Problem with CP2 installation on linux

I’m trying to set up CP2 on a desktop computer running linux mint debian edition. I’ve followed the instructions on the github page “CellProfiler Developer’s version installation for Linux” (option 2), but I’m getting the following error messages when I open CP2.

The main problem seems to be the “permission denied” for the javabridge. If it matters, I downloaded the repository to /usr/local/CellProfiler, which now belongs to user “root” and group “staff”. My user is a member of the “staff” group.

It’s also weird to me that it says the subversion revision is 11675 (the CP2 gui says the same thing), even though when I update the repository, it says I have revision 11715. Thanks for any help.

/usr/local/CellProfiler $ python CellProfiler.py
running build_ext
skipping ‘_cpmorphology2.c’ Cython extension (up-to-date)
skipping ‘_watershed.c’ Cython extension (up-to-date)
skipping ‘_propagate.c’ Cython extension (up-to-date)
skipping ‘_filter.c’ Cython extension (up-to-date)
skipping ‘_lapjv.c’ Cython extension (up-to-date)
running build_ext
cythoning javabridge.pyx to javabridge.c
error: /usr/local/CellProfiler/cellprofiler/utilities/javabridge.c: Permission denied
Failed to load bioformats
Traceback (most recent call last):
File “/usr/local/CellProfiler/cellprofiler/modules/loadimages.py”, line 64, in
import bioformats.formatreader as formatreader
File “/usr/local/CellProfiler/bioformats/init.py”, line 20, in
import cellprofiler.utilities.jutil as jutil
File “/usr/local/CellProfiler/cellprofiler/utilities/jutil.py”, line 163, in
import javabridge
ImportError: No module named javabridge
Could not load cellprofiler.modules.run_imagej
Traceback (most recent call last):
File “/usr/local/CellProfiler/cellprofiler/modules/init.py”, line 303, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/usr/local/CellProfiler/cellprofiler/modules/run_imagej.py”, line 21, in
import bioformats
File “/usr/local/CellProfiler/bioformats/init.py”, line 20, in
import cellprofiler.utilities.jutil as jutil
File “/usr/local/CellProfiler/cellprofiler/utilities/jutil.py”, line 163, in
import javabridge
ImportError: No module named javabridge
Failed to load bioformats. SaveImages will not be able to save movies.
Traceback (most recent call last):
File “/usr/local/CellProfiler/cellprofiler/modules/saveimages.py”, line 44, in
from bioformats.formatreader import *
File “/usr/local/CellProfiler/bioformats/init.py”, line 20, in
import cellprofiler.utilities.jutil as jutil
File “/usr/local/CellProfiler/cellprofiler/utilities/jutil.py”, line 163, in
import javabridge
ImportError: No module named javabridge
could not load these modules: cellprofiler.modules.run_imagej

(python:10329): Gtk-CRITICAL **: IA__gtk_range_set_range: assertion `min < max’ failed
Subversion revision: 11675
Caught exception while killing ijbridge.
Traceback (most recent call last):
File “CellProfiler.py”, line 490, in
import imagej.ijbridge as ijbridge
File “/usr/local/CellProfiler/imagej/ijbridge.py”, line 13, in
import cellprofiler.utilities.jutil as J
File “/usr/local/CellProfiler/cellprofiler/utilities/jutil.py”, line 163, in
import javabridge
ImportError: No module named javabridge
Caught exception while killing VM.
Traceback (most recent call last):
File “CellProfiler.py”, line 500, in
import cellprofiler.utilities.jutil as jutil
File “/usr/local/CellProfiler/cellprofiler/utilities/jutil.py”, line 163, in
import javabridge
ImportError: No module named javabridge

Hi,

It looks like the Linux instructions here were still pointing to our old svn repository, sorry. So you were not actually pointed to our most recent code. I corrected Step 7 in the instructions, so try checking out CP again using svn, or equivalently, using git pull.

I don’t know if this will fix the java error for sure, but first things first.

Thanks,
David

Hi David,
Thanks for the help. It seems to work fine with the latest version from the new repository.

Jake

Great, thanks for letting us know it works.
-David