installation problems w/ Mac OS 15.2

wgraves · January 2, 2025, 11:17pm

Hello AFNI experts,

I tried following your "quick setup" recipe for installing AFNI on Mac OS 12+ (1.1.8. macOS 12+ (Apple Silicon/ARM processor/chip: M1, M2, …) — AFNI, SUMA and FATCAT: v24.3.10), but it's not working for me. When I get to the end (step E) if fails to compile. Here's what it shows:

wgraves@Mac:~% 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  5072  100  5072    0     0  39438      0 --:--:-- --:--:-- --:--:-- 39625
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
if ( ! -f /Users/wgraves/abin/init_user_dotfiles.py ) then
echo -- skipping install of AFNI anyos_text_atlas
-- skipping install of AFNI anyos_text_atlas
endif
echo ++ setting up user dotfiles
++ setting up user dotfiles
/Users/wgraves/abin/init_user_dotfiles.py -shell_list bash zsh tcsh -do_updates path apsearch -dir_bin /Users/wgraves/abin
-- 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 4 dot files

which init_user_dotfiles.py
/Users/wgraves/abin/init_user_dotfiles.py
if ( 0 ) then
if ( arm64 == x86_64 ) then
set package = macos_13_ARM
endif
echo ++ compiling AFNI package macos_13_ARM
++ compiling AFNI package macos_13_ARM
echo ++ running: build_afni.py -build_root ~/afni_build -package macos_13_ARM
++ running: build_afni.py -build_root ~/afni_build -package macos_13_ARM
build_afni.py -build_root /Users/wgraves/afni_build -package macos_13_ARM

-- build_afni.py, version 0.14, November 17, 2024
-- current AFNI: AFNI_24.3.10, anyos_text, Dec 17 2024
-- cleaning old build root dir, /Users/wgraves/afni_build
-- preparing build_root dir, /Users/wgraves/afni_build
-- have default git tag LAST_TAG, will checkout AFNI_24.3.10
-- checking out git tag AFNI_24.3.10
-- using repo branch (detached), tag AFNI_24.3.10
-- removing old atlas dir, prev/afni_atlases_dist
** error: failed run_cmd(p): rmtree prev/afni_atlases_dist

-- shell/system command history is in:
      /Users/wgraves/afni_build/hist_commands.txt

++ screen text history is in:
      /Users/wgraves/afni_build/hist_messages.txt

rehash
if ( ! 1 ) then
echo -- already have R_LIBS=/Users/wgraves/sw/R-4.3.1
-- already have R_LIBS=/Users/wgraves/sw/R-4.3.1
endif
if ( ! -d /Users/wgraves/sw/R-4.3.1 ) then
echo -- already have directory /Users/wgraves/sw/R-4.3.1
-- already have directory /Users/wgraves/sw/R-4.3.1
endif
if ( -f /opt/X11/bin/Xvfb ) then
which Xvfb
if ( 0 ) then
echo -- already have Xvfb in PATH
-- already have Xvfb in PATH
endif
else
if ( ! -f ~/.afnirc ) then
if ( ! -f ~/.sumarc ) then
echo ++ running: suma -update_env
++ running: suma -update_env
suma -update_env
suma: Command not found.

And of course running "afni_system_check.py -check_all" doesn't go well either, giving this output:

-------------------------------- general ---------------------------------
architecture:         64bit Mach-O
cpu type:             arm64
system:               Darwin
release:              24.2.0
version:              Darwin Kernel Version 24.2.0: Fri Dec  6 18:51:28 PST 2024; root:xnu-11215.61.5~2/RELEASE_ARM64_T8112
distribution:         15.2
number of CPUs:       8
apparent login shell: tcsh
shell RC file:        .tcshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           :
                     : 
AFNI_version.txt     : AFNI_24.3.10, anyos_text, Dec 17 2024, local
which python         : /Users/wgraves/miniconda3/envs/py3_afni_tiny/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  : 2 
      /Users/wgraves/miniconda3/envs/py3_afni_tiny/bin/python3.13
      /opt/homebrew/Cellar/python@3.13/3.13.1/Frameworks/Python.framework/Versions/3.13/bin/python3.13
    python2 : 0 
    python3 : 3 
      /opt/homebrew/Cellar/python@3.13/3.13.1/Frameworks/Python.framework/Versions/3.13/bin/python3.13
      /Users/wgraves/miniconda3/envs/py3_afni_tiny/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
        

------------------------ 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 : /Users/wgraves/miniconda3/envs/py3_afni_tiny/lib/python3.13/site-packages/matplotlib/pyplot.py
   matplotlib version : 3.9.2

++ module loaded: flask
   module file : /Users/wgraves/miniconda3/envs/py3_afni_tiny/lib/python3.13/site-packages/flask/__init__.py
   flask version : 3.0.3

++ module loaded: flask_cors
   module file : /Users/wgraves/miniconda3/envs/py3_afni_tiny/lib/python3.13/site-packages/flask_cors/__init__.py
   flask_cors version : 3.0.10

-------------------------------- env vars --------------------------------
PATH                       = /opt/homebrew/bin:/opt/homebrew/sbin:/Users/wgraves/miniconda3/envs/py3_afni_tiny/bin:/Users/wgraves/miniconda3/condabin:/usr/local/sbin:/opt/homebrew/bin/brew:/Applications:/Users/wgraves/pipestat/bin:/Users/wgraves/scripts/execs:/usr/local/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:/Library/TeX/texbin:/Users/wgraves/abin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin

PYTHONPATH                 = 
R_LIBS                     = /Users/wgraves/sw/R-4.3.1
LD_LIBRARY_PATH            = 
DYLD_LIBRARY_PATH (sub-shell) = /opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) = 
CONDA_SHLVL                = 1
CONDA_DEFAULT_ENV          = py3_afni_tiny
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 2 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 4.4.14


=========================  summary, please fix:  =========================
*  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

I'd appreciate any help you can give!

Best,
Will

rickr · January 3, 2025, 3:04pm

Hi Will,

Maybe there is a permission issue in the build tree. What is the output from:

ls -l ~/afni_build
ls -l ~/afni_build/prev

Thanks,
-rick

wgraves · January 3, 2025, 6:19pm

Thanks for getting back to me, Rick. Here's the output from ls -l ~/afni_build

total 3872
drwxr-xr-x  48 20892    _lpoperator     1536 May 10  2024 afni_atlases_dist
drwxr-xr-x   3 wgraves  staff             96 Dec 31 17:31 git
-rw-r--r--   1 wgraves  staff            517 Jan  2 18:10 hist_commands.txt
-rw-r--r--   1 wgraves  staff            648 Jan  2 18:10 hist_messages.txt
-rw-r--r--   1 root     staff        1972601 Jan  2 15:45 niivue_afni.umd.js
drwxr-xr-x   7 wgraves  staff            224 Jan  2 18:10 prev

And from ls -l ~/afni_build/prev

total 3872
drwxr-xr-x    48 20892    _lpoperator     1536 May 10  2024 afni_atlases_dist
drwxr-xr-x  1774 wgraves  staff          56768 Jan  2 15:47 build_src
-rw-r--r--     1 wgraves  staff            517 Jan  2 17:49 hist_commands.txt
-rw-r--r--     1 wgraves  staff            648 Jan  2 17:49 hist_messages.txt
-rw-r--r--     1 root     staff        1972601 Jan  2 15:27 niivue_afni.umd.js

Best,
Will

rickr · January 3, 2025, 8:33pm

I think you must have run build_afni.py using sudo at some point, which means you might have run that b_user script via sudo. Look for root owned files under your home directory and change them to be owned by you. For example, that afni_build tree should be fixed:

sudo chown -R wgraves:staff ~/afni_build

-rick

wgraves · January 3, 2025, 10:24pm

Thanks, Rick, that did the trick! It compiled and passed all the AFNI system checks except for several R packages that didn't install. But Paul Taylor's helpful advice for manually installing them in this thread (missing R packages (see rPkgsInstall) - #3 by osman) fixed those remaining issues.

Thanks again,
Will

rickr · January 6, 2025, 3:00pm

That's great. It looks like rPkgsInstall does not have an option for including dependencies, as that other command shows. Such an option should probably be added.

Thanks,

-rick