PyQt4 issue with uber_subject.py

AFNI Message Board
1

Hi AFNI team. I have been struggling to get uber_subject.py to run on my macbook.

[Michaels-MacBook-Pro-2:~] amlung% uber_subject.py

**** 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 executed all the steps described in the -help_install. I have confirmed that I have python2.7 installed, and PyQt4 is in the site-packages folder. I have also confirmed that PYTHONPATH points to /usr/local/lib/python2.7/site-packages

I am guessing I am missing something basic, but it is escaping me.

Can you please provide some guidance? Thank you!

Michael Amlung

2

Hi Michael,

What does the system check show?

afni_system_check.py -check_all

  • rick
3

Looks like theres an issue with install of PyQt4

bash-3.2$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 16.0.0
version: Darwin Kernel Version 16.0.0: Mon Aug 29 17:56:20 PDT 2016; root:xnu-3789.1.32~3/RELEASE_X86_64
distribution: 10.12 x86_64
number of CPUs: 4
apparent login shell: tcsh (current shell is bash)
shell RC file: .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/amlung/abin/afni
afni version : Precompiled binary macos_10.12_local: Aug 14 2018
: AFNI_18.2.10
AFNI_version.txt : AFNI_18.2.10, macos_10.12_local, Aug 14 2018
which python : /usr/local/bin/python
python version : 2.7.16
which R : /usr/local/bin/R
R version : R version 3.3.2 (2016-10-31) – “Sincere Pumpkin Patch”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/amlung/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.3/Resources/bin/R)
python : 2
/usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/bin/python2.7
/usr/bin/python
python2 : 1 (/usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python3 : 1 (/usr/local/Cellar/python/3.7.4_1/Frameworks/Python.framework/Versions/3.7/bin/python3.7)

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 : missing
.afni/help/all_progs.COMP : found

------------------------------ python libs -------------------------------
++ module ‘PyQt4’ found at /usr/local/lib/python2.7/site-packages/PyQt4
++ module loaded: PyQt4

** have PyQt4, but cannot load QtCore, QtGui; error is:

Traceback (most recent call last):
File “”, line 1, in
ImportError: No module named sip

-------------------------------- env vars --------------------------------
PATH = /Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/amlung/abin:/Applications/workbench/bin_macosx64/:/Applications/workbench/bin_macosx64:/Applications/workbench/bin_macosx64:/Applications/workbench/bin_macosx64:/Applications/workbench/bin_macosx64

PYTHONPATH = /usr/local/lib/python2.7/site-packages/

R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) =
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =

------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /Users/amlung/abin

------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 2.1.11

++ found PyQt4 under /usr/local/lib/python2.7/site-packages
– consider installing gcc under homebrew
– consider installing glib under homebrew
++ found 1 dylib files under ‘/opt/X11/lib/flat_namespace’
– found ‘libXt’ dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
– recent OS X, cheating to check DYLD_LIBRARY_PATH in cur shell ‘bash’…
** env var DYLD_LIBRARY_PATH not set to contain /opt/X11/lib/flat_namespace
– recent OS X, cheating to check DYLD_LIBRARY_PATH in shell ‘tcsh’…
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace

========================= summary, please fix: =========================

  • missing R packages (see rPkgsInstall)
  • consider running “suma -update_env” for .sumarc
  • check for partial install of PyQt4
  • insufficient data for AFNI bootcamp
  • consider adding /usr/local/lib/python2.7/site-packages to PYTHONPATH
  • please set DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace in bash
4

Hi Rick, Any ideas on why its not working for us?

5

Hi Michael,

Sorry for not getting back to this.

It looks like you have this set up under homebrew, but maybe sip is not installed. Can you install that? I am not sure, but it might be just via “brew install sip”).

Can you give that a try? I do not have homebrew-based system to try these things out on.

  • rick
6

HI Rick,
Nope that was not the solution. Sip already installed and up to date. Should I try to wipe AFNI and do a clean install?

7

Well, AFNI isn’t the problem, set pyqt4 setup with homebrew is. You could try doing it via fink, instead, but that is doing a lot for a little package (pyqt4).

I think Brian has set up a virtual mac for us to test with. Maybe we can try installing pyqt4 via homebrew on there, and see how it goes.

What is the output from:

python -c 'from PyQt4 import QtCore, QtGui'

I think that is basically what needs to work.

Note that the afni_system_check.py output shows homebrew python2, homebrew pyqt4, and yet shows this error for loading PyQt4:

Traceback (most recent call last):
File “”, line 1, in
ImportError: No module named sip

Maybe you have sip installed for python3, but not python2?

  • rick