Nevermind, figured it out. Didn’t need to be drastic and remove everything and reinstall…
I had modified my ~/.condarc file some time ago and the ‘r’ channel was above in the priority list than the ‘defaults’. Putting the ‘defaults’ back on top of the list did the trick.
Hope that might be useful for someone in the future if they run into a similar problem.
Best
Juan
On 1 Nov 2016, at 12:59, Eiros Zamora, Juan <j.eiros-zamora14.imperial.ac.uk<mailto:j.eiros-zamora14.imperial.ac.uk>> wrote:
Hi Jason,
I upgraded the environment as suggested (here’s the complete log
http://lpaste.net/2338255014272696320) , but I’m afraid this has somehow screwed up matplotlib even further. Now mdout_analyzer.py won’t load, with the following Traceback:
Traceback (most recent call last):
File "/usr/local/amber16/bin/mdout_analyzer.py", line 9, in <module>
from mdoutanalyzer.graphproperties import GraphControlWindow
File "/usr/local/amber16/lib/python3.5/site-packages/mdoutanalyzer/graphproperties.py", line 6, in <module>
from mdoutanalyzer.widgets import LabeledEntry
File "/usr/local/amber16/lib/python3.5/site-packages/mdoutanalyzer/widgets.py", line 7, in <module>
import matplotlib.pyplot as plt
File "/Users/je714/anaconda3/lib/python3.5/site-packages/matplotlib/pyplot.py", line 29, in <module>
import matplotlib.colorbar
File "/Users/je714/anaconda3/lib/python3.5/site-packages/matplotlib/colorbar.py", line 34, in <module>
import matplotlib.collections as collections
File "/Users/je714/anaconda3/lib/python3.5/site-packages/matplotlib/collections.py", line 27, in <module>
import matplotlib.backend_bases as backend_bases
File "/Users/je714/anaconda3/lib/python3.5/site-packages/matplotlib/backend_bases.py", line 62, in <module>
import matplotlib.textpath as textpath
File "/Users/je714/anaconda3/lib/python3.5/site-packages/matplotlib/textpath.py", line 18, in <module>
from matplotlib.mathtext import MathTextParser
File "/Users/je714/anaconda3/lib/python3.5/site-packages/matplotlib/mathtext.py", line 60, in <module>
import matplotlib._png as _png
ImportError: dlopen(/Users/je714/anaconda3/lib/python3.5/site-packages/matplotlib/_png.so, 2): Library not loaded: @rpath/libpng16.16.dylib
Referenced from: /Users/je714/anaconda3/lib/python3.5/site-packages/matplotlib/_png.so
Reason: Incompatible library version: _png.so requires version 39.0.0 or later, but libpng16.16.dylib provides version 34.0.0
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/amber16/bin/mdout_analyzer.py", line 18, in <module>
(amberhome, amberhome))
ImportError: Could not import Amber Python modules. Please make sure you have sourced /usr/local/amber16/amber.sh (if you are using sh/ksh/bash/zsh) or /usr/local/amber16/amber.csh (if you are using csh/tcsh)
I do have sourced $AMBERHOME/amber.sh previously.
I’ve googled the libpng16.16.dylib error, and followed suggestions like this
https://github.com/pyskell/slouchy/issues/11 or this
https://codedump.io/share/5ap8ZmVDafxz/1
Seems to me that the error is with some of the stuff I have in my root environment is crashing with libraries installed with brew, as not only mdout_analyzer.py is crashing now.
I also get the same Traceback if I open a Python shell and run `import seaborn` or try to use %pylab inline in a Jupyter notebook.
My next step is going to be erasing my Anaconda distribution and start one from fresh, as apparently something’s gone pretty wrong. But I just wanted to ask you in case you have any suggestion :)
Best
Juan
On 31 Oct 2016, at 18:48, Jason Swails <jason.swails.gmail.com<mailto:jason.swails.gmail.com><mailto:jason.swails.gmail.com>> wrote:
Hi Juan,
This looks like a problem with Anaconda's matplotlib TkAgg backend. Here
is where it's described in Google Groups:
https://groups.google.com/a/continuum.io/forum/#!topic/anaconda/xssOnleIPFw
I saw the same behavior on my Anaconda distribution. I was able to fix it
by running the command:
conda upgrade -n py35 --all
In this case, replace "py35" with the name of your conda environment (which
you can find as the environment with the * next to it when you run the
command "conda env list").
