Compile Successful but CP2 fails to run on Linux

Hi,

CellProfiler2 is a fantastic program that I’ve been able to use successfully in windows as a binary version. However now I’m trying to get CP2 working under linux but have run up against some challenges in compiling CP2 for linux.

So I’ve now spent about a month off and on, working to get CP to compile in Linux on a Mandriva 2011 64 bit system, kernel 2.6.39.4. Probably about 100 compilation attempts now. It’s required a bit of tweaking of the Makefile.CP2 to download and compile currently available packages but finally the compilation process reaches the end without aborting.

I thought I was just about there with the program, however when I attempt to start CP2 at the terminal, I get the output shown below. The CellProfiler startup image pops up briefly but disappears when the startup terminates:

############################################################################################################

[andrew@localhost CellProfiler-CellProfiler-802161f]$ python CellProfiler.py

WARNING:root:Distributed support disabled: please install nuageux

running build_ext

building ‘_cpmorphology’ extension

gcc -pthread -fno-strict-aliasing -O2 -g -frecord-gcc-switches -Wstrict-aliasing=2 -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -DNDEBUG -O2 -g -frecord-gcc-switches -Wstrict-aliasing=2 -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -g -fPIC -Isrc -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c src/cpmorphology.c -o build/temp.linux-x86_64-2.7/src/cpmorphology.o -O3

src/cpmorphology.c: In function ‘to_stdout’:

src/cpmorphology.c:29:6: error: format not a string literal and no format arguments -Werror=format-security]

cc1: some warnings being treated as errors

error: command ‘gcc’ failed with exit status 1

running build_ext

skipping ‘javabridge.c’ Cython extension (up-to-date)

ERROR:root:Could not parse SVN XML output while finding version.

<?xml version="1.0"?>

svn: ‘.’ is not a working copy

Could not parse SVN XML output while finding version.

<?xml version="1.0"?>

svn: ‘.’ is not a working copy

Traceback (most recent call last):

File “CellProfiler.py”, line 293, in

show_splashbox = (options.pipeline_filename is None))

File “/home/andrew/CellProfiler-CellProfiler-802161f/cellprofiler/cellprofilerapp.py”, line 18, in init

super(CellProfilerApp, self).init(*args, **kwargs)

File “/usr/lib64/python2.7/site-packages/wx-2.8-gtk2-unicode/wx/_core.py”, line 7981, in init

self._BootstrapApp()

File “/usr/lib64/python2.7/site-packages/wx-2.8-gtk2-unicode/wx/_core.py”, line 7555, in _BootstrapApp

return core.PyApp__BootstrapApp(*args, **kwargs)

File “/home/andrew/CellProfiler-CellProfiler-802161f/cellprofiler/cellprofilerapp.py”, line 39, in OnInit

from cellprofiler.gui.cpframe import CPFrame

File “/home/andrew/CellProfiler-CellProfiler-802161f/cellprofiler/gui/cpframe.py”, line 22, in

from cellprofiler.modules import get_data_tool_names, instantiate_module

File “/home/andrew/CellProfiler-CellProfiler-802161f/cellprofiler/modules/init.py”, line 22, in

import cellprofiler.cpmodule as cpm

File “/home/andrew/CellProfiler-CellProfiler-802161f/cellprofiler/cpmodule.py”, line 25, in

import cellprofiler.settings as cps

File “/home/andrew/CellProfiler-CellProfiler-802161f/cellprofiler/settings.py”, line 28, in

import cellprofiler.measurements

File “/home/andrew/CellProfiler-CellProfiler-802161f/cellprofiler/measurements.py”, line 22, in

from scipy.io.matlab import loadmat

ImportError: No module named scipy.io.matlab

[andrew@localhost CellProfiler-CellProfiler-802161f]$

#####################################################################

I wondered if maybe I didn’t have a full XML installation (including available libraries) but installation of every relevant XML file I could find, and recompilation of CellProfiler (again successful), there was no difference to the result when I again attempted to start CellProfiler.

Hopefully, the terminal output shown above might be familiar to someone. I’d love to hear from anyone who can provide some useful insights here.

Cheers

I’m not one of the developers but I was struck by the last couple of lines –

[code]## from scipy.io.matlab import loadmat

ImportError: No module named scipy.io.matlab[/code]

Do you have Scipy installed?

Hi TimSmith,

Mmmm. You’re right, scipy hadn’t compiled at all and neither had many of the the other packages.

This failure stems from me introducing ‘-m compileall’ (see below) into Makefile.CP2; it’s obvious that I haven’t done that appropriately at all :frowning: Having had so much frustration with compiling CP2, I dropped my guard when, to my relief, the changes I’d made allowed the Makefile.CP2 to reach it’s end without aborting. Didn’t realise the compilation had simply skipped some packages.

The reason for attempting to add ‘-m compileall’ was that, without it, the script reached ‘decorator’ and aborted, complaining that ‘byte-compiling is disabled’. From what I’ve found by googling, I thought I would need to include ‘-m compileall’ in order to enable byte-compiling.

The way I included this, for example, with decorator in Makefile.CP2 (and with other packages such as scipy), was as follows:

export LD_LIBRARY_PATH="$(PYTHONPREFIX)/lib:$${LD_LIBRARY_PATH}" &&
$(PYTHONPREFIX)/bin/python -m compileall setup.py install

It appears that inclusion of ‘-m compileall’ in packages specified in Makefile.CP2 merely makes the compilation process skip that package (or is it just that I’m using -m compileall incorrectly ??).

I understand (perhaps incorrectly) that, by default, byte-compiling is disabled in mandriva so would need to be explicitly included in compilation instructions. Anyone have an idea as to how to include -m compileall, or of a more appropriate way to enable byte-compiling so that packages such as decorator are dealt with properly ?

