Can't run uber_subject because of Segmentation Fault

AFNI Message Board
1

Hey guys:

I used to be able to run Uber-subject.py without issue but today when I went to run it it literally just gives me “Segmentation Fault.”
Running it with sudo is slightly more helpful and gives me


`**** failed to import PyQt4.QtGui ****

   PyQt4 must be installed to run the uber_subject.py GUI
   --> see the output of: uber_subject.py -help_install`

I’m pretty sure PyQT4 is installed on my computer. Running the system check gives me the following output:
`


-------------------------------- general ---------------------------------
architecture:         64bit 
system:               Darwin
release:              17.3.0
version:              Darwin Kernel Version 17.3.0: Thu Nov  9 18:09:22 PST 2017; root:xnu-4570.31.3~1/RELEASE_X86_64
distribution:         10.13.2 x86_64
number of CPUs:       8
apparent login shell: bash  (current shell is csh)
shell RC file:        .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /Users/nixonsghost/abin/afni
afni version         : Precompiled binary macos_10.12_local: Mar 20 2019 
                     : AFNI_19.0.26 'Tiberius'
AFNI_version.txt     : AFNI_19.0.26, macos_10.12_local, Mar 20 2019
which python         : /Users/nixonsghost/anaconda2/bin/python
python version       : 2.7.15
which R              : /Users/nixonsghost/anaconda2/bin/R
R version            : R version 3.5.1 (2018-07-02) -- "Feather Spray"
which tcsh           : /bin/tcsh

instances of various programs found in PATH:
    afni    : 1   (/Users/nixonsghost/abin/afni)
    R       : 2 
      /Users/nixonsghost/anaconda2/bin/R
      /Library/Frameworks/R.framework/Versions/3.4/Resources/bin/R
    python  : 3 
      /Users/nixonsghost/anaconda2/bin/python2.7
      /sw/bin/python2.7
      /usr/bin/python
    python2 : 1   (/Users/nixonsghost/anaconda2/bin/python2.7)
    python3 : 1   (/Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6)


testing ability to start various programs...
    afni                 : success
    suma                 : success
    3dSkullStrip         : success
    uber_subject.py      : success
    3dAllineate          : success
    3dRSFC               : success
    SurfMesh             : success
    3dClustSim           : success

checking for R packages...
    rPkgsInstall -pkgs ALL -check : FAILURE
        
        oo Warning: 
           These packages are not installed on the computer: brms!
        

checking for $HOME files...
    .afnirc                   : found
    .sumarc                   : found
    .afni/help/all_progs.COMP : found

------------------------------ python libs -------------------------------
++ module 'PyQt4' found at /sw/lib/qt4-mac/lib/python2.7/site-packages/PyQt4
++ module loaded: PyQt4
Segmentation fault`

I notice I have a load of Pythons in my PATH. Could this be the problem? I’m just confused as to what I changed because it was working a month ago.

Thanks for any insight. usually this is a problem I’d try to solve on my own but I’m horrid at versions and everything else seems to be working so I don’t want to mess anything up.

Lauren

2

Hi Lauren,

Most likely, you are running python out of your conda environment, but have PYTHONPATH set to point to your fink tree, and they are not compatible. Remove use of PYTHONPATH from your “dot” file (.cshrc or .bashrc or .bash_profile), and try again.

This would require installing pyqt4 under that conda environment.

  • rick
3

Hey Rick:

Thank you for that. This solved the problem. Specifically thanks for the explicit instructions as I did have to change the dot file and “reinstall” pyqt4 via conda.

I appreciate it very much - I never would have figured this out on my own.

Thanks for your time.
Lauren