HTH,
Jason
On Mon, Oct 31, 2016 at 8:09 AM, Eiros Zamora, Juan <
j.eiros-zamora14.imperial.ac.uk<mailto:
j.eiros-zamora14.imperial.ac.uk><mailto:
j.eiros-zamora14.imperial.ac.uk>> wrote:
Dear Amberists,
I’m using mdout_analyzer.py to read an mdout file, and I see some warnings
and errors and I was hoping you could help me figure out what’s wrong.
First, when I call the program, I get the following warnings (but the GUI
opens just fine):
/Users/je714/anaconda3/lib/python3.5/site-packages/matplotlib/__init__.py:461:
UserWarning: matplotlibrc ps.usedistiller can not be set to xpdf unless
xpdf-3.0 or later is installed on your system
'your system') % pdftops_req)
objc[17603]: Class TKApplication is implemented in both
/System/Library/Frameworks/Tk.framework/Versions/8.5/Tk and
/Users/je714/anaconda3/lib/libtk8.5.dylib. One of the two will be used.
Which one is undefined.
objc[17603]: Class TKMenu is implemented in both
/System/Library/Frameworks/Tk.framework/Versions/8.5/Tk and
/Users/je714/anaconda3/lib/libtk8.5.dylib. One of the two will be used.
Which one is undefined.
objc[17603]: Class TKContentView is implemented in both
/System/Library/Frameworks/Tk.framework/Versions/8.5/Tk and
/Users/je714/anaconda3/lib/libtk8.5.dylib. One of the two will be used.
Which one is undefined.
objc[17603]: Class TKWindow is implemented in both
/System/Library/Frameworks/Tk.framework/Versions/8.5/Tk and
/Users/je714/anaconda3/lib/libtk8.5.dylib. One of the two will be used.
Which one is undefined.
I can chose any item in the ‘Select Data to Analyze’ list and click on
'Show Statistics’ or ’Save to File', for example. But when I try to plot
them with the ‘Graph Them!’, ‘Histogram Data’ or ‘Autocorrelation’,
‘Running Average’ or ‘Cumulative Running Average' buttons, I first get this
error:
Exception in Tkinter callback
Traceback (most recent call last):
File "/Users/je714/anaconda3/lib/python3.5/site-packages/matplotlib/backends/tkagg.py",
line 22, in blit
id(data), colormode, id(bbox_array))
_tkinter.TclError: invalid command name "PyAggImagePhoto"
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/je714/anaconda3/lib/python3.5/tkinter/__init__.py", line
1550, in __call__
return self.func(*args)
File "/usr/local/amber16/lib/python3.5/site-packages/mdoutanalyzer/widgets.py",
line 91, in new_fcn
return fcn(self)
File "/usr/local/amber16/lib/python3.5/site-packages/mdoutanalyzer/widgets.py",
line 63, in new_fcn
if fcn(self, newfig, ax, self.graph_props.nexcl()) == 1:
File "/usr/local/amber16/lib/python3.5/site-packages/mdoutanalyzer/widgets.py",
line 469, in execute
fig.show()
File "/Users/je714/anaconda3/lib/python3.5/site-packages/
matplotlib/backends/backend_tkagg.py", line 355, in draw
tkagg.blit(self._tkphoto, self.renderer._renderer, colormode=2)
File "/Users/je714/anaconda3/lib/python3.5/site-packages/matplotlib/backends/tkagg.py",
line 30, in blit
id(data), colormode, id(bbox_array))
_tkinter.TclError
Then an empty window titled ‘Mdout Analyzer’ pops up. I can then close it,
and re-click any of the buttons, followed by a close down of the program
with the following error:
python(17641,0x7fff79860000) malloc: *** error for object 0x100c21cd0:
pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
Abort trap: 6
I’m not familiar with the tkinter module so I’m not too sure what’s going
wrong.
My Mac is running on OS X El Capitan Version 10.11.6, my Python is Python
3.5.2 :: Anaconda 4.0.0 (x86_64), here (http://lpaste.net/raw/
5192122385733517312) is the result of conda list command (I’m running
mdout_analyzer.py on my root environment), result of uname -a command is:
Darwin ch-knuth.ch.ic.ac.uk<
http://ch-knuth.ch.ic.ac.uk/><
http://ch-knuth.ch.ic.ac.uk/><
http://ch-knuth.ch.ic.ac.uk<
http://ch-knuth.ch.ic.ac.uk/>> 15.6.0 Darwin
Kernel Version 15.6.0: Mon Aug 29 20:21:34 PDT 2016;
root:xnu-3248.60.11~1/RELEASE_X86_64 x86_64.
Please let me know if you need more information to replicate this error,
Thanks for any comments,
Juan Eiros
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Received on Tue Nov 01 2016 - 06:30:03 PDT
