Complile Cellprofiler SplashScreen at 5759


#1

Hi,
I complile Cellprofiler source on a linux server where matlab is instal.
(first i had add the directory of cellprofiler on the path)

mcc -m Cellprofiler.

And then run CellProfiler
./CellProfiler

and get the error :
122_MATLAB]$ ./CellProfiler

Error in ==> CellProfiler>SplashScreen at 5759

Error in ==> CellProfiler at 29

-bash: [fr56668@tlpl08: command not found

MATLAB:imread:fileOpen
Warning: 1 visible figure(s) exist at MCR termination.

If your application has terminated unexpectedly, please note that
applications generated by the MATLAB Compiler terminate when there are no
[fr56668@tlpl08 CellProfiler_1.0.5122_MATLAB]$ Extracting CTF archive. This may take a few seconds, depending on the
WAITFORCALLBACKS for more information.
-bash: Extracting: command not found

Have you got an idea of what’s going wrong ?
Regards,

Marie Laure


#2

Hi Marie,

Cellprofiler is looking for CPsplash.jpg, which is located in the CPsubfunctions folder. Perhaps you didn’t add this folder to Matlab’s path before you compiled? You need to add paths for all the subfolders, namely something like this (if you’re in CP’s main folder):

addpath(pwd)
addpath(fullfile(pwd,‘ImageTools’))
addpath(fullfile(pwd,‘DataTools’))
addpath(fullfile(pwd,‘CPsubfunctions’))
addpath(fullfile(pwd,‘Modules’))
addpath(fullfile(pwd,‘Help’))

Then run mcc, and see how things go.

David


#3

Hi David,

Thank you David for your answer.
I had already add all this path by the matlab window
file / setPath / add with subfolder.

But, I try with your way
addpath(pwd)
addpath(fullfile(pwd,‘ImageTools’))
addpath(fullfile(pwd,‘DataTools’))
addpath(fullfile(pwd,‘CPsubfunctions’))
addpath(fullfile(pwd,‘Modules’))
addpath(fullfile(pwd,‘Help’))

and then I Compile :

mcc -m CellProfiler.m
Warning: Duplicate directory name:
/software/master/linux/discovery/mathworks/matlab/2007b/toolbox/local.

on a bash shell :

[fr56668@tlpl08 CellProfiler_1.0.5122_MATLAB]$ ./CellProfiler
Extracting CTF archive. This may take a few seconds, depending on the
size of your application. Please wait…
…CTF archive extraction complete.
??? Error using ==> imread at 362
File “CPsplash.jpg” does not exist.

Error in ==> CellProfiler>SplashScreen at 5759

Error in ==> CellProfiler at 29

MATLAB:imread:fileOpen
Warning: 1 visible figure(s) exist at MCR termination.

If your application has terminated unexpectedly, please note that
applications generated by the MATLAB Compiler terminate when there are no
visible figure windows. See the documentation for WaitForFiguresToDie and
WAITFORCALLBACKS for more information.

[fr56668@tlpl08 CellProfiler_1.0.5122_MATLAB]$

I don’t understand rules of WaitForFiguresToDie and WAITFORCALLBACKS.

and then an other execution of cellprofiler :
ellProfiler_1.0.5122_MATLAB] ./CellProfiler ellProfiler_1.0.5122_MATLAB]

and nothing happen …

FYI, I work on RHEL 4U4, and you ?

Marie Laure.


#4

Hi Marie,

You need to compile with this command:

mcc -m CellProfiler.m -a ‘CPsubfunctions\CPsplash.jpg’

More detailed instructions for compiling are being compiled (so to speak), as the only directions for this are on some old Forum posts apparently.

David


#5

Hi David,

here is the way I had use in order to compile CellProfiler

But, with that version I can not add modules.
Regards
Marie Laure


#6

Hi Marie,

Are you still having these troubles, or the ones here: CellProfiler on Linux

Thanks,
David