Hi,
I've tried the various solutions offered in the forum, but can't seem to get AFNI to install.
Here's the output from afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: i386
system: Darwin
release: 23.2.0
version: Darwin Kernel Version 23.2.0: Wed Nov 15 21:53:18 PST 2023; root:xnu-10002.61.3~2/RELEASE_ARM64_T6000
distribution: 10.16
number of CPUs: 10
apparent login shell: zsh
shell RC file: .zshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni :
:
AFNI_version.txt : AFNI_24.1.17, anyos_text, Jun 06 2024, local
which python : /opt/anaconda3/bin/python
python version : 3.11.7
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 : 4
/opt/anaconda3/bin/python3.11
/Applications/fsl/bin/python3.11
/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
/opt/homebrew/Cellar/python@3.12/3.12.4/Frameworks/Python.framework/Versions/3.12/bin/python3.12
python2 : 1 (/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python3 : 5
/opt/anaconda3/bin/python3.11
/opt/homebrew/Cellar/python@3.12/3.12.4/Frameworks/Python.framework/Versions/3.12/bin/python3.12
/Library/Frameworks/Python.framework/Versions/3.12/bin/python3.12
/Applications/fsl/bin/python3.11
/usr/bin/python3
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
Error in library(data.table) : there is no package called ‘data.table’
Calls: source ... suppressPackageStartupMessages -> withCallingHandlers -> library
Execution halted
------------------------ dependent program tests -------------------------
checking for dependent programs...
which tcsh : /opt/homebrew/bin/tcsh
tcsh version : 6.24.13
which Xvfb : /opt/X11/bin/Xvfb
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
R RHOME : /Library/Frameworks/R.framework/Resources
------------------------------ python libs -------------------------------
++ module loaded: matplotlib.pyplot
module file : /opt/anaconda3/lib/python3.11/site-packages/matplotlib/pyplot.py
matplotlib version : 3.8.0
++ module loaded: flask
module file : /opt/anaconda3/lib/python3.11/site-packages/flask/init.py
flask version : 2.2.5
** failed to load module flask_cors
-- flask_cors is not required, but is desirable
-- python binaries under /usr/local/bin:
/usr/local/bin/python (sym link to /Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
/usr/local/bin/python3 (sym link to /Library/Frameworks/Python.framework/Versions/3.12/bin/python3.12)
/usr/local/bin/python2 (sym link to /Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
/usr/local/bin/python2.7 (sym link to /Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
-------------------------------- env vars --------------------------------
PATH = /opt/anaconda3/bin:/opt/anaconda3/condabin:/opt/homebrew/bin:/opt/homebrew/sbin:/Library/Frameworks/Python.framework/Versions/3.12/bin:/Applications/freesurfer/7.2.0/bin:/Applications/freesurfer/7.2.0/fsfast/bin:/Applications/fsl/bin:/Applications/fsl/share/fsl/bin:/Applications/freesurfer/7.2.0/mni/bin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/Applications/fsl/share/fsl/bin:/Applications/fsl/share/fsl/bin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/X11/bin:/Library/Apple/usr/bin:/Applications/VMware Fusion.app/Contents/Public:/Users/moayedilab/abin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin
PYTHONPATH (sub-shell) =
R_LIBS = /Users/moayedilab/sw/R-4.3.1
LD_LIBRARY_PATH (sub-shell) =
DYLD_LIBRARY_PATH (sub-shell) =
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
CONDA_SHLVL = 1
CONDA_DEFAULT_ENV = base
----------------------------- eval dot files -----------------------------
----------- AFNI $HOME files -----------
.afnirc : found
.sumarc : missing
.afni/help/all_progs.COMP : missing
--------- shell startup files ----------
-- good: .cshrc seems to contain 'source .tcshrc'
-- 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
which brew : /opt/homebrew/bin/brew
brew version : Homebrew 4.3.5
========================= 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 R packages (see rPkgsInstall)
- 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
- consider installing gcc under homebrew
- consider installing glib under homebrew
Thanks,
Massieh