/Applications/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
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/.dylibs/liblzma.5.dylib  
  

ImportError:
dlopen(/Applications/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:
/Applications/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
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/.dylibs/liblzma.5.dylib  
  
File
"/Applications/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 session /Users/ucsf/Desktop/Ps_acetylated_aligned.cxs

Session file format is not finalized, and thus might not be restorable in
other versions of ChimeraX.  

Traceback (most recent call last):  
  File
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/save_dialog.py", line 93, in _session_save  
    run(session, "save session %s" % quote_if_necessary(filename))  
  File
"/Applications/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
"/Applications/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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/session.py", line 905, in save_session  
    save(session, filename, **kw)  
  File
"/Applications/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
"/Applications/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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/session.py", line 717, in save  
    session.save(output, version=version)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/session.py", line 464, in save  
    from . import serialize  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/serialize.py", line 53, in <module>  
    from PIL import Image  
  File
"/Applications/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(/Applications/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:
/Applications/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
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/.dylibs/liblzma.5.dylib  
  

ImportError:
dlopen(/Applications/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:
/Applications/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
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/.dylibs/liblzma.5.dylib  
  
File
"/Applications/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 session /Users/ucsf/Desktop/Ps_acetylated_aligned.cxs

Session file format is not finalized, and thus might not be restorable in
other versions of ChimeraX.  

Traceback (most recent call last):  
  File
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/save_dialog.py", line 93, in _session_save  
    run(session, "save session %s" % quote_if_necessary(filename))  
  File
"/Applications/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
"/Applications/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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/session.py", line 905, in save_session  
    save(session, filename, **kw)  
  File
"/Applications/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
"/Applications/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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/session.py", line 717, in save  
    session.save(output, version=version)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/session.py", line 464, in save  
    from . import serialize  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/serialize.py", line 53, in <module>  
    from PIL import Image  
  File
"/Applications/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(/Applications/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:
/Applications/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
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/.dylibs/liblzma.5.dylib  
  

ImportError:
dlopen(/Applications/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:
/Applications/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
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/.dylibs/liblzma.5.dylib  
  
File
"/Applications/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 session /Users/ucsf/Desktop/Ps_acetylated_aligned.cxs

Session file format is not finalized, and thus might not be restorable in
other versions of ChimeraX.  

Traceback (most recent call last):  
  File
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/save_dialog.py", line 93, in _session_save  
    run(session, "save session %s" % quote_if_necessary(filename))  
  File
"/Applications/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
"/Applications/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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/session.py", line 905, in save_session  
    save(session, filename, **kw)  
  File
"/Applications/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
"/Applications/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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/session.py", line 717, in save  
    session.save(output, version=version)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/session.py", line 464, in save  
    from . import serialize  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/serialize.py", line 53, in <module>  
    from PIL import Image  
  File
"/Applications/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(/Applications/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:
/Applications/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
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/.dylibs/liblzma.5.dylib  
  

ImportError:
dlopen(/Applications/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:
/Applications/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
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/PIL/.dylibs/liblzma.5.dylib  
  
File
"/Applications/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: 3.3 INTEL-10.0.35
OpenGL renderer: Intel HD Graphics 3000 OpenGL Engine
OpenGL vendor: Intel Inc.

Change History (2)

comment:1 by Eric Pettersen, 7 years ago

Component: Unassigned → Platform
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → OS X 10.10 symbol (_clock_gettime) problem

comment:2 by Eric Pettersen, 7 years ago

Resolution: → wontfix
Status: assigned → closed

We don't support OS X 10.10

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