I have a similar problem. It seems that I upgraded to 10.12, which is not right?
Here is the information:

afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 18.6.0
version: Darwin Kernel Version 18.6.0: Thu Apr 25 23:16:27 PDT 2019; root:xnu-4903.261.4~2/RELEASE_X86_64
distribution: unknown Darwin
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/fanglab/abin/afni
afni version : Precompiled binary macos_10.12_local: Aug 10 2020
: AFNI_20.2.11 'Aulus Vitellius'
AFNI_version.txt : AFNI_20.2.11, macos_10.12_local, Aug 10 2020
which python : /opt/anaconda3/bin/python
python version : 3.8.3
which R : /usr/local/bin/R
R version : R version 3.4.1 (2017-06-30) -- "Single Candle"
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/fanglab/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.4/Resources/bin/R)
python : 2
/opt/anaconda3/bin/python3.8
/usr/bin/python
python2 : 0
python3 : 2
/opt/anaconda3/bin/python3.8
/usr/local/Cellar/python@3.8/3.8.5/Frameworks/Python.framework/Versions/3.8/bin/python3.8

** 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 : FAILURE
Error in dyn.load(ll) :
unable to load shared object '/Users/fanglab/abin/R_io.so':
dlopen(/Users/fanglab/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
Referenced from: /Users/fanglab/abin/R_io.so
Reason: Incompatible library version: R_io.so requires version 3.6.0 or later, but libR.dylib provides version 3.4.0
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
Execution halted

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 : /opt/anaconda3/lib/python3.8/site-packages/matplotlib/pyplot.py

-- python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /usr/local/Cellar/python@3.8/3.8.5/Frameworks/Python.framework/Versions/3.8/bin/python3.8)
/usr/local/bin/python3.8 (sym link to /usr/local/Cellar/python@3.8/3.8.5/Frameworks/Python.framework/Versions/3.8/bin/python3.8)

-------------------------------- env vars --------------------------------
PATH = /opt/anaconda3/bin:/opt/anaconda3/condabin:/path/to/my/anaconda3/lib/Python3.7/site-packages/mripy/scripts:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/fanglab/abin

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ 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/fanglab/abin

------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11

which brew : /usr/local/bin/brew
brew version : Homebrew 2.4.9

-- for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
++ found 1 dylib files under '/opt/X11/lib/flat_namespace'
-- found 'libXt' dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
** env var DYLD_LIBRARY_PATH is not set to contain /opt/X11/lib/flat_namespace
(so afni and suma may fail)

========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* have python version 3.8.3, but a few programs need 2.7.x
* AFNI programs show FAILURE
* insufficient data for AFNI bootcamp
* OS X version might be old
* consider setting DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace



Edited 1 time(s). Last edit at 08/11/2020 08:22AM by SarahChang.