:smile:

Well, some progress made now. The byte-compiling issue is solved:

In a shell:
unset PYTHONDONTWRITEBYTECODE export PATH=/usr/bin:/…
export LD_LIBRARY_PATH=/usr/lib/jvm/java-1.6.0-sun-1.6.0.29.................... export JAVA_HOME=/usr/lib/jvm/java-1.6.0-sun-1.6.0.29
export HOSTTYPE=x86_64 make -f Makefile.CP2

and we now get byte-compiling occuring as required! Success! :smiley:

So now the make file runs to the end without complaint of byte-compiling being disabled. However, boot still fails: while there’s no longer any reporting that scipy modules aren’t able to be found (see earlier post), there’s now a failure to find the _cpmorphology module (see startup output, below).

:question: I’m not sure what the location and ‘literal name’ of the _cpmorphology module is in the CP2 installation so would appreciate any help in this direction ? I could then check to see if it has actually been compiled or whether CP2 just can’t find it for some reason.

The output when I attempt to start CP2 at the command line ( python CellProfiler.py -b ) is as shown below (see 1).

I’ve also shown the latter portion of the compile output (see 2), as there may be some clues here as to what the problem is.

:question: For trouble shooting, would it be possible for someone from the development team to make a successfully compiled version of CP2 available online ? This way, we would be able to check to see whether our own directories contain the same files and directories as those in a working version of CP2. Maybe this already is available and I simply am unaware of the link ?

  1. Terminal output when attempting to start CP2

$ python CellProfiler.py -b
WARNING:root:Distributed support disabled: please install nuageux
ERROR:root:Could not parse SVN XML output while finding version.

<?xml version="1.0"?> svn: '.' is not a working copy

Could not parse SVN XML output while finding version.

<?xml version="1.0"?> svn: '.' is not a working copy

Traceback (most recent call last):
File “CellProfiler.py”, line 293, in
show_splashbox = (options.pipeline_filename is None))
File “/home/andrew/CellProfiler-CellProfiler-802161f/cellprofiler/cellprofilerapp.py”, line 18, in init
super(CellProfilerApp, self).init(*args, **kwargs)
File “/usr/lib64/python2.7/site-packages/wx-2.8-gtk2-unicode/wx/_core.py”, line 7981, in init
self._BootstrapApp()
File “/usr/lib64/python2.7/site-packages/wx-2.8-gtk2-unicode/wx/_core.py”, line 7555, in _BootstrapApp
return core.PyApp__BootstrapApp(*args, **kwargs)
File “/home/andrew/CellProfiler-CellProfiler-802161f/cellprofiler/cellprofilerapp.py”, line 39, in OnInit
from cellprofiler.gui.cpframe import CPFrame
File “/home/andrew/CellProfiler-CellProfiler-802161f/cellprofiler/gui/cpframe.py”, line 22, in
from cellprofiler.modules import get_data_tool_names, instantiate_module
File “/home/andrew/CellProfiler-CellProfiler-802161f/cellprofiler/modules/init.py”, line 22, in
import cellprofiler.cpmodule as cpm
File “/home/andrew/CellProfiler-CellProfiler-802161f/cellprofiler/cpmodule.py”, line 27, in
import cellprofiler.objects
File “/home/andrew/CellProfiler-CellProfiler-802161f/cellprofiler/objects.py”, line 20, in
from cellprofiler.cpmath.cpmorphology import all_connected_components
File “/home/andrew/CellProfiler-CellProfiler-802161f/cellprofiler/cpmath/cpmorphology.py”, line 21, in
import _cpmorphology
ImportError: No module named _cpmorphology

###################################################################
2. ######## Final portion of output when compiling using Makefile.CP2 #########

A CellProfiler/decorator.py
A CellProfiler/CellProfiler.py
A CellProfiler/CellProfilerIcon_old.png
A CellProfiler/CellProfilerIcon.png
Checked out revision 11715.
WARNING:root:Distributed support disabled: please install nuageux
running build_ext
building ‘_cpmorphology’ extension
creating build
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/src
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Isrc -I/home/andrew/CellProfiler-CellProfiler-802161f/lib/python2.7/site-packages/numpy/core/include -I/home/andrew/CellProfiler-CellProfiler-802161f/include/python2.7 -c src/cpmorphology.c -o build/temp.linux-x86_64-2.7/src/cpmorphology.o -O3
In file included from /home/andrew/CellProfiler-CellProfiler-802161f/include/python2.7/Python.h:8:0,
from src/cpmorphology.c:24:
/home/andrew/CellProfiler-CellProfiler-802161f/include/python2.7/pyconfig.h:1155:0: warning: “_POSIX_C_SOURCE” redefined [enabled by default]
/usr/include/features.h:214:0: note: this is the location of the previous definition
src/cpmorphology.c:27:13: warning: ‘to_stdout’ defined but not used -Wunused-function]
gcc -pthread -shared build/temp.linux-x86_64-2.7/src/cpmorphology.o -L/home/andrew/CellProfiler-CellProfiler-802161f/lib -lpython2.7 -o /home/andrew/CellProfiler-CellProfiler-802161f/CellProfiler/cellprofiler/cpmath/_cpmorphology.so
cythoning _cpmorphology2.pyx to _cpmorphology2.c
building ‘_cpmorphology2’ extension
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/andrew/CellProfiler-CellProfiler-802161f/lib/python2.7/site-packages/numpy/core/include -I/home/andrew/CellProfiler-CellProfiler-802161f/include/python2.7 -c _cpmorphology2.c -o build/temp.linux-x86_64-2.7/_cpmorphology2.o -O3
_cpmorphology2.c: In function ‘__pyx_pf_14_cpmorphology2_skeletonize_loop’:
_cpmorphology2.c:981:14: warning: variable ‘__pyx_bshape_0_order’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:980:14: warning: variable ‘__pyx_bstride_0_order’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:978:14: warning: variable ‘__pyx_bshape_0_table’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:977:14: warning: variable ‘__pyx_bstride_0_table’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:975:14: warning: variable ‘__pyx_bshape_1_result’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:974:14: warning: variable ‘__pyx_bshape_0_result’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:973:14: warning: variable ‘__pyx_bstride_1_result’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:970:14: warning: variable ‘__pyx_bshape_0_j’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:969:14: warning: variable ‘__pyx_bstride_0_j’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:967:14: warning: variable ‘__pyx_bshape_0_i’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:966:14: warning: variable ‘__pyx_bstride_0_i’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c: In function ‘__pyx_pf_14_cpmorphology2_table_lookup_index’:
_cpmorphology2.c:1502:14: warning: variable ‘__pyx_bshape_1_indexer’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:1501:14: warning: variable ‘__pyx_bshape_0_indexer’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:1500:14: warning: variable ‘__pyx_bstride_1_indexer’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:1497:14: warning: variable ‘__pyx_bshape_1_image’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:1496:14: warning: variable ‘__pyx_bshape_0_image’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:1495:14: warning: variable ‘__pyx_bstride_1_image’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c: In function ‘__pyx_pf_14_cpmorphology2_grey_reconstruction_loop’:
_cpmorphology2.c:2559:14: warning: variable ‘__pyx_bshape_0_aprev’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:2558:14: warning: variable ‘__pyx_bstride_0_aprev’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:2556:14: warning: variable ‘__pyx_bshape_0_avalues’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:2555:14: warning: variable ‘__pyx_bstride_0_avalues’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:2553:14: warning: variable ‘__pyx_bshape_0_astrides’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:2552:14: warning: variable ‘__pyx_bstride_0_astrides’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:2550:14: warning: variable ‘__pyx_bshape_0_anext’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:2549:14: warning: variable ‘__pyx_bstride_0_anext’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c: In function ‘__pyx_pf_14_cpmorphology2__all_connected_components’:
_cpmorphology2.c:3105:14: warning: variable ‘__pyx_bshape_0_stack_being_processed_a’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:3104:14: warning: variable ‘__pyx_bstride_0_stack_being_processed_a’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:3102:14: warning: variable ‘__pyx_bshape_0_being_processed_a’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:3101:14: warning: variable ‘__pyx_bstride_0_being_processed_a’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:3099:14: warning: variable ‘__pyx_bshape_0_v_idx_a’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:3098:14: warning: variable ‘__pyx_bstride_0_v_idx_a’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:3096:14: warning: variable ‘__pyx_bshape_0_stack_v_a’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:3095:14: warning: variable ‘__pyx_bstride_0_stack_v_a’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:3093:14: warning: variable ‘__pyx_bshape_0_label_a’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:3092:14: warning: variable ‘__pyx_bstride_0_label_a’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:3090:14: warning: variable ‘__pyx_bshape_0_indexes_a’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:3089:14: warning: variable ‘__pyx_bstride_0_indexes_a’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:3087:14: warning: variable ‘__pyx_bshape_0_visit_index_a’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:3086:14: warning: variable ‘__pyx_bstride_0_visit_index_a’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:3084:14: warning: variable ‘__pyx_bshape_0_i_a’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:3083:14: warning: variable ‘__pyx_bstride_0_i_a’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:3081:14: warning: variable ‘__pyx_bshape_0_counts_a’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:3080:14: warning: variable ‘__pyx_bstride_0_counts_a’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:3078:14: warning: variable ‘__pyx_bshape_0_j_a’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:3077:14: warning: variable ‘__pyx_bstride_0_j_a’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:3065:28: warning: variable ‘__pyx_v_i’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c: In function ‘__pyx_pf_14_cpmorphology2_index_lookup’:
_cpmorphology2.c:3856:14: warning: variable ‘__pyx_bshape_0_table’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:3853:14: warning: variable ‘__pyx_bshape_0_index_i’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:3850:14: warning: variable ‘__pyx_bshape_0_index_j’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:3847:14: warning: variable ‘__pyx_bshape_1_image’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:3846:14: warning: variable ‘__pyx_bshape_0_image’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c: In function ‘__pyx_pf_14_cpmorphology2_fill_labeled_holes_loop’:
_cpmorphology2.c:5186:14: warning: variable ‘__pyx_bshape_0_is_not_hole’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:5185:14: warning: variable ‘__pyx_bstride_0_is_not_hole’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:5183:14: warning: variable ‘__pyx_bshape_0_i_count’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:5182:14: warning: variable ‘__pyx_bstride_0_i_count’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:5180:14: warning: variable ‘__pyx_bshape_0_to_do’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:5179:14: warning: variable ‘__pyx_bstride_0_to_do’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:5177:14: warning: variable ‘__pyx_bshape_0_j’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:5176:14: warning: variable ‘__pyx_bstride_0_j’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:5174:14: warning: variable ‘__pyx_bshape_0_i’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:5173:14: warning: variable ‘__pyx_bstride_0_i’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:5171:14: warning: variable ‘__pyx_bshape_0_idx’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:5170:14: warning: variable ‘__pyx_bstride_0_idx’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:5168:14: warning: variable ‘__pyx_bshape_0_adjacent_non_hole’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:5167:14: warning: variable ‘__pyx_bstride_0_adjacent_non_hole’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c:5164:8: warning: variable ‘__pyx_v_p_i’ set but not used -Wunused-but-set-variable]
_cpmorphology2.c: At top level:
/home/andrew/CellProfiler-CellProfiler-802161f/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:196:1: warning: ‘_import_umath’ defined but not used -Wunused-function]
gcc -pthread -shared build/temp.linux-x86_64-2.7/_cpmorphology2.o -L/home/andrew/CellProfiler-CellProfiler-802161f/lib -lpython2.7 -o /home/andrew/CellProfiler-CellProfiler-802161f/CellProfiler/cellprofiler/cpmath/_cpmorphology2.so
cythoning _watershed.pyx to _watershed.c
building ‘_watershed’ extension
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Isrc -I/home/andrew/CellProfiler-CellProfiler-802161f/lib/python2.7/site-packages/numpy/core/include -I/home/andrew/CellProfiler-CellProfiler-802161f/include/python2.7 -c _watershed.c -o build/temp.linux-x86_64-2.7/_watershed.o -O3
_watershed.c: In function ‘__pyx_pf_10_watershed_watershed’:
_watershed.c:1504:14: warning: variable ‘__pyx_bshape_1_structure’ set but not used -Wunused-but-set-variable]
_watershed.c:1503:14: warning: variable ‘__pyx_bshape_0_structure’ set but not used -Wunused-but-set-variable]
_watershed.c:1502:14: warning: variable ‘__pyx_bstride_1_structure’ set but not used -Wunused-but-set-variable]
_watershed.c:1499:14: warning: variable ‘__pyx_bshape_0_output’ set but not used -Wunused-but-set-variable]
_watershed.c:1498:14: warning: variable ‘__pyx_bstride_0_output’ set but not used -Wunused-but-set-variable]
_watershed.c:1496:14: warning: variable ‘__pyx_bshape_0_image_shape’ set but not used -Wunused-but-set-variable]
_watershed.c:1495:14: warning: variable ‘__pyx_bstride_0_image_shape’ set but not used -Wunused-but-set-variable]
_watershed.c:1493:14: warning: variable ‘__pyx_bshape_0_mask’ set but not used -Wunused-but-set-variable]
_watershed.c:1492:14: warning: variable ‘__pyx_bstride_0_mask’ set but not used -Wunused-but-set-variable]
_watershed.c:1490:14: warning: variable ‘__pyx_bshape_0_image’ set but not used -Wunused-but-set-variable]
_watershed.c:1489:14: warning: variable ‘__pyx_bstride_0_image’ set but not used -Wunused-but-set-variable]
_watershed.c:1487:14: warning: variable ‘__pyx_bshape_1_pq’ set but not used -Wunused-but-set-variable]
_watershed.c:1486:14: warning: variable ‘__pyx_bshape_0_pq’ set but not used -Wunused-but-set-variable]
_watershed.c:1485:14: warning: variable ‘__pyx_bstride_1_pq’ set but not used -Wunused-but-set-variable]
_watershed.c: At top level:
/home/andrew/CellProfiler-CellProfiler-802161f/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:196:1: warning: ‘_import_umath’ defined but not used -Wunused-function]
_watershed.c:4792:18: warning: ‘__Pyx_UnpackItem’ defined but not used -Wunused-function]
_watershed.c:4802:12: warning: ‘__Pyx_EndUnpack’ defined but not used -Wunused-function]
gcc -pthread -shared build/temp.linux-x86_64-2.7/_watershed.o -L/home/andrew/CellProfiler-CellProfiler-802161f/lib -lpython2.7 -o /home/andrew/CellProfiler-CellProfiler-802161f/CellProfiler/cellprofiler/cpmath/_watershed.so
cythoning _propagate.pyx to _propagate.c
building ‘_propagate’ extension
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Isrc -I/home/andrew/CellProfiler-CellProfiler-802161f/lib/python2.7/site-packages/numpy/core/include -I/home/andrew/CellProfiler-CellProfiler-802161f/include/python2.7 -c _propagate.c -o build/temp.linux-x86_64-2.7/_propagate.o -O3
_propagate.c: In function ‘__pyx_pf_10_propagate_propagate’:
_propagate.c:2567:14: warning: variable ‘__pyx_bshape_0_delta_j’ set but not used -Wunused-but-set-variable]
_propagate.c:2566:14: warning: variable ‘__pyx_bstride_0_delta_j’ set but not used -Wunused-but-set-variable]
_propagate.c:2564:14: warning: variable ‘__pyx_bshape_0_delta_i’ set but not used -Wunused-but-set-variable]
_propagate.c:2563:14: warning: variable ‘__pyx_bstride_0_delta_i’ set but not used -Wunused-but-set-variable]
_propagate.c:2561:14: warning: variable ‘__pyx_bshape_0_elem’ set but not used -Wunused-but-set-variable]
_propagate.c:2560:14: warning: variable ‘__pyx_bstride_0_elem’ set but not used -Wunused-but-set-variable]
_propagate.c:2558:14: warning: variable ‘__pyx_bshape_1_mask’ set but not used -Wunused-but-set-variable]
_propagate.c:2557:14: warning: variable ‘__pyx_bshape_0_mask’ set but not used -Wunused-but-set-variable]
_propagate.c:2556:14: warning: variable ‘__pyx_bstride_1_mask’ set but not used -Wunused-but-set-variable]
_propagate.c:2553:14: warning: variable ‘__pyx_bshape_1_labels’ set but not used -Wunused-but-set-variable]
