Problem with CP 2.2


#1

Hello there.

I previously had Windows 10 on my computer and I had CP running withou anyproblem. Recently I removed Windows and installed a Linux distribuition. I installed CP and had no problems, although since the installation and up until now I had never tried to use it. Today however, I was presented with a problem I didn’t know about. After a quick look in this forum, I discovered someone had the same problem (this one: Zernike error on measureobjectsizeshape module in linux ). I updated scipy and numpy, as Mark suggested. After this, I am not able to run CP again, every single time it stops here (see image) and does nothing. What happened? I just updated scipy and numpy.


#2

Hi,

Could you please try running:

$ python2 CellProfiler.py --log-level=DEBUG

from the CellProfiler directory and paste the output.


#3

Hello, here is the output


#4

Can you also compare your pip freeze with the list from this post? I’m suspicious that you were able to run it (right? That’s how you found the Zernike issue?) until the numpy and scipy updates; I wonder if there’s a version issue.

Is updating to CP 3.0 an option?


#5

Yes, that’s exactly what happen. I could run until the numpy and scipy updates.

Comparing the output from my pip freeze and the list on that post, there are some on that list that I don’t have as there are some I have that are not on that list. I have Cython, Pillow, python-dateutil and urllib3 with older versions. Here’s my list.

And yes, updating might be an option.

apsw==3.8.11.1.post1
attrs==17.3.0
BeautifulSoup==3.2.1
beautifulsoup4==4.4.1
blinker==1.3
cellh5==1.3.0
-e git+https://github.com/CellProfiler/CellProfiler.git@478e2fe1779b3505d1bc13fdabf263af22dc32df#egg=CellProfiler
centrosome==1.0.9
chardet==2.3.0
CherryPy==3.5.0
configglue==1.1.2
configobj==5.0.6
cryptography==1.2.3
cssselect==0.9.1
cssutils==1.0
cycler==0.9.0
Cython==0.23.4
debtags==2.0
decorator==4.1.2
defer==1.0.6
dirspec==13.10
dnspython==1.12.0
duplicity==0.7.6
ecdsa==0.13
enum34==1.1.2
ez-setup==0.9
feedparser==5.1.3
funcsigs==1.0.2
future==0.16.0
h5py==2.6.0
hmmlearn==0.2.0
httplib2==0.9.1
idna==2.0
inflect==0.2.5
ipaddress==1.0.16
javabridge==1.0.15
libtiff==0.4.2
lockfile==0.12.2
lxml==3.5.0
Mako==1.0.3
Markdown==2.6.6
MarkupSafe==0.23
matplotlib==1.5.1
mechanize==0.2.5
MySQL-python==1.2.5
mysqlclient==1.3.7
nemo-emblems==3.6.0
netifaces==0.10.4
networkx==2.0
numpy==1.14.0
oauthlib==1.0.3
oneconf==0.3.9
PAM==0.4.2
pandas==0.21.1
paramiko==1.16.0
pexpect==4.0.1
Pillow==3.1.2
piston-mini-client==0.7.5
pluggy==0.6.0
prokaryote==2.3.2
protobuf==2.6.1
ptyprocess==0.5
py==1.5.2
pyasn1==0.1.9
pyasn1-modules==0.0.7
pycrypto==2.6.1
pycups==1.9.73
pycurl==7.43.0
pygobject==3.20.0
pyinotify==0.9.6
PyJWT==1.3.0
pyOpenSSL==0.15.1
pyparsing==2.0.3
pyparted==3.10.7
pyserial==3.0.1
pysmbc==1.0.15.5
pytest==3.3.1
python-apt==1.1.0b1
python-bioformats==1.3.2
python-dateutil==2.4.2
python-debian==0.1.27
python-xlib==0.14
pytz==2014.10
PyWavelets==0.5.2
pyxdg==0.25
pyzmq==15.2.0
reportlab==3.3.0
repoze.lru==0.6
Routes==2.2
scikit-image==0.13.1
scikit-learn==0.19.1
scipy==1.0.0
service-identity==16.0.0
setproctitle==1.1.8
six==1.10.0
Twisted==16.0.0
urllib3==1.13.1
uTidylib==0.2
wxPython==3.0.2.0
wxPython-common==3.0.2.0
zope.interface==4.1.3

#6

I’m reasonably confident it has to due with the numpy/scipy update then; can you roll those back (if systemwide is a problem, then put CP in conda/pyenv etc) and see if that works? Otherwise I think CP 3.0 is your answer.


#7

I don’t really know how to do any of that :S And as for upgrading to CP 3.0. I followed the git tutorial on how to install on Ubuntu. I thought changing git checkout 2.2.0 to git checkout 3.0.0 would work, but it doesn’t, so how can I upgrade to CP 3.0 on Linux?


#8

git checkout master


#9

Thank you. Now I got this when running CP 3.0 and it stays there indefinitely.


#10

Can you run pip install --upgrade --editable . to upgrade all of CellProfiler’s dependencies?


#11

This is strange, 'cause I did that when upgrading but it seems not all of them were upgraded. Now it’s working and I tried running the same pipeline and there wasn’t any trouble for the first 10 images, so I assume everything’s okay now. Thank you very much for your help :grin: