I recently installed CellProfiler on my desktop running Ubuntu 12.10 (Precise Pangolin) and I’ve encountered some problems. I’ve managed to overcome most of them, and the ones I haven’t been able to fix isn’t preventing me from using the program, but I thought I’d post them here in case others were having similar problems and they could be fixed.
I followed the instructions for installation via Option 2 as described here, and encountered a few issues with the installation:
When I tried to compile I received I received an ld error saying that libjvm.so was missing. I had set LD_LIBRARY_PATH and checked my Makefile and it all appeared to be correct. In the end, I was able to fix this error using the tweak to cellprofiler/utilities/setup.py described in this post. I think maybe this file needs a fix itself to have a non amd64 option?
After succesffully compiling when I ran CellProfiler I was still getting an error about libjvm.so not being found. The error was being spit up by cellprofiler/utilities/jutil.py. After playing around with that, I determined that it was failing because the
java -cp ... findlibjvmcall was producing nothing. So, I was able to fix this with a real kludge by changing line 99 in cellprofiler/utilities/jutil.py:
#jvm_dir = stdout.strip() jvm_dir = "/usr/lib/jvm/java-6-sun/jre/lib/i386/server"
Though it works for me, this is obviously a terrible solution. Maybe something is wrong with the findlibjvm class for my version of java? Here’s some info on that:
$ java -version java version "1.7.0_15" OpenJDK Runtime Environment (IcedTea7 2.3.7) (7u15-2.3.7-0ubuntu1~12.10.1) OpenJDK Server VM (build 23.7-b01, mixed mode)
- After fixing the libjvm.so issue I was able to run CellProfiler and process images. There are a few minor things remaining that I 100% don’t care about (no “Tahoma” font, I’ll live… ). However, I am still getting tons of Gtk errors spit out at me that are a bit more concerning (though not killing my ability to use the program). Here’s what happens when I run CellProfiler.py:
$ 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) skipping '_convex_hull.c' Cython extension (up-to-date) running build_ext skipping 'javabridge.c' Cython extension (up-to-date) (python:9886): Gtk-CRITICAL **: IA__gtk_range_set_range: assertion `min < max' failed Version: 2013-03-20T16:20:08 SVN:10199 / 20130320162008 (python:9886): Gtk-CRITICAL **: IA__gtk_widget_get_direction: assertion `GTK_IS_WIDGET (widget)' failed
I continue to get these sorts of errors as windows are opened and closed and manipulated, etc. For example, if I open an image and then close it I get this:
(python:9886): LIBDBUSMENU-GTK-CRITICAL **: watch_submenu: assertion `GTK_IS_MENU_SHELL(menu)' failed
I haven’t done any thorough research into fixing this problem (because hey, I’m processing images), but a look across the posts here didn’t turn up anything. If anyone had any insight I’d be curious…
That’s all, thanks for this amazing program!!!