Hi Rick,
Many thanks for getting back regarding this issue. I am using a M1 mac with macOS Big Sur (version 11.2) installed.
I rebooted my machine after running the command below:
cp $HOME/abin/AFNI.afnirc $HOME/.afnirc
suma -update_env
Of note, I did not run the curl command. Therefore, I am wondering whether it might have something to do with this.
Concerning XQuartz and R, I did install both of them and selected R version 3.6.3 as recommended. I can see both of them in my Applications' directory.
Please find below the full output from afni_system_check.py.
Many thanks!
Claudie
bash-3.2$ 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: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/claudie/abin/afni
afni version : dyld: Library not loaded: /opt/X11/lib/libXp.6.dylib
:
AFNI_version.txt : AFNI_21.0.12, macos_10.12_local, Feb 25 2021
which python : /opt/anaconda3/bin/python
python version : 3.8.5
which R :
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/Users/claudie/abin/afni)
R : 0
python : 2
/opt/anaconda3/bin/python3.8
/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 : 2
/opt/anaconda3/bin/python3.8
/usr/bin/python3
testing ability to start various programs...
afni : FAILURE
dyld: Library not loaded: /opt/X11/lib/libXp.6.dylib
Referenced from: /Users/claudie/abin/afni
Reason: image not found
suma : FAILURE
dyld: Library not loaded: /opt/X11/lib/libXp.6.dylib
Referenced from: /Users/claudie/abin/suma
Reason: image not found
3dSkullStrip : FAILURE
dyld: Library not loaded: /opt/X11/lib/libXp.6.dylib
Referenced from: /Users/claudie/abin/3dSkullStrip
Reason: image not found
uber_subject.py : success
3dAllineate : FAILURE
dyld: Library not loaded: /opt/X11/lib/libXp.6.dylib
Referenced from: /Users/claudie/abin/3dAllineate
Reason: image not found
3dRSFC : FAILURE
dyld: Library not loaded: /opt/X11/lib/libXp.6.dylib
Referenced from: /Users/claudie/abin/3dRSFC
Reason: image not found
SurfMesh : FAILURE
dyld: Library not loaded: /opt/X11/lib/libXp.6.dylib
Referenced from: /Users/claudie/abin/SurfMesh
Reason: image not found
3dClustSim : FAILURE
dyld: Library not loaded: /opt/X11/lib/libXp.6.dylib
Referenced from: /Users/claudie/abin/3dClustSim
Reason: image not found
3dMVM : success
checking for R packages...
rPkgsInstall -pkgs ALL -check : success
R RHOME : R: Command not found.
checking for $HOME files...
.afnirc : found
.sumarc : missing
.afni/help/all_progs.COMP : missing
------------------------------ python libs -------------------------------
** failed to load module PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp
++ module loaded: matplotlib.pyplot
module file : /opt/anaconda3/lib/python3.8/site-packages/matplotlib/pyplot.py
-------------------------------- env vars --------------------------------
PATH = /opt/anaconda3/bin:/opt/anaconda3/condabin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/claudie/abin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = :/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/claudie/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.8.0_rc2
** no package manager found (okay for bootcamp)
++ 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 'bash'...
++ found evar DYLD_LIBRARY_PATH = :/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
========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
* failure under initial "AFNI and related program tests"
* AFNI programs show FAILURE
* please run: "suma -update_env" for .sumarc
* please run: apsearch -update_all_afni_help
* insufficient data for AFNI bootcamp
Claudie
