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