Thanks Rick, here is the output:
Michaels-iMac-2:1000p cnalab$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 18.7.0
version: Darwin Kernel Version 18.7.0: Sun Dec 1 18:59:03 PST 2019; root:xnu-4903.278.19~1/RELEASE_X86_64
distribution: 10.14.6 x86_64
number of CPUs: 6
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/cnalab/abin/afni
afni version : Precompiled binary macos_10.12_local: Nov 8 2019
: AFNI_19.3.12 'Nero'
AFNI_version.txt : AFNI_19.3.12, macos_10.12_local, Nov 08 2019
which python : /usr/bin/python
python version : 2.7.16
which R : /usr/local/bin/R
R version : R version 3.5.3 (2019-03-11) -- "Great Truth"
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/Users/cnalab/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.5/Resources/bin/R)
python : 1 (/usr/bin/python)
python2 : 0
python3 : 1 (/usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/bin/python3.7)
** have python3 but not python2
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
3dMVM : success
checking for R packages...
rPkgsInstall -pkgs ALL -check : success
R RHOME : /Library/Frameworks/R.framework/Resources
checking for $HOME files...
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
** failed to load module PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp
++ module loaded: matplotlib.pyplot
module file : /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/pyplot.pyc
-- python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/bin/python3.7)
/usr/local/bin/python3.7 (sym link to /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/bin/python3.7)
-------------------------------- env vars --------------------------------
PATH = /usr/local/fsl/bin:/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/cnalab/abin:/Applications/workbench/bin_macosx64
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = /Applications/freesurfer/lib/gcc/lib::/opt/X11/lib/flat_namespace
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/cnalab/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11
which brew : /usr/local/bin/brew
brew version : Homebrew 2.2.4
++ found PyQt4 under /usr/local/lib/python2.7/site-packages
** warning: have brew? PyQt4, but non-brew python /usr/bin/python
-- 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'...
++ found evar DYLD_LIBRARY_PATH = /Applications/freesurfer/lib/gcc/lib::/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: =========================
* login shell 'bash', trusting user to translate code examples from 'tcsh'
* shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
* insufficient data for AFNI bootcamp
* consider adding /usr/local/lib/python2.7/site-packages to PYTHONPATH
* have brew? PyQt4, but non-brew python /usr/bin/python