_propagate.c:2552:14: warning: variable ‘__pyx_bshape_0_labels’ set but not used -Wunused-but-set-variable]
_propagate.c:2551:14: warning: variable ‘__pyx_bstride_1_labels’ set but not used -Wunused-but-set-variable]
_propagate.c:2548:14: warning: variable ‘__pyx_bshape_1_image’ set but not used -Wunused-but-set-variable]
_propagate.c:2547:14: warning: variable ‘__pyx_bshape_0_image’ set but not used -Wunused-but-set-variable]
_propagate.c:2546:14: warning: variable ‘__pyx_bstride_1_image’ set but not used -Wunused-but-set-variable]
_propagate.c:2545:14: warning: variable ‘__pyx_bstride_0_image’ set but not used -Wunused-but-set-variable]
_propagate.c:2543:14: warning: variable ‘__pyx_bshape_0_new_elem’ set but not used -Wunused-but-set-variable]
_propagate.c:2542:14: warning: variable ‘__pyx_bstride_0_new_elem’ set but not used -Wunused-but-set-variable]
_propagate.c:2540:14: warning: variable ‘__pyx_bshape_1_pq’ set but not used -Wunused-but-set-variable]
_propagate.c:2539:14: warning: variable ‘__pyx_bshape_0_pq’ set but not used -Wunused-but-set-variable]
_propagate.c:2538:14: warning: variable ‘__pyx_bstride_1_pq’ set but not used -Wunused-but-set-variable]
_propagate.c:2537:14: warning: variable ‘__pyx_bstride_0_pq’ set but not used -Wunused-but-set-variable]
_propagate.c:2535:14: warning: variable ‘__pyx_bshape_1_distances’ set but not used -Wunused-but-set-variable]
_propagate.c:2534:14: warning: variable ‘__pyx_bshape_0_distances’ set but not used -Wunused-but-set-variable]
_propagate.c:2533:14: warning: variable ‘__pyx_bstride_1_distances’ set but not used -Wunused-but-set-variable]
_propagate.c: At top level:
/home/andrew/CellProfiler-CellProfiler-802161f/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:196:1: warning: ‘_import_umath’ defined but not used -Wunused-function]
_propagate.c:6355:18: warning: ‘__Pyx_UnpackItem’ defined but not used -Wunused-function]
_propagate.c:6365:12: warning: ‘__Pyx_EndUnpack’ defined but not used -Wunused-function]
gcc -pthread -shared build/temp.linux-x86_64-2.7/_propagate.o -L/home/andrew/CellProfiler-CellProfiler-802161f/lib -lpython2.7 -o /home/andrew/CellProfiler-CellProfiler-802161f/CellProfiler/cellprofiler/cpmath/_propagate.so
cythoning _filter.pyx to _filter.c
building ‘_filter’ extension
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Isrc -I/home/andrew/CellProfiler-CellProfiler-802161f/lib/python2.7/site-packages/numpy/core/include -I/home/andrew/CellProfiler-CellProfiler-802161f/include/python2.7 -c _filter.c -o build/temp.linux-x86_64-2.7/_filter.o -O3
_filter.c: In function ‘__pyx_f_7_filter_update_current_location’:
_filter.c:2895:26: warning: variable ‘__pyx_v_radius’ set but not used -Wunused-but-set-variable]
_filter.c: In function ‘__pyx_pf_7_filter_median_filter’:
_filter.c:3665:14: warning: variable ‘__pyx_bshape_1_output’ set but not used -Wunused-but-set-variable]
_filter.c:3664:14: warning: variable ‘__pyx_bshape_0_output’ set but not used -Wunused-but-set-variable]
_filter.c:3663:14: warning: variable ‘__pyx_bstride_1_output’ set but not used -Wunused-but-set-variable]
_filter.c:3662:14: warning: variable ‘__pyx_bstride_0_output’ set but not used -Wunused-but-set-variable]
_filter.c:3660:14: warning: variable ‘__pyx_bshape_1_data’ set but not used -Wunused-but-set-variable]
_filter.c:3659:14: warning: variable ‘__pyx_bshape_0_data’ set but not used -Wunused-but-set-variable]
_filter.c:3658:14: warning: variable ‘__pyx_bstride_1_data’ set but not used -Wunused-but-set-variable]
_filter.c:3657:14: warning: variable ‘__pyx_bstride_0_data’ set but not used -Wunused-but-set-variable]
_filter.c:3655:14: warning: variable ‘__pyx_bshape_1_mask’ set but not used -Wunused-but-set-variable]
_filter.c:3654:14: warning: variable ‘__pyx_bshape_0_mask’ set but not used -Wunused-but-set-variable]
_filter.c:3653:14: warning: variable ‘__pyx_bstride_1_mask’ set but not used -Wunused-but-set-variable]
_filter.c:3652:14: warning: variable ‘__pyx_bstride_0_mask’ set but not used -Wunused-but-set-variable]
_filter.c: In function ‘__pyx_pf_7_filter_masked_convolution’:
_filter.c:4105:14: warning: variable ‘__pyx_bshape_1_output’ set but not used -Wunused-but-set-variable]
_filter.c:4104:14: warning: variable ‘__pyx_bshape_0_output’ set but not used -Wunused-but-set-variable]
_filter.c:4103:14: warning: variable ‘__pyx_bstride_1_output’ set but not used -Wunused-but-set-variable]
_filter.c:4102:14: warning: variable ‘__pyx_bstride_0_output’ set but not used -Wunused-but-set-variable]
_filter.c:4100:14: warning: variable ‘__pyx_bshape_1_mask’ set but not used -Wunused-but-set-variable]
_filter.c:4099:14: warning: variable ‘__pyx_bshape_0_mask’ set but not used -Wunused-but-set-variable]
_filter.c:4098:14: warning: variable ‘__pyx_bstride_1_mask’ set but not used -Wunused-but-set-variable]
_filter.c:4097:14: warning: variable ‘__pyx_bstride_0_mask’ set but not used -Wunused-but-set-variable]
_filter.c:4095:14: warning: variable ‘__pyx_bshape_1_data’ set but not used -Wunused-but-set-variable]
_filter.c:4094:14: warning: variable ‘__pyx_bshape_0_data’ set but not used -Wunused-but-set-variable]
_filter.c:4093:14: warning: variable ‘__pyx_bstride_1_data’ set but not used -Wunused-but-set-variable]
_filter.c:4092:14: warning: variable ‘__pyx_bstride_0_data’ set but not used -Wunused-but-set-variable]
_filter.c:4090:14: warning: variable ‘__pyx_bshape_1_big_mask’ set but not used -Wunused-but-set-variable]
_filter.c:4089:14: warning: variable ‘__pyx_bshape_0_big_mask’ set but not used -Wunused-but-set-variable]
_filter.c:4088:14: warning: variable ‘__pyx_bstride_1_big_mask’ set but not used -Wunused-but-set-variable]
_filter.c:4087:14: warning: variable ‘__pyx_bstride_0_big_mask’ set but not used -Wunused-but-set-variable]
_filter.c:4085:14: warning: variable ‘__pyx_bshape_1_kernel’ set but not used -Wunused-but-set-variable]
_filter.c:4084:14: warning: variable ‘__pyx_bshape_0_kernel’ set but not used -Wunused-but-set-variable]
_filter.c:4083:14: warning: variable ‘__pyx_bstride_1_kernel’ set but not used -Wunused-but-set-variable]
_filter.c:4082:14: warning: variable ‘__pyx_bstride_0_kernel’ set but not used -Wunused-but-set-variable]
_filter.c: At top level:
/home/andrew/CellProfiler-CellProfiler-802161f/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:196:1: warning: ‘_import_umath’ defined but not used -Wunused-function]
_filter.c:7605:18: warning: ‘__Pyx_UnpackItem’ defined but not used -Wunused-function]
_filter.c:7615:12: warning: ‘__Pyx_EndUnpack’ defined but not used -Wunused-function]
gcc -pthread -shared build/temp.linux-x86_64-2.7/_filter.o -L/home/andrew/CellProfiler-CellProfiler-802161f/lib -lpython2.7 -o /home/andrew/CellProfiler-CellProfiler-802161f/CellProfiler/cellprofiler/cpmath/_filter.so
