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