Hi Rick,

I'm having the same problem with the R libraries. (I had to reinstall afni because I suddenly was having a bunch of issues that I couldn't figure out.) Upon reinstalling and doing the check, I get the issue below.

Any input would be much appreciated!
-Nancy

[OBYL100MAC:~] canlabuser% afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 17.7.0
version: Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64
distribution: 10.13.6 x86_64
number of CPUs: 12
apparent login shell: tcsh
shell RC file: .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/canlabuser/abin/afni
afni version : Precompiled binary macos_10.12_local: Sep 27 2018
: AFNI_18.2.19
AFNI_version.txt : AFNI_18.2.19, macos_10.12_local, Sep 27 2018
which python : /usr/bin/python
python version : 2.7.10
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/canlabuser/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.4/Resources/bin/R)
python : 1 (/usr/bin/python)
python2 : 0
python3 : 0


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
Error in dyn.load(ll) :
unable to load shared object '/Users/canlabuser/abin/R_io.so':
dlopen(/Users/canlabuser/abin/R_io.so, 6): Library not loaded: /sw/lib/libXt.6.dylib
Referenced from: /Users/canlabuser/abin/R_io.so
Reason: image not found
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
Execution halted

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

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

python binaries under /sw/bin:
/sw/bin/python (sym link to /sw/bin/python2.7)
/sw/bin/python2.7

-------------------------------- env vars --------------------------------
PATH = /usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/canlabuser/abin

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = /opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: 20 Jun 2016 [rickr]: optional de-mean in PPI
data dir : found AFNI_demos under $HOME
top history: 26 Sep 2014 [ziad] : added Do_11 to FATCAT_DEMO
data dir : found suma_demo under $HOME
top history: .../SUMA_data/Build_tmp on Wed Aug 20 10:04:23 EDT 2014
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /Users/canlabuser/abin

------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 1.7.6

++ found existent library /usr/local/lib/libgomp.1.dylib
++ found valid link /usr/local/lib/libglib-2.0.dylib
to ../Cellar/glib/2.58.0/lib/libglib-2.0.dylib
++ 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 'tcsh'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace

========================= summary, please fix: =========================
* missing R packages (see rPkgsInstall)