AFNI Installation Issue (Apple MacBook Air M2, macOS 13.6.9)

minkim · August 28, 2024, 9:43am

Hi everyone, I’m new to AFNI and am running into some permission errors during the installation process. I’ve included the output from the check-up below. Could someone please assist me with this issue?

<user>@dhcp-10-8-032-137 ~ % cd abin
<user>@dhcp-10-8-032-137 abin % python afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture:         64bit 
cpu type:             arm (uname -m == arm64)
system:               Darwin
release:              22.6.0
version:              Darwin Kernel Version 22.6.0: Mon Jun 24 01:20:40 PDT 2024; root:xnu-8796.141.3.706.2~1/RELEASE_ARM64_T8112
distribution:         13.6.9
number of CPUs:       8
apparent login shell: zsh
shell RC file:        .zshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           :
                     : 
AFNI_version.txt     : AFNI_24.2.03, anyos_text, Aug 20 2024, local
which python         : /opt/homebrew/anaconda3/bin/python
python version       : 3.12.2
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  : 2 
      /opt/homebrew/anaconda3/bin/python3.12
      /opt/homebrew/Cellar/python@3.12/3.12.5/Frameworks/Python.framework/Versions/3.12/bin/python3.12
    python2 : 0 
    python3 : 3 
      /opt/homebrew/anaconda3/bin/python3.12
      /opt/homebrew/Cellar/python@3.12/3.12.5/Frameworks/Python.framework/Versions/3.12/bin/python3.12
      /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
        Error in library(data.table) : there is no package called ‘data.table’
        Calls: source ... suppressPackageStartupMessages -> withCallingHandlers -> library
        Execution halted

have failures, testing programs under implied /Users/<user>/abin...
    afni                 : FAILURE
        /bin/sh: /Users/<user>/abin/afni: No such file or directory
    suma                 : FAILURE
        /bin/sh: /Users/<user>/abin/suma: No such file or directory
    3dSkullStrip         : FAILURE
        /bin/sh: /Users/<user>/abin/3dSkullStrip: No such file or directory
    3dAllineate          : FAILURE
        /bin/sh: /Users/<user>/abin/3dAllineate: No such file or directory
    3dRSFC               : FAILURE
        /bin/sh: /Users/<user>/abin/3dRSFC: No such file or directory
    SurfMesh             : FAILURE
        /bin/sh: /Users/<user>/abin/SurfMesh: No such file or directory
    3dClustSim           : FAILURE
        /bin/sh: /Users/<user>/abin/3dClustSim: No such file or directory
    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           : /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 -------------------------------

++ module loaded: matplotlib.pyplot
   module file : /opt/homebrew/anaconda3/lib/python3.12/site-packages/matplotlib/pyplot.py
   matplotlib version : 3.8.4

++ module loaded: flask
   module file : /opt/homebrew/anaconda3/lib/python3.12/site-packages/flask/__init__.py
   flask version : 3.0.3

** failed to load module flask_cors
-- flask_cors is not required, but is desirable

-------------------------------- env vars --------------------------------
PATH                       = /opt/homebrew/anaconda3/bin:/Users/<user>/.local/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/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/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin:/Users/<user>/abin/

PYTHONPATH                 = 
R_LIBS                     = 
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                   : missing
    .sumarc                   : missing
    .afni/help/all_progs.COMP : missing

--------- shell startup files ----------

   -- no .tcshrc, will create one as a follower of .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)
   
   dot file test : want 3 modifications across 3 files:
   
      file             path  flatdir  apsearch        follower
      ---------------  ----  -------  --------        --------
      .cshrc           1     0        1               0     
      .tcshrc          0     0        0               1     
      .zshrc           0     0        1               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           : /opt/homebrew/bin/brew
brew version         : Homebrew 4.3.18


=========================  summary, please fix:  =========================
*  CPU differs between python and uname?
*  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
*  consider adding /Users/<user>/abin to your PATH
*  missing R packages (see rPkgsInstall)
*  please run: cp /Users/<user>/abin//AFNI.afnirc ~/.afnirc
*  please run: "suma -update_env" for .sumarc
*  please run: apsearch -update_all_afni_help
*  dot file test : want 3 modifications across 3 files:
*  insufficient data for AFNI bootcamp
   (see "Prepare for Bootcamp" on install pages)
*  consider installing gcc under homebrew
*  consider installing glib under homebrew

<user>@dhcp-10-8-032-137 abin % python init_user_dotfiles.py -test


-- no .tcshrc, will create one as a follower of .cshrc
-- considered operations: path, flatdir, 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 7 modifications across 5 files:

   file             path  flatdir  apsearch        follower
   ---------------  ----  -------  --------        --------
   .bashrc          0     1        0               0     
   .cshrc           1     1        0               0     
   .tcshrc          0     0        0               1     
   .profile         1     1        0               0     
   .zshrc           0     1        1               0     

<user>@dhcp-10-8-032-137 abin % ls -al ~/.tcshrc
ls: /Users/<user>/.tcshrc: No such file or directory

If that matters, I have previously installed several programs including homebrew, anaconda, docker, freesurfer, fmriprep, and R.

