AFNI install issues M2

Hi AFNI folk!

I am trying to install AFNI on my new computer (chip Apple M2, OS 13.5, R v4.2.3). I was able to build AFNI ok (I think), but run into hiccups once I get to the rPkgsInstall portion where it's unable to load the shared R_io.so object. The problem seems similar to what was happening here (AFNI install issues on M1 with R-4.2.3) but I tried following the troubleshooting advised and am still getting the same issue, so I'm not sure if I did something wrong or there's something different about my setup.

Here's the output of the AFNI system check. Thanks for any help!

-------------------------------- general ---------------------------------
architecture:         64bit 
cpu type:             arm
system:               Darwin
release:              22.6.0
version:              Darwin Kernel Version 22.6.0: Wed Jul  5 22:17:35 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T8112
distribution:         13.5
number of CPUs:       8
apparent login shell: zsh
shell RC file:        .zshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /Users/ashley/abin/afni
afni version         : Precompiled binary macos_13_ARM_clang: Sep 19 2023 
                     : AFNI_23.2.10 'Marcus Didius Severus Julianus'
AFNI_version.txt     : AFNI_23.2.10, macos_13_ARM_clang, Sep 19 2023, build
which python         : /opt/homebrew/opt/python/libexec/bin/python
python version       : 3.11.5
which R              : /usr/local/bin/R
R version            : R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"

instances of various programs found in PATH:
    afni    : 1   (/Users/ashley/abin/afni)
    R       : 1   (/Library/Frameworks/R.framework/Versions/4.2/Resources/bin/R)
    python  : 1   (/opt/homebrew/Cellar/python@3.11/3.11.5/Frameworks/Python.framework/Versions/3.11/bin/python3.11)
    python2 : 0 
    python3 : 2 
      /opt/homebrew/Cellar/python@3.11/3.11.5/Frameworks/Python.framework/Versions/3.11/bin/python3.11
      /usr/bin/python3

** have python3 but not python2

testing ability to start various programs...
    afni                 : success
    suma                 : success
    3dSkullStrip         : success
    3dAllineate          : success
    3dRSFC               : success
    SurfMesh             : success
    3dClustSim           : success
    uber_subject.py      : success
    3dMVM                : FAILURE
        Error in dyn.load(ll) : 
          unable to load shared object '/Users/ashley/abin/R_io.so':
          dlopen(/Users/ashley/abin/R_io.so, 0x0006): symbol not found in flat namespace '_EDIT_floatize_dataset'
        Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
        Execution halted

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

which tcsh           : /opt/homebrew/bin/tcsh
which Xvfb           : /opt/X11/bin/Xvfb

checking for R packages...
    rPkgsInstall -pkgs ALL -check : FAILURE
        Error in dyn.load(ll) : 
          unable to load shared object '/Users/ashley/abin/R_io.so':
          dlopen(/Users/ashley/abin/R_io.so, 0x0006): symbol not found in flat namespace '_EDIT_floatize_dataset'
        Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
        Execution halted

R RHOME : /Library/Frameworks/R.framework/Resources

------------------------------ python libs -------------------------------

++ module loaded: matplotlib.pyplot
   module file : /opt/homebrew/lib/python3.11/site-packages/matplotlib/pyplot.py
   matplotlib version : 3.7.2

-------------------------------- env vars --------------------------------
PATH = /opt/homebrew/bin:/opt/homebrew/sbin:/Users/ashley/fsl/share/fsl/bin:/Users/ashley/fsl/share/fsl/bin:/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:/Library/Frameworks/R.framework/Resources:/usr/local/gfortran/bin:/usr/local/opt/python/libexec/bin:/Users/ashley/abin:/usr/local/opt/python/libexec/bin

PYTHONPATH = 
R_LIBS = /Users/ashley/sw/R-4.2.3

LD_LIBRARY_PATH = 
DYLD_LIBRARY_PATH (sub-shell) = /opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) = 

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

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

    .afnirc                   : missing
    .sumarc                   : missing
    .afni/help/all_progs.COMP : missing

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

   -- good: .tcshrc seems to contain 'source .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)
   
   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    : found TT_N27+tlrc  under /Users/Ashley/abin

------------------------------ OS specific -------------------------------
XQuartz version      : 2.8.5

which brew           : /opt/homebrew/bin/brew
brew version         : Homebrew >=2.5.0 (shallow or no git repository)

++ found 1 dylib files under '/opt/X11/lib/flat_namespace'
   -- found 'libXt' dylib files:
      /opt/X11/lib/flat_namespace/libXt.6.dylib
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in cur shell 'zsh'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in shell 'tcsh'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace

=========================  summary, please fix:  =========================
*  just be aware: login shell 'zsh', but our code examples use 'tcsh'
*  AFNI programs show FAILURE
*  missing R packages (see rPkgsInstall)
*  please run: cp /Users/ashley/abin/AFNI.afnirc ~/.afnirc
*  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)
*  consider installing gcc under homebrew
*  consider installing glib under homebrew

Please verify that the R version you have installed is the ARM64 (Apple) version. Then can you try deleting the R_io.so in your ~/abin folder and then copying the R_io.so over from the build directory again?

Running the same commands as Rick suggested before will give us more insight:

cd ~/abin
file afni R_io.so

Also would be helpful to see your command for building AFNI and then copying the files over to the ~/abin folder.

Oh wow, that was a simple error. I did have the wrong (Intel) version of R installed. I was following along with this https://github.com/afni/afni/blob/master/src/other_builds/OS_notes.macos_12_x86_64_a_admin.txt and missed that I needed to change the R version download/install.

Thanks so much!

1 Like

Oh sorry, I thought that mac installer package was universal!
I will change those instructions, thanks!

  • rick
1 Like