Installation issues on an M3 Sequoia 15.1.1

Dear experts

Wonder whether you could assist with the follow, greatly appreciated. Below the output of afni_system_check.py -check_all:

-------------------------------- general ---------------------------------
architecture: 64bit Mach-O
cpu type: arm64
system: Darwin
release: 24.1.0
version: Darwin Kernel Version 24.1.0: Thu Oct 10 21:02:26 PDT 2024; root:xnu-11215.41.3~2/RELEASE_ARM64_T8122
distribution: 15.1.1
number of CPUs: 8
user: miguel
apparent login shell: zsh
shell RC file: .zshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni :
:
AFNI_version.txt : AFNI_25.0.02, anyos_text, Feb 01 2025, local
which python : /opt/homebrew/opt/python/libexec/bin/python
python version : 3.13.1
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@3.13/3.13.1/Frameworks/Python.framework/Versions/3.13/bin/python3.13)
python2 : 0
python3 : 2
/opt/homebrew/Cellar/python@3.13/3.13.1/Frameworks/Python.framework/Versions/3.13/bin/python3.13
/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

rPkgsInstall         : FAILURE

------------------------ dependent program tests -------------------------
checking for dependent programs...

which tcsh : /bin/tcsh
tcsh version : 6.21.00
which Xvfb : /opt/X11/bin/Xvfb

checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE

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

-------------------------------- env vars --------------------------------
PATH = /opt/homebrew/bin:/opt/homebrew/sbin:/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:/Applications/quarto/bin:/opt/homebrew/opt/python/libexec/bin:/Users/miguel/abin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin

PYTHONPATH =
R_LIBS = /Users/miguel/sw/R-4.3.1
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) =
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
CONDA_SHLVL =
CONDA_DEFAULT_ENV =
CC =

----------------------------- eval dot files -----------------------------

----------- AFNI $HOME files -----------

.afnirc                   : found
.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

which brew : /opt/homebrew/bin/brew
brew version : Homebrew 4.4.19

which git : /usr/bin/git
git version : git version 2.39.3 (Apple Git-146)
which gcc : /usr/bin/gcc
gcc version : Apple clang version 15.0.0 (clang-1500.3.9.4)

brew gcc(s) : /opt/homebrew/bin/gcc-13
/opt/homebrew/bin/gcc-14
CommandLineTools SDK : MacOSX14.4.sdk

========================= 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)
  • 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
  • insufficient data for AFNI bootcamp
    (see "Prepare for Bootcamp" on install pages)
  • possibly missing atlases

Many thanks
miguel

According to brew doctor, CommandLineTools needed updating. This seemed to have fixed the problem :)