My $PATH currently looks like this, if echoed:

/opt/homebrew/anaconda3/bin:/Users/<user>/.local/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/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/homebrew/opt/python/libexec/bin

Thanks!

ptaylor · August 28, 2024, 5:52pm

Hi-

I don't see anything with "abin" in your PATH, so either those AFNI install updates have not been set, or they havebut your shell has not re-read its ~/.*rc command file to know about those updates. I suspect the latter might be the case here. Can you open up a new terminal (so the shell's command file will be read), and run:

afni_system_check.py -check_all

... and then copy+paste that result here?

Also, that command should not need to be run from abin itself. That is a sign of the PATH information not being updated, itself.

--pt

minkim · August 29, 2024, 5:28am

Even if I re-open my terminal, abin doesn't show up in my $PATH.

<user>@dhcp-10-8-032-137 ~ % afni_system_check.py -check_all
zsh: command not found: afni_system_check.py
<user>@dhcp-10-8-032-137 ~ % echo $PATH
/opt/homebrew/anaconda3/bin:/Users/<user>/.local/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/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/homebrew/opt/python/libexec/bin

I think there is an issue with the third installation file. This is the output I get:

<user>@dhcp-10-8-032-137 ~ % tcsh OS_notes.macos_12_ARM_b_user.tcsh
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  3521  100  3521    0     0  22075      0 --:--:-- --:--:-- --:--:-- 22144
set os = `uname -s`
uname -s
if ( 0 ) then
if ( Darwin != Darwin ) then
set cpu = `uname -m`
uname -m
if ( 0 ) then
set rver = `R --version | head -n 1 | cut -d ' ' -f 3`
R --version
cut -d   -f 3
head -n 1
if ( 0 ) then
echo OS    : Darwin
OS    : Darwin
echo CPU   : arm64
CPU   : arm64
echo R ver : 4.3.1
R ver : 4.3.1
echo 

defaults write org.macosforge.xquartz.X11 wm_ffm -bool true
defaults write org.x.X11 wm_ffm -bool true
defaults write com.apple.Terminal FocusFollowsMouse -string YES
curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 53097  100 53097    0     0  85816      0 --:--:-- --:--:-- --:--:-- 85917
tcsh @update.afni.binaries -no_recur -package anyos_text_atlas -bindir /Users/<user>/abin
-- running @update.afni.binaries version 3.24, December 7, 2023
-- no current AFNI package found in path...
-- any downloads will be from https://afni.nimh.nih.gov via wget

-- attempting to install package anyos_text_atlas under
   install dir: /Users/<user>/abin...
-- have install dir
++ working in new temp dir, .tmp.install
-- skipping update of @update.afni.binaries
++ downloading test file: wget anyos_text_atlas/AFNI_version.txt ...
--2024-08-28 22:27:54--  https://afni.nimh.nih.gov/pub/dist/bin/anyos_text_atlas/AFNI_version.txt
Resolving afni.nimh.nih.gov (afni.nimh.nih.gov)... 156.40.187.114
Connecting to afni.nimh.nih.gov (afni.nimh.nih.gov)|156.40.187.114|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 42 [text/plain]
Saving to: ‘AFNI_version.txt’

     0K                                                       100% 1.08M=0s

2024-08-28 22:27:55 (1.08 MB/s) - ‘AFNI_version.txt’ saved [42/42]

++ no update needed
/Users/<user>/abin/init_user_dotfiles.py -shell_list bash zsh tcsh -do_updates path apsearch -dir_bin /Users/<user>/abin
-- no .tcshrc, will create one as a follower of .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)

dot file mods : want 5 modifications across 4 files:

   file             path  flatdir  apsearch        follower
   ---------------  ----  -------  --------        --------
   .bashrc          1     0        0               0     
   .zshrc           1     0        1               0     
   .cshrc           1     0        1               0     
   .tcshrc          0     0        0               1     

-- backing up .bashrc to .bashrc.adot.bak
** failed to open text file '.bashrc' for writing
** error: failed to append shell text to file .bashrc

How should I append .zshrc or .bashrc in order to make things work?