The build process should take on the order of a few minutes, not hours. There are no perl scripts involved in our builds, so I suspect your Perl.exe process must be separate from CellProfiler. Quit this process (or better, reboot), and try again. And be sure to follow the rest of the directions in BuildCellProfiler.m’s Help file for ‘single’ machine usage:
% BuildCellProfiler Build a self-contained executable of CellProfiler for
% use on a single machine or for cluster computing.
% The argument ‘Usage’ is a string and can either be:
% ‘single’: Create a CellProfiler executable appropriate for the host
% machine it’s compiled on (e.g., PC, Macs, Unix)
% ‘cluster’: Create a CellProfiler executable appropriate for use on a
% cluster (assumed to be Unix-based)
% The output will be an executable called CellProfiler (Usage: ‘single’)
% or CPCluster (Usage: ‘cluster’), along with any associated files
% neccesary to set up environment variables.
% Before running this function, set the current directory to
% your root (or trunk) CellProfiler directory, which includes
% CellProfiler.m and the Modules, CPsubfunctions, etc folders.
% NOTES ON “SINGLE” USAGE
% A new folder called CompiledCellProfiler will be created at the
% same level as the CP root folder. This placement is to avoid duplicate
% function names if you run CP from the root directory after building.
% Read the readme.txt file created, and set your path variables either
% manually, try the CellProfiler*.command scripts, or use the
% run_CellProfiler.sh script at a terminal prompt.
% See readme.txt file for more details.
You might also be sure to Run Matlab as Administrator, which can often help on Vista, though I’m not certain it’s necessary.