Followed the instructions from the AFNI installation website:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_macOS_12_Silicon.html
Summary of errors:
========================= summary, please fix: =========================
- just be aware: login shell 'zsh', but our code examples use 'tcsh'
- missing program: afni
- failure under initial "AFNI and related program tests"
- AFNI programs show FAILURE
- missing program: Xvfb
- missing R packages (see rPkgsInstall)
- please run: cp /Users/menonsn/abin/AFNI.afnirc ~/.afnirc
- please run: "suma -update_env" for .sumarc
- please run: apsearch -update_all_afni_help
- insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages) - possibly missing atlases
Full out.ASC.txt:
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: arm
system: Darwin
release: 22.6.0
version: Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020
distribution: 13.5
number of CPUs: 12
apparent login shell: zsh
shell RC file: .zshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni :
:
AFNI_version.txt : AFNI_23.3.02, anyos_text, Oct 17 2023, local
which python : /usr/local/bin/python
python version : 3.11.6
which R : /usr/local/bin/R
R version : R version 4.3.1 (aarch64-apple-darwin20)
instances of various programs found in PATH:
afni : 0
R : 1 (/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/bin/R)
python : 1 (/opt/homebrew/Cellar/python@3.11/3.11.6/Frameworks/Python.framework/Versions/3.11/bin/python3.11)
python2 : 0
python3 : 2
/usr/bin/python3
/Library/Frameworks/Python.framework/Versions/3.11/bin/python3.11
** have python3 but not python2
testing ability to start various programs...
afni : FAILURE
/bin/sh: afni: command not found
suma : FAILURE
/bin/sh: suma: command not found
3dSkullStrip : FAILURE
/bin/sh: 3dSkullStrip: command not found
3dAllineate : FAILURE
/bin/sh: 3dAllineate: command not found
3dRSFC : FAILURE
/bin/sh: 3dRSFC: command not found
SurfMesh : FAILURE
/bin/sh: SurfMesh: command not found
3dClustSim : FAILURE
/bin/sh: 3dClustSim: command not found
uber_subject.py : success
3dMVM : FAILURE
setenv: Too many arguments.
------------------------ dependent program tests -------------------------
checking for dependent programs...
which tcsh : /bin/tcsh
which Xvfb :
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
setenv: Too many arguments.
R RHOME : /Library/Frameworks/R.framework/Resources
------------------------------ python libs -------------------------------
++ module loaded: matplotlib.pyplot
module file : /opt/homebrew/lib/python3.11/site-packages/matplotlib/pyplot.py
matplotlib version : 3.8.0
-- python binaries under /usr/local/bin:
/usr/local/bin/python (sym link to /opt/homebrew/Cellar/python@3.11/3.11.6/Frameworks/Python.framework/Versions/3.11/bin/python3.11)
/usr/local/bin/python3 (sym link to /Library/Frameworks/Python.framework/Versions/3.11/bin/python3.11)
-------------------------------- env vars --------------------------------
PATH = /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/local/jamf/bin:/opt/homebrew/opt/python@3.11/libexec/bin:/opt/homebrew/opt/python@3.11/libexec/bin:/Users/menonsn/abin
PYTHONPATH =
R_LIBS = /Users/menonsn/sw/R-4.3.1
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) =
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
----------------------------- eval dot files -----------------------------
----------- AFNI $HOME files -----------
.afnirc : missing
.sumarc : missing
.afni/help/all_progs.COMP : missing
--------- shell startup files ----------
-- good: .tcshrc seems to contain 'source .cshrc'
-- considered operations: path, apsearch
-- note: followers should not need edits, so edit flags should be 0
(have 1 follower(s), which can be ignored)
no modifications needed across 3 dot files
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : did not find TT_N27+tlrc
------------------------------ OS specific -------------------------------
XQuartz version : 2.8.5
** no package manager found (okay for bootcamp)
========================= summary, please fix: =========================
- just be aware: login shell 'zsh', but our code examples use 'tcsh'
- missing program: afni
- failure under initial "AFNI and related program tests"
- AFNI programs show FAILURE
- missing program: Xvfb
- missing R packages (see rPkgsInstall)
- please run: cp /Users/menonsn/abin/AFNI.afnirc ~/.afnirc
- please run: "suma -update_env" for .sumarc
- please run: apsearch -update_all_afni_help
- insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages) - possibly missing atlases