Hi,
I'm new to AFNI and having some problems with the install on a mac M3 running Sonoma. There's likely to be quite a few things going wrong I'm sure, but below is the output:
I appreciate any help!
afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: arm
system: Darwin
release: 23.1.0
version: Darwin Kernel Version 23.1.0: Mon Oct 9 21:33:00 PDT 2023; root:xnu-10002.41.9~7/RELEASE_ARM64_T6031
distribution: 14.1
number of CPUs: 14
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni :
:
AFNI_version.txt : AFNI_24.0.06, anyos_text, Feb 08 2024, local
which python : /Users/LisanneJ/miniconda3/bin/python
python version : 3.11.5
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 (/Users/LisanneJ/miniconda3/bin/python3.11)
python2 : 0
python3 : 3
/Users/LisanneJ/miniconda3/bin/python3.11
/usr/local/Cellar/python@3.8/3.8.5/Frameworks/Python.framework/Versions/3.8/bin/python3.8
/usr/bin/python3
** 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 -------------------------------
** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is required
** failed to load module flask
-- flask is not required, but is desirable
** failed to load module flask_cors
-- flask_cors is not required, but is desirable
-- python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /usr/local/Cellar/python@3.8/3.8.5/Frameworks/Python.framework/Versions/3.8/bin/python3.8)
/usr/local/bin/python3.8 (sym link to /usr/local/Cellar/python@3.8/3.8.5/Frameworks/Python.framework/Versions/3.8/bin/python3.8)
-------------------------------- env vars --------------------------------
PATH = /Users/LisanneJ/miniconda3/bin:/Users/LisanneJ/miniconda3/condabin:/Users/LisanneJ/dcm2niix/build/bin:/Users/LisanneJ/.local/bin:/usr/local/fsl/share/fsl/bin:/usr/local/fsl/share/fsl/bin:/usr/local/bin/python3:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Users/LisanneJ/abin:/Applications/workbench/bin_macosx64
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = :/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
----------------------------- 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)
dot file test : want 2 modifications across 3 files:
file path flatdir apsearch follower
--------------- ---- ------- -------- --------
.cshrc 0 0 0 1
.tcshrc 1 0 1 0
.bashrc 0 0 0 0
------------------------------ 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 .
------------------------------ OS specific -------------------------------
XQuartz version : 2.8.5
which brew : /usr/local/bin/brew
brew version : Homebrew 2.5.2
++ found valid link /usr/local/lib/libglib-2.0.dylib
to ../Cellar/glib/2.64.5/lib/libglib-2.0.dylib
========================= summary, please fix: =========================
- just be aware: login shell 'bash', 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)
- python library matplotlib is required
(see AFNI install docs for details) - please run: "suma -update_env" for .sumarc
- please run: apsearch -update_all_afni_help
- dot file test : want 2 modifications across 3 files:
- insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages) - consider installing gcc under homebrew