Hi pt,

Thank you so much for the response! Unfortunately, it still has the same error even after update. Could you please let me know if there is another issue here? Below is the result of afni_system_check.py -check_all.

-------------------------------- general ---------------------------------

architecture: 64bit

system: Darwin

release: 16.7.0

version: Darwin Kernel Version 16.7.0: Wed Apr 24 20:50:53 PDT 2019; root:xnu-3789.73.49~1/RELEASE_X86_64

distribution: 10.12.6 x86_64

number of CPUs: 12

apparent login shell: bash

shell RC file: .bashrc (exists)



--------------------- AFNI and related program tests ---------------------

which afni : /Users/titus/abin/afni

afni version : Precompiled binary macos_10.12_local: May 17 2019

: AFNI_19.1.09 'Caligula'

AFNI_version.txt : AFNI_19.1.09, macos_10.12_local, May 17 2019

which python : /usr/bin/python

python version : 2.7.10

which R : /usr/local/bin/R

R version : R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"

which tcsh : /bin/tcsh



instances of various programs found in PATH:

afni : 1 (/Users/titus/abin/afni)

R : 1 (/Library/Frameworks/R.framework/Versions/3.4/Resources/bin/R)

python : 1 (/usr/bin/python)

python2 : 0

python3 : 1 (/Library/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



checking for R packages...

rPkgsInstall -pkgs ALL -check : FAILURE



oo Warning:

These packages are not installed on the computer: corrplot!





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 = /usr/local/fsl/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Users/titus/abin:/Users/titus/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 : found AFNI_data6 under $HOME/afni_materials

top history: ... [rickr]: updated FT_white.nii w/out 16 (brain stem)

data dir : found AFNI_demos under $HOME/afni_materials

top history: ... [pault]: remove rank from FATCAT_DEMO, FAT_MVM_DEMO

data dir : found suma_demo under $HOME/afni_materials

top history: .../SUMA_data/Build_tmp on Wed Aug 20 10:04:23 EDT 2014

data dir : found afni_handouts under $HOME/afni_materials

atlas : found TT_N27+tlrc under /Users/titus/abin



------------------------------ OS specific -------------------------------

which brew : /usr/local/bin/brew

brew version : Homebrew 1.7.3



++ found PyQt4 under /sw/lib/qt4-mac/lib/python2.7/site-packages

** warning: have fink PyQt4, but non-fink 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

++ yay, env var DYLD_LIBRARY_PATH contains /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

* missing R packages (see rPkgsInstall)

* consider adding /sw/lib/qt4-mac/lib/python2.7/site-packages to PYTHONPATH

* have fink PyQt4, but non-fink python /usr/bin/python




Thanks,
JW