cythoning _lapjv.pyx to _lapjv.c
building ‘_lapjv’ extension
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Isrc -I/home/andrew/CellProfiler-CellProfiler-802161f/lib/python2.7/site-packages/numpy/core/include -I/home/andrew/CellProfiler-CellProfiler-802161f/include/python2.7 -c _lapjv.c -o build/temp.linux-x86_64-2.7/_lapjv.o -O3
_lapjv.c: In function ‘__pyx_pf_6_lapjv_reduction_transfer’:
_lapjv.c:865:14: warning: variable ‘__pyx_bshape_0_x’ set but not used -Wunused-but-set-variable]
_lapjv.c:864:14: warning: variable ‘__pyx_bstride_0_x’ set but not used -Wunused-but-set-variable]
_lapjv.c:862:14: warning: variable ‘__pyx_bshape_0_v’ set but not used -Wunused-but-set-variable]
_lapjv.c:861:14: warning: variable ‘__pyx_bstride_0_v’ set but not used -Wunused-but-set-variable]
_lapjv.c:859:14: warning: variable ‘__pyx_bshape_0_u’ set but not used -Wunused-but-set-variable]
_lapjv.c:858:14: warning: variable ‘__pyx_bstride_0_u’ set but not used -Wunused-but-set-variable]
_lapjv.c:856:14: warning: variable ‘__pyx_bshape_0_j’ set but not used -Wunused-but-set-variable]
_lapjv.c:855:14: warning: variable ‘__pyx_bstride_0_j’ set but not used -Wunused-but-set-variable]
_lapjv.c:853:14: warning: variable ‘__pyx_bshape_0_idx’ set but not used -Wunused-but-set-variable]
_lapjv.c:852:14: warning: variable ‘__pyx_bstride_0_idx’ set but not used -Wunused-but-set-variable]
_lapjv.c:850:14: warning: variable ‘__pyx_bshape_0_c’ set but not used -Wunused-but-set-variable]
_lapjv.c:849:14: warning: variable ‘__pyx_bstride_0_c’ set but not used -Wunused-but-set-variable]
_lapjv.c:847:14: warning: variable ‘__pyx_bshape_0_count’ set but not used -Wunused-but-set-variable]
_lapjv.c:846:14: warning: variable ‘__pyx_bstride_0_count’ set but not used -Wunused-but-set-variable]
_lapjv.c:844:14: warning: variable ‘__pyx_bshape_0_ii’ set but not used -Wunused-but-set-variable]
_lapjv.c:843:14: warning: variable ‘__pyx_bstride_0_ii’ set but not used -Wunused-but-set-variable]
_lapjv.c: In function ‘__pyx_pf_6_lapjv_augmenting_row_reduction’:
_lapjv.c:1449:14: warning: variable ‘__pyx_bshape_0_x’ set but not used -Wunused-but-set-variable]
_lapjv.c:1448:14: warning: variable ‘__pyx_bstride_0_x’ set but not used -Wunused-but-set-variable]
_lapjv.c:1446:14: warning: variable ‘__pyx_bshape_0_y’ set but not used -Wunused-but-set-variable]
_lapjv.c:1445:14: warning: variable ‘__pyx_bstride_0_y’ set but not used -Wunused-but-set-variable]
_lapjv.c:1443:14: warning: variable ‘__pyx_bshape_0_v’ set but not used -Wunused-but-set-variable]
_lapjv.c:1442:14: warning: variable ‘__pyx_bstride_0_v’ set but not used -Wunused-but-set-variable]
_lapjv.c:1440:14: warning: variable ‘__pyx_bshape_0_u’ set but not used -Wunused-but-set-variable]
_lapjv.c:1439:14: warning: variable ‘__pyx_bstride_0_u’ set but not used -Wunused-but-set-variable]
_lapjv.c:1437:14: warning: variable ‘__pyx_bshape_0_idx’ set but not used -Wunused-but-set-variable]
_lapjv.c:1436:14: warning: variable ‘__pyx_bstride_0_idx’ set but not used -Wunused-but-set-variable]
_lapjv.c:1434:14: warning: variable ‘__pyx_bshape_0_c’ set but not used -Wunused-but-set-variable]
_lapjv.c:1433:14: warning: variable ‘__pyx_bstride_0_c’ set but not used -Wunused-but-set-variable]
_lapjv.c:1431:14: warning: variable ‘__pyx_bshape_0_count’ set but not used -Wunused-but-set-variable]
_lapjv.c:1430:14: warning: variable ‘__pyx_bstride_0_count’ set but not used -Wunused-but-set-variable]
_lapjv.c:1428:14: warning: variable ‘__pyx_bshape_0_jj’ set but not used -Wunused-but-set-variable]
_lapjv.c:1427:14: warning: variable ‘__pyx_bstride_0_jj’ set but not used -Wunused-but-set-variable]
_lapjv.c:1425:14: warning: variable ‘__pyx_bshape_0_ii’ set but not used -Wunused-but-set-variable]
_lapjv.c:1424:14: warning: variable ‘__pyx_bstride_0_ii’ set but not used -Wunused-but-set-variable]
_lapjv.c:1409:11: warning: variable ‘__pyx_v_p_u_base’ set but not used -Wunused-but-set-variable]
_lapjv.c: In function ‘__pyx_pf_6_lapjv_augment’:
_lapjv.c:2400:14: warning: variable ‘__pyx_bstride_0_x’ set but not used -Wunused-but-set-variable]
_lapjv.c:2398:14: warning: variable ‘__pyx_bshape_0_y’ set but not used -Wunused-but-set-variable]
_lapjv.c:2397:14: warning: variable ‘__pyx_bstride_0_y’ set but not used -Wunused-but-set-variable]
_lapjv.c:2394:14: warning: variable ‘__pyx_bstride_0_v’ set but not used -Wunused-but-set-variable]
_lapjv.c:2391:14: warning: variable ‘__pyx_bstride_0_u’ set but not used -Wunused-but-set-variable]
_lapjv.c:2389:14: warning: variable ‘__pyx_bshape_0_idx’ set but not used -Wunused-but-set-variable]
_lapjv.c:2388:14: warning: variable ‘__pyx_bstride_0_idx’ set but not used -Wunused-but-set-variable]
_lapjv.c:2385:14: warning: variable ‘__pyx_bstride_0_c’ set but not used -Wunused-but-set-variable]
_lapjv.c:2383:14: warning: variable ‘__pyx_bshape_0_count’ set but not used -Wunused-but-set-variable]
_lapjv.c:2382:14: warning: variable ‘__pyx_bstride_0_count’ set but not used -Wunused-but-set-variable]
_lapjv.c:2380:14: warning: variable ‘__pyx_bshape_0_jj’ set but not used -Wunused-but-set-variable]
_lapjv.c:2379:14: warning: variable ‘__pyx_bstride_0_jj’ set but not used -Wunused-but-set-variable]
_lapjv.c:2377:14: warning: variable ‘__pyx_bshape_0_ii’ set but not used -Wunused-but-set-variable]
_lapjv.c:2376:14: warning: variable ‘__pyx_bstride_0_ii’ set but not used -Wunused-but-set-variable]
_lapjv.c:2359:11: warning: variable ‘__pyx_v_p_u_base’ set but not used -Wunused-but-set-variable]
_lapjv.c: At top level:
/home/andrew/CellProfiler-CellProfiler-802161f/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:196:1: warning: ‘_import_umath’ defined but not used -Wunused-function]
_lapjv.c:7220:18: warning: ‘__Pyx_UnpackItem’ defined but not used -Wunused-function]
_lapjv.c:7230:12: warning: ‘__Pyx_EndUnpack’ defined but not used -Wunused-function]
_lapjv.c: In function ‘__pyx_pf_6_lapjv_augment’:
_lapjv.c:3757:22: warning: ‘__pyx_v_umin’ may be used uninitialized in this function -Wuninitialized]
_lapjv.c: In function ‘__pyx_pf_6_lapjv_augmenting_row_reduction’:
_lapjv.c:2124:41: warning: ‘__pyx_v_j2’ may be used uninitialized in this function -Wuninitialized]
_lapjv.c:2200:39: warning: ‘__pyx_v_j1’ may be used uninitialized in this function -Wuninitialized]
gcc -pthread -shared build/temp.linux-x86_64-2.7/_lapjv.o -L/home/andrew/CellProfiler-CellProfiler-802161f/lib -lpython2.7 -o /home/andrew/CellProfiler-CellProfiler-802161f/CellProfiler/cellprofiler/cpmath/_lapjv.so
running build_ext
cythoning javabridge.pyx to javabridge.c
building ‘javabridge’ extension
creating build
creating build/temp.linux-x86_64-2.7
