Installation from source (CentOS) failed

centos
source
installation

#1

Hi,
I followed the instructions to install cellprofiler from source on a CentOS but when it comes to this command:\

'pip install -e . --process-dependency-links'

I end up with this error message (I just replaced my user name with …):

Obtaining file:///home/.../MyApplications/CellProfiler
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/home/.../MyApplications/CellProfiler/setup.py", line 36, in <module>
        from libtiff.libtiff_ctypes import tiff_h_name
    ImportError: No module named libtiff.libtiff_ctypes
    
    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /home.../MyApplications/CellProfiler/

Any idea what could help?


#2

@July your error indicates that you’re missing libtiff. Does installing this python package, pip install libtiff, before calling pip install -e . --process-dependency-links resolve your issue?


#3

Installing libtiff like suggested changed the error message only:

Obtaining file:///home/.../MyApplications/CellProfiler
    Complete output from command python setup.py egg_info:
    
    ----------------------------------------
Command "python setup.py egg_info" failed with error code -11 in /home/niederle/MyApplications/CellProfiler/

One more comment: I try to build release version 2.1.1 as this is also the version running on our cluster. I checked out the branch “release_2.1.1” before.


#4

You’re not going to be able to follow those instructions to build 2.1.1, those are for 2.2 and after. It looks like the previous installation instructions for CentOS called for pre-compiling CP elsewhere then installing it, but the link to the instructions is dead.

I’ll ping our SWEs on this to see if they can help you at all, but I do want to say that given we’re about to release 3.0, and that there were major changes in how CP works/was installed between 2.1.1 and 2.2, I think it’s less and less likely that there’ll be comprehensive continuing support of 2.1.1. It may be worth looking into whether your cluster version can be upgraded…


#5

Unfortunately the newer versions were somehow more problematic to get them running on our cluster (as far as I know - I’m not the cluster admin). With 2.1.1 or 2.2 we had a setup, that we could create multiple single jobs which ran Cellprofiler with a batch of input files. I might be wrong, but I thought that is somehow not possible anymore?
Anyhow, I’m not the right person looking into this.
So, for the moment, I’ll stick to another machine (with another OS) having Cellprofiler installed.


#6

With 2.1.1 or 2.2 we had a setup, that we could create multiple single jobs which ran Cellprofiler with a batch of input files. I might be wrong, but I thought that is somehow not possible anymore?

That should definitely still be possible.