Problems with setting path so that PyQt can work for uber_subject.py

AFNI Message Board
1

Hi,

I am attempting to use uber_subject.py on my Mac and after installing PyQt4 I am still having issues, and I believe it is due to an incorrect path. From other questions asked on this forum, I’ve noticed that when I type “which python” in terminal it should output “/sw/bin/python” and I have tried editing my ~/.bashrc , ~/.profile , and ~/.bash_profile files but I believe I am doing this incorrectly because “which python” still returns “/usr/local/bin/python” for me.

Does anyone know how I may fix it so that the path is correct?

Thanks,

Will

2

Hi Will,

/usr/local/bin/python is correct. What is the output of:

afni_system_check.py -check_all

  • rick
3

Hi Rick,

This is the output I received:

-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 15.0.0
version: Darwin Kernel Version 15.0.0: Wed Aug 26 16:57:32 PDT 2015; root:xnu-3247.1.106~1/RELEASE_X86_64
distribution: 10.11 x86_64
number of CPUs: 4
apparent login shell: tcsh
shell RC file: .tcshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/willsnyder/abin/macosx_10.7_Intel_64/afni
afni version : Precompiled binary macosx_10.7_Intel_64: Nov 23 2016
AFNI_version.txt : AFNI_16.3.13, macosx_10.7_Intel_64, Nov 23 2016
which python : /usr/local/bin/python
python version : 2.7.12
which R : /usr/local/bin/R
R version : R version 3.3.1 (2016-06-21) – “Bug in Your Hair”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/willsnyder/abin/macosx_10.7_Intel_64/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.3/Resources/bin/R)
python : 2
/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
/usr/bin/python

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

checking for R packages…
rPkgsInstall -pkgs ALL -check : FAILURE

    oo Warning: 
       These packages are not installed on the computer: afex!
    These packages are not installed on the computer: phia!
    These packages are not installed on the computer: snow!
    These packages are not installed on the computer: lme4!
    These packages are not installed on the computer: paran!
    These packages are not installed on the computer: psych!

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

------------------------------ python libs -------------------------------
** python module not found: PyQt4

-------------------------------- env vars --------------------------------
PATH = /usr/local/bin:/usr/local/bin:/usr/local/bin:/usr/local/bin:/usr/local/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/willsnyder/abin:/Users/willsnyder/abin:/Users/willsnyder/abin:/Users/willsnyder/abin:/Users/willsnyder/abin:/Users/willsnyder/abin/macosx_10.7_Intel_64

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

R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: … 2016 [rickr]: updated proc scripts and PPI examples
data dir : missing suma_demo
data dir : missing FATCAT_DEMO
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /Users/willsnyder/abin/macosx_10.7_Intel_64

------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 1.1.2

++ found valid link /usr/local/lib/libgomp.1.dylib
to /usr/local/Cellar/gcc/6.2.0/lib/gcc/6/libgomp.1.dylib
++ found valid link /usr/local/lib/libglib-2.0.dylib
to …/Cellar/glib/2.50.2/lib/libglib-2.0.dylib

============================ summary comments ============================

  • missing R packages (see rPkgsInstall)
  • consider running “suma -update_env” for .sumarc
  • consider running: apsearch -update_all_afni_help
  • insufficient data for AFNI bootcamp
  • consider running: brew install pyqt

Also, I noticed I have PyQt5 installed and not PyQt4 (brew install pyqt only lets me install the former), not sure if that is important though

Thanks,

Will