Hello,
I have been trying to install AFNI and run tafni_system_check.py -check_all but it seems like it is unable to recognize that I have downloaded R on to the laptop. Please see the output below. Would greatly appreciate any advice on how to troubleshoot.
darshil@1ST21RI-MBP02 ~ % afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 20.3.0
version: Darwin Kernel Version 20.3.0: Thu Jan 21 00:06:51 PST 2021; root:xnu-7195.81.3~1/RELEASE_ARM64_T8101
distribution: 10.16
number of CPUs: 8
apparent login shell: zsh
shell RC file: .zshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/darshil/abin/afni
afni version : Precompiled binary macos_10.12_local: Mar 17 2021
: AFNI_21.0.20 'Titus'
AFNI_version.txt : AFNI_21.0.20, macos_10.12_local, Mar 17 2021
which python : /usr/bin/python
python version : 2.7.16
which R :
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/Users/darshil/abin/afni)
R : 0
python : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python2 : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python3 : 1 (/usr/bin/python3)
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 : success
checking for R packages...
rPkgsInstall -pkgs ALL -check : success
R RHOME : R: Command not found.
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 : /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/pyplot.pyc
-------------------------------- env vars --------------------------------
PATH = /opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/darshil/abin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = ...completed.
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) = ...completed.
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: 20 Feb 2020 [rickr]: updated FT_analysis examples
data dir : found AFNI_demos under $HOME
top history: ...ct 2020 [taylorp]: updated scripts under FATCAT_DEMO
data dir : found suma_demo under $HOME
top history: ...s_New/data/Build_tmp on Mon Mar 4 11:56:45 EST 2013
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /Users/darshil/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.7.10
which brew : /opt/homebrew/bin/brew
brew version : Homebrew 3.0.8
-- for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
-- 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
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in cur shell 'zsh'...
** env var DYLD_LIBRARY_PATH is set, but without /opt/X11/lib/flat_namespace
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in shell 'tcsh'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace
========================= summary, please fix: =========================
* just be aware: login shell 'zsh', but our code examples use 'tcsh'
* failure under initial "AFNI and related program tests"
* please set DYLD_LIBRARY_PATH to include /opt/X11/lib/flat_namespace
