hi again guys
omg i'm an idiot. i hadn't fully installed xquartz, sorry. i may have also messed up some path stuff last night as i tried to troubleshoot, so i'm still getting an error about DYLD_LIBRARY_PATH but overall it's looking better. first i'll paste my current output of afni_system_check, and then at the bottom of this message i'll respond to rick's newest inquiry:
[MacBook-Pro:~] torrisi% afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.5.0
version: Darwin Kernel Version 19.5.0: Tue May 26 20:41:44 PDT 2020; root:xnu-6153.121.2~2/RELEASE_X86_64
distribution: unknown Darwin
number of CPUs: 8
apparent login shell: tcsh
shell RC file: .cshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/torrisi/abin/afni
afni version : Precompiled binary macos_10.12_local: Jun 30 2020
: AFNI_20.1.18 'Otho'
AFNI_version.txt : AFNI_20.1.18, macos_10.12_local, Jun 30 2020
which python : /usr/bin/python
python version : 2.7.16
which R : /usr/local/bin/R
R version : R version 4.0.2 (2020-06-22) -- "Taking Off Again"
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/Users/torrisi/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/4.0/Resources/bin/R)
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 : FAILURE
Error in dyn.load(ll) :
unable to load shared object '/Users/torrisi/abin/R_io.so':
dlopen(/Users/torrisi/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
Referenced from: /Users/torrisi/abin/R_io.so
Reason: image not found
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
Execution halted
checking for R packages...
rPkgsInstall -pkgs ALL -check : success
R RHOME : /Library/Frameworks/R.framework/Resources
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 = /usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/torrisi/abin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ 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/torrisi/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11
which brew : /usr/local/bin/brew
brew version : Homebrew 2.4.2
-- for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
++ found 1 dylib files under '/opt/X11/lib/flat_namespace'
-- found 'libXt' dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
** env var DYLD_LIBRARY_PATH is not set to contain /opt/X11/lib/flat_namespace
(so afni and suma may fail)
========================= summary, please fix: =========================
* AFNI programs show FAILURE
* insufficient data for AFNI bootcamp
* OS X version might be old
* consider setting DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace
and:
[MacBook-Pro:~] torrisi% ls -l /opt/X11/lib/libXt*
-rwxr-xr-x 1 root wheel 698896 Oct 29 2016 /opt/X11/lib/libXt.6.dylib
-rwxr-xr-x 1 root wheel 34224 Oct 29 2016 /opt/X11/lib/libXt.7.dylib
lrwxr-xr-x 1 torrisi wheel 13 Jul 1 10:46 /opt/X11/lib/libXt.dylib -> libXt.6.dylib
-rwxr-xr-x 1 root wheel 71104 Oct 29 2016 /opt/X11/lib/libXtst.6.dylib
lrwxr-xr-x 1 torrisi wheel 15 Jul 1 10:46 /opt/X11/lib/libXtst.dylib -> libXtst.6.dylib