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/andrew/CellProfiler-CellProfiler-802161f/lib/python2.7/site-packages/numpy/core/include -I/usr/lib/jvm/java-1.6.0-sun-1.6.0.29/include -I/usr/lib/jvm/java-1.6.0-sun-1.6.0.29/include/linux -I/home/andrew/CellProfiler-CellProfiler-802161f/include/python2.7 -c javabridge.c -o build/temp.linux-x86_64-2.7/javabridge.o
javabridge.c: In function ‘__pyx_pf_10javabridge_get_default_java_vm_init_args’:
javabridge.c:1655:8: warning: variable ‘__pyx_v_result’ set but not used -Wunused-but-set-variable]
javabridge.c: In function ‘pyx_pf_10javabridge_9JB_Object___repr’:
javabridge.c:1858:31: warning: cast from pointer to integer of different size -Wpointer-to-int-cast]
javabridge.c: In function ‘__pyx_pf_10javabridge_9JB_Object_addr’:
javabridge.c:1973:31: warning: cast from pointer to integer of different size -Wpointer-to-int-cast]
javabridge.c: In function ‘pyx_pf_10javabridge_8JB_Class___repr’:
javabridge.c:2053:31: warning: cast from pointer to integer of different size -Wpointer-to-int-cast]
javabridge.c: In function ‘pyx_pf_10javabridge_13__JB_MethodID___repr’:
javabridge.c:2163:31: warning: cast from pointer to integer of different size -Wpointer-to-int-cast]
javabridge.c: In function ‘pyx_pf_10javabridge_12__JB_FieldID___repr’:
javabridge.c:2281:31: warning: cast from pointer to integer of different size -Wpointer-to-int-cast]
javabridge.c: In function ‘__pyx_pf_10javabridge_6JB_Env_set_static_char_field’:
javabridge.c:10201:13: warning: variable ‘__pyx_v_value’ set but not used -Wunused-but-set-variable]
javabridge.c: In function ‘__pyx_pf_10javabridge_6JB_Env_get_string_utf’:
javabridge.c:11426:17: warning: cast from pointer to integer of different size -Wpointer-to-int-cast]
javabridge.c:11451:17: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default]
javabridge.c: In function ‘__pyx_pf_10javabridge_6JB_Env_get_boolean_array_elements’:
javabridge.c:11569:14: warning: variable ‘__pyx_bshape_0_result’ set but not used -Wunused-but-set-variable]
javabridge.c:11568:14: warning: variable ‘__pyx_bstride_0_result’ set but not used -Wunused-but-set-variable]
javabridge.c: In function ‘__pyx_pf_10javabridge_6JB_Env_get_byte_array_elements’:
javabridge.c:11737:14: warning: variable ‘__pyx_bshape_0_result’ set but not used -Wunused-but-set-variable]
javabridge.c:11736:14: warning: variable ‘__pyx_bstride_0_result’ set but not used -Wunused-but-set-variable]
javabridge.c: In function ‘__pyx_pf_10javabridge_6JB_Env_get_short_array_elements’:
javabridge.c:11889:14: warning: variable ‘__pyx_bshape_0_result’ set but not used -Wunused-but-set-variable]
javabridge.c:11888:14: warning: variable ‘__pyx_bstride_0_result’ set but not used -Wunused-but-set-variable]
javabridge.c: In function ‘__pyx_pf_10javabridge_6JB_Env_get_int_array_elements’:
javabridge.c:12041:14: warning: variable ‘__pyx_bshape_0_result’ set but not used -Wunused-but-set-variable]
javabridge.c:12040:14: warning: variable ‘__pyx_bstride_0_result’ set but not used -Wunused-but-set-variable]
javabridge.c: In function ‘__pyx_pf_10javabridge_6JB_Env_get_long_array_elements’:
javabridge.c:12193:14: warning: variable ‘__pyx_bshape_0_result’ set but not used -Wunused-but-set-variable]
javabridge.c:12192:14: warning: variable ‘__pyx_bstride_0_result’ set but not used -Wunused-but-set-variable]
javabridge.c: In function ‘__pyx_pf_10javabridge_6JB_Env_get_float_array_elements’:
javabridge.c:12345:14: warning: variable ‘__pyx_bshape_0_result’ set but not used -Wunused-but-set-variable]
javabridge.c:12344:14: warning: variable ‘__pyx_bstride_0_result’ set but not used -Wunused-but-set-variable]
javabridge.c: In function ‘__pyx_pf_10javabridge_6JB_Env_get_double_array_elements’:
javabridge.c:12497:14: warning: variable ‘__pyx_bshape_0_result’ set but not used -Wunused-but-set-variable]
javabridge.c:12496:14: warning: variable ‘__pyx_bstride_0_result’ set but not used -Wunused-but-set-variable]
javabridge.c: In function ‘__pyx_pf_10javabridge_6JB_Env_make_boolean_array’:
javabridge.c:12858:14: warning: variable ‘__pyx_bshape_0_barray’ set but not used -Wunused-but-set-variable]
javabridge.c:12857:14: warning: variable ‘__pyx_bstride_0_barray’ set but not used -Wunused-but-set-variable]
javabridge.c: In function ‘__pyx_pf_10javabridge_6JB_Env_make_byte_array’:
javabridge.c:13119:14: warning: variable ‘__pyx_bshape_0_array’ set but not used -Wunused-but-set-variable]
javabridge.c:13118:14: warning: variable ‘__pyx_bstride_0_array’ set but not used -Wunused-but-set-variable]
javabridge.c: In function ‘__pyx_pf_10javabridge_6JB_Env_make_short_array’:
javabridge.c:13330:14: warning: variable ‘__pyx_bshape_0_array’ set but not used -Wunused-but-set-variable]
javabridge.c:13329:14: warning: variable ‘__pyx_bstride_0_array’ set but not used -Wunused-but-set-variable]
javabridge.c: In function ‘__pyx_pf_10javabridge_6JB_Env_make_int_array’:
javabridge.c:13541:14: warning: variable ‘__pyx_bshape_0_array’ set but not used -Wunused-but-set-variable]
javabridge.c:13540:14: warning: variable ‘__pyx_bstride_0_array’ set but not used -Wunused-but-set-variable]
javabridge.c: In function ‘__pyx_pf_10javabridge_6JB_Env_make_long_array’:
javabridge.c:13752:14: warning: variable ‘__pyx_bshape_0_array’ set but not used -Wunused-but-set-variable]
javabridge.c:13751:14: warning: variable ‘__pyx_bstride_0_array’ set but not used -Wunused-but-set-variable]
javabridge.c: In function ‘__pyx_pf_10javabridge_6JB_Env_make_float_array’:
javabridge.c:13963:14: warning: variable ‘__pyx_bshape_0_array’ set but not used -Wunused-but-set-variable]
javabridge.c:13962:14: warning: variable ‘__pyx_bstride_0_array’ set but not used -Wunused-but-set-variable]
javabridge.c: In function ‘__pyx_pf_10javabridge_6JB_Env_make_double_array’:
javabridge.c:14174:14: warning: variable ‘__pyx_bshape_0_array’ set but not used -Wunused-but-set-variable]
javabridge.c:14173:14: warning: variable ‘__pyx_bstride_0_array’ set but not used -Wunused-but-set-variable]
javabridge.c: At top level:
/home/andrew/CellProfiler-CellProfiler-802161f/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:196:1: warning: ‘_import_umath’ defined but not used -Wunused-function]
javabridge.c: In function ‘__pyx_pf_10javabridge_6JB_Env_set_static_char_field’:
javabridge.c:20695:30: warning: ‘__pyx_v_jvalue’ may be used uninitialized in this function -Wuninitialized]
javabridge.c:10202:9: note: ‘__pyx_v_jvalue’ was declared here
gcc -pthread -shared build/temp.linux-x86_64-2.7/javabridge.o -L/usr/lib/jvm/java-1.6.0-sun-1.6.0.29/jre/lib/amd64/server -L/home/andrew/CellProfiler-CellProfiler-802161f/lib -ljvm -lpython2.7 -o /home/andrew/CellProfiler-CellProfiler-802161f/CellProfiler/cellprofiler/utilities/javabridge.so
#############################################

