Rick/Peter -

Progress. I re-installed Xcode. Homebrew then installed without problems, and I installed glib and gcc (in that order).

Trouble now with the installation of python module PyQt4 as below. With the command

brew install pyqt

I get

qt: This formula either does not compile or function as expected on macOS
versions newer than El Capitan due to an upstream incompatibility.
Error: An unsatisfied requirement failed this build.


I still have trouble with the .sumarc installation. When I run

suma -update_env

I get

sh: ___sumarc: Permission denied
-- Error suma (SUMA_suma.c:732):
Failed to create env file.

The full output of

afni_system_check.py -check-all

is


-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 16.1.0
version: Darwin Kernel Version 16.1.0: Thu Oct 13 21:26:57 PDT 2016; root:xnu-3789.21.3~60/RELEASE_X86_64
distribution: 10.12.1 x86_64
number of CPUs: 8
apparent login shell: tcsh
shell RC file: .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/gkalamangalam/abin/afni
afni version : Precompiled binary macosx_10.7_Intel_64: Nov 4 2016
AFNI_version.txt : AFNI_16.3.08, macosx_10.7_Intel_64, Nov 04 2016
which python : /usr/bin/python
python version : 2.7.10
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/gkalamangalam/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.3/Resources/bin/R)
python : 1 (/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 : success

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

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

-------------------------------- env vars --------------------------------
PATH = /usr/local/fsl/bin:/Users/gkalamangalam/freesurfer/bin:/Users/gkalamangalam/freesurfer/fsfast/bin:/Users/gkalamangalam/freesurfer/tktools:/usr/local/fsl/bin:/Users/gkalamangalam/freesurfer/bin/freeview.app/Contents/MacOS/:/Users/gkalamangalam/freesurfer/mni/bin:/usr/local/fsl/bin:/Users/gkalamangalam/freesurfer/bin:/Users/gkalamangalam/freesurfer/fsfast/bin:/Users/gkalamangalam/freesurfer/tktools:/usr/local/fsl/bin:/Users/gkalamangalam/freesurfer/bin/freeview.app/Contents/MacOS/:/Users/gkalamangalam/freesurfer/mni/bin:/usr/local/fsl/bin:/Users/gkalamangalam/freesurfer/bin:/Users/gkalamangalam/freesurfer/fsfast/bin:/Users/gkalamangalam/freesurfer/tktools:/usr/local/fsl/bin:/Users/gkalamangalam/freesurfer/bin/freeview.app/Contents/MacOS/:/Users/gkalamangalam/freesurfer/mni/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/local/fsl/bin:/Users/gkalamangalam/freesurfer/bin:/Users/gkalamangalam/freesurfer/fsfast/bin:/Users/gkalamangalam/freesurfer/tktools:/Users/gkalamangalam/freesurfer/bin/freeview.app/Contents/MacOS/:/Users/gkalamangalam/freesurfer/mni/bin:/Users/gkalamangalam/abin:/Users/gkalamangalam/abin:/Users/gkalamangalam/abin:/Users/gkalamangalam/abin

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

R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

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

------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 1.1.0

++ 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/2.50.1/lib/libglib-2.0.dylib

============================ summary comments ============================
* consider running "suma -update_env" for .sumarc
* insufficient data for AFNI bootcamp
* consider running: brew install pyqt