Thanks Paul!
Here are the outputs after executing command: afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 16.6.0
version: Darwin Kernel Version 16.6.0: Fri Apr 14 16:13:31 PDT 2017; root:xnu-3789.60.24~4/RELEASE_X86_64
distribution: 10.12.5 x86_64
number of CPUs: 4
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/shoaibur/abin/afni
afni version : Precompiled binary macosx_10.7_local: Aug 28 2018
: AFNI_18.2.15
AFNI_version.txt : AFNI_18.2.15, macosx_10.7_local, Aug 28 2018
which python : /usr/bin/python
python version : 2.7.10
which R : /usr/local/bin/R
R version : R version 3.4.2 (2017-09-28) -- "Short Summer"
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/Users/shoaibur/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
oo Warning:
These packages are not installed on the computer: brms!
checking for $HOME files...
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
** python module not found: PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp
python binaries under /sw/bin:
/sw/bin/python (sym link to /sw/bin/python2.7)
/sw/bin/python2.7
-------------------------------- env vars --------------------------------
PATH = /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/shoaibur/abin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH = /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/shoaibur/abin
------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 1.5.14
++ found PyQt4 under /sw/lib/qt4-mac/lib/python2.7/site-packages
-- consider installing gcc under homebrew
++ found 1 dylib files under '/opt/X11/lib/flat_namespace'
-- found 'libXt' dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
++ yay, env var DYLD_LIBRARY_PATH contains /opt/X11/lib/flat_namespace
========================= summary, please fix: =========================
* login shell 'bash', trusting user to translate from 'tcsh'
* shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
* missing R packages (see rPkgsInstall)
* insufficient data for AFNI bootcamp
* consider adding /sw/lib/qt4-mac/lib/python2.7/site-packages to PYTHONPATH
* consider linking /usr/local/Cellar/glib/2.56.0/lib/libglib-2.0.dylib under /usr/local/lib
