CellProfiler 2.0 Mac OS X installation

Hi everyone,

I am trying to install CellProfiler 2.0 on my MacBook, used the makefile to create the virtual environment (from the installation wiki) which seemed to work fine. I then jumped down to the pip commands and had problems installing Cython, and get the following error (see below). Also, it says on the installation page that I can “check out and run CellProfiler in the virtualenv”. How would I do that? I want to make sure I can run CellProfiler before I build the app/executable. I’m reasonably good with Mac/Linux but these installation instructions are quite daunting, its not clear whether this should take me a day (or several days to install). So far I have spent an entire evening on it and don’t seem very close. I think adding a little bit more detailed comments to each step would be very helpful. Have people had success with installations?

Thanks and any help would be greatly appreciated. I’m very much looking forward to running/developing with the new CellProfiler!

-Salil

Salil Desai, Ph.D.
MGH-MIT ECOR Fellow in Translational Medicine
Massachusetts General Hospital | Massachusetts Institute of Technology
email: desai@mit.edu
voice: 617-653-4098

pip install Cython==0.12.1

Downloading/unpacking Cython==0.12.1
Running setup.py egg_info for package Cython
warning: no files found matching ‘Demos/Setup.py’
warning: no files found matching ‘Cython/Mac/Makefile’
warning: no files found matching ‘Cython/Mac/_Filemodule_patched.c’
Installing collected packages: Cython
Running setup.py install for Cython
building ‘Cython.Plex.Scanners’ extension
gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd -fno-common -dynamic -DNDEBUG -g -O3 -I/Library/Frameworks/Python.framework/Versions/2.5/include/python2.5 -c /Users/salildesai/Desktop/VENV254/CellProfilerVirtualenv/build/Cython/Cython/Plex/Scanners.c -o build/temp.macosx-10.3-i386-2.5/Users/salildesai/Desktop/VENV254/CellProfilerVirtualenv/build/Cython/Cython/Plex/Scanners.o
cc1: error: unrecognized command line option "-Wno-long-double"
cc1: error: unrecognized command line option "-Wno-long-double"
lipo: can’t figure out the architecture type of: /var/folders/Yc/Yc8bPjRvGoWN8lJ4Yy0RIE+++TI/-Tmp-//ccCtispd.out
error: command ‘gcc’ failed with exit status 1
Complete output from command /Users/salildesai/Desktop/VENV254/CellProfilerVirtualenv/bin/python -c "import setuptools; file=’/Users/salildesai/Desktop/VENV254/CellProfilerVirtualenv/build/Cython/setup.py’; execfile(’/Users/salildesai/Desktop/VENV254/CellProfilerVirtualenv/build/Cython/setup.py’)" install --single-version-externally-managed --record /var/folders/Yc/Yc8bPjRvGoWN8lJ4Yy0RIE+++TI/-Tmp-/pip-MNRtXQ-record/install-record.txt --install-headers /Users/salildesai/Desktop/VENV254/CellProfilerVirtualenv/bin/…/include/site/python2.5:
running install

running build

running build_py

running build_ext

building ‘Cython.Plex.Scanners’ extension

gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd -fno-common -dynamic -DNDEBUG -g -O3 -I/Library/Frameworks/Python.framework/Versions/2.5/include/python2.5 -c /Users/salildesai/Desktop/VENV254/CellProfilerVirtualenv/build/Cython/Cython/Plex/Scanners.c -o build/temp.macosx-10.3-i386-2.5/Users/salildesai/Desktop/VENV254/CellProfilerVirtualenv/build/Cython/Cython/Plex/Scanners.o

cc1: error: unrecognized command line option “-Wno-long-double”

cc1: error: unrecognized command line option “-Wno-long-double”

lipo: can’t figure out the architecture type of: /var/folders/Yc/Yc8bPjRvGoWN8lJ4Yy0RIE+++TI/-Tmp-//ccCtispd.out

error: command ‘gcc’ failed with exit status 1


Command /Users/salildesai/Desktop/VENV254/CellProfilerVirtualenv/bin/python -c “import setuptools; file=’/Users/salildesai/Desktop/VENV254/CellProfilerVirtualenv/build/Cython/setup.py’; execfile(’/Users/salildesai/Desktop/VENV254/CellProfilerVirtualenv/build/Cython/setup.py’)” install --single-version-externally-managed --record /var/folders/Yc/Yc8bPjRvGoWN8lJ4Yy0RIE+++TI/-Tmp-/pip-MNRtXQ-record/install-record.txt --install-headers /Users/salildesai/Desktop/VENV254/CellProfilerVirtualenv/bin/…/include/site/python2.5 failed with error code 1
Storing complete log in /Users/salildesai/.pip/pip.log

I seem to have fixed my installation problems and can now install Cython and everything else. It required making sure that I was using gcc-4.0 in the makefile (as pointed out in the installation wiki). If someone has these types of problems feel free to drop me a note and I would be happy to help debug.

However, I can’t seem to run the pythonw example, the window appears and closes instantaneously (I’m suspecting this an Expose’ issue, with having multiple desktops open … though I could be wrong). Also, still don’t know how to “check out” the CellProfiler executable and run it in the virtualenv to check if I’ve got everything working. I can’t seem to find any type of top-level executable in the bin directories. I probably being a complete idiot but if someone has any suggestions that would be very helpful.

Thanks for your help,

-Salil

Salil Desai, Ph.D.
MGH-MIT ECOR Fellow in Translational Medicine
Massachusetts General Hospital | Massachusetts Institute of Technology
email: desai@mit.edu
voice: 617-653-4098

Hi everyone,

So again, I seem to have fixed my own problem. There was copy/paste error in the pythonw example and once I fixed my error the example ran just fine. After that I magically found a CellProfiler app in my Applications folder. Not sure how it got there, I’m assuming that’s how I checked out CellProfiler. I was under the impression that I actually needed to build the app. If anyone can shed any light on this that would be helpful but with things working now I’m not going to fret too much.

If anybody has questions with their installations I would be happy to help out, as I went over 4-5 times before I got it done perfectly.
Happy cell profiling,

-Salil

Great! We’re glad you got it working- thanks so much for posting your troubleshooting.