Hi,

So after a search of the CellProfiler directories, I have found various _cpmorphology files. They are:

/home/andrew/CellProfiler-CellProfiler-802161f/CellProfiler/cellprofiler/cpmath/_cpmorphology.so
/home/andrew/CellProfiler-CellProfiler-802161f/CellProfiler/cellprofiler/cpmath/_cpmorphology2.c
/home/andrew/CellProfiler-CellProfiler-802161f/CellProfiler/cellprofiler/cpmath/_cpmorphology2.pyx
/home/andrew/CellProfiler-CellProfiler-802161f/CellProfiler/cellprofiler/cpmath/_cpmorphology2.so
/home/andrew/CellProfiler-CellProfiler-802161f/CellProfiler/cellprofiler/cpmath/build/temp.linux-x86_64-2.7/_cpmorphology2.o
/home/andrew/CellProfiler-CellProfiler-802161f/CellProfiler/cellprofiler/cpmath/tests/test_cpmorphology.py
/home/andrew/CellProfiler-CellProfiler-802161f/cellprofiler/cpmath/_cpmorphology2.pyx
/home/andrew/CellProfiler-CellProfiler-802161f/cellprofiler/cpmath/tests/test_cpmorphology.py

:question: So when CP complains about not being able to find the _cpmorphology module, which of the above files is it actually looking for ?

Thanks,

Andrew