Hello,
I’m having issues with R programs because R_io.so is not loading. I’m using a MacBook pro M1 Max and zsh.
Error in dyn.load(ll) :
unable to load shared object '/Users/ccg/abin/R_io.so':
dlopen(/Users/ccg/abin/R_io.so, 0x0006): tried: '/Users/ccg/abin/R_io.so' (mach-o file, but is an incompatible architecture (have (x86_64), need (arm64e)))
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
Ejecución interrumpida
Do you have any suggestions? Thanks very much in advance,
Best wishes,
Cesar
Ps. Below is the output of afni_system_check.py -check_all
afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 21.6.0
version: Darwin Kernel Version 21.6.0: Sat Jun 18 17:07:22 PDT 2022; root:xnu-8020.140.41~1/RELEASE_ARM64_T6000
distribution: 12.5
number of CPUs: 10
apparent login shell: zsh
shell RC file: .zshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/ccg/abin/afni
afni version : Precompiled binary macos_10.12_local: Sep 18 2022
: AFNI_22.2.12 ‘Marcus Aurelius’
AFNI_version.txt : AFNI_22.2.12, macos_10.12_local, Sep 18 2022
which python : /Users/ccg/.pyenv/versions/3.9.10/bin/python
python version : 3.9.10
which R : /usr/local/bin/R
R version : R version 4.1.3 (2022-03-10) – “One Push-Up”
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/Users/ccg/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/bin/R)
python : 2
/Users/ccg/.pyenv/versions/3.9.10/bin/python3.9
/Users/ccg/.pyenv/shims/python
python2 : 0
python3 : 4
/Users/ccg/.pyenv/versions/3.9.10/bin/python3.9
/Users/ccg/.pyenv/shims/python3
/opt/homebrew/Cellar/python@3.9/3.9.12/Frameworks/Python.framework/Versions/3.9/bin/python3.9
/usr/bin/python3
** have python3 but not python2
testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
3dMVM : FAILURE
Error in dyn.load(ll) :
unable to load shared object ‘/Users/ccg/abin/R_io.so’:
dlopen(/Users/ccg/abin/R_io.so, 0x0006): tried: ‘/Users/ccg/abin/R_io.so’ (mach-o file, but is an incompatible architecture (have (x86_64), need (arm64e)))
Calls: source … withVisible → eval → eval → set_R_io → dyn.load
Ejecución interrumpida
checking for R packages…
rPkgsInstall -pkgs ALL -check : success
R RHOME : /Library/Frameworks/R.framework/Resources
checking for $HOME files…
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
** failed to load module PyQt4
– PyQt4 is no longer needed for an AFNI bootcamp
++ module loaded: matplotlib.pyplot
module file : /Users/ccg/.pyenv/versions/3.9.10/lib/python3.9/site-packages/matplotlib/pyplot.py
matplotlib version : 3.5.2
-------------------------------- env vars --------------------------------
PATH = /Users/ccg/.pyenv/versions/3.9.10/bin:/opt/homebrew/Cellar/pyenv/2.2.5/libexec:/opt/homebrew/Cellar/pyenv/2.2.5/plugins/python-build/bin:/usr/local/opt/python/libexec/bin:/usr/local/bin:/Users/ccg/Downloads/y/bin:/Users/ccg/.pyenv/shims:/Users/ccg/.pyenv/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/X11/bin:/Library/Apple/usr/bin:/Applications/Visual Studio Code.app/Contents/Resources/app/bin:/usr/local/texlive/2020/bin/x86_64-darwin:/Users/ccg/abin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME/cesar_data/data (948584M Avail)
top history: 19 Mar 2015 [rickr]: enhanced unix_tutorial
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : found afni_handouts under $HOME/cesar_data (948584M Avail)
atlas : found TT_N27+tlrc under /Users/ccg/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.8.1
which brew : /opt/homebrew/bin/brew
brew version : Homebrew 3.4.7
– for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
++ found 1 dylib files under ‘/opt/X11/lib/flat_namespace’
– found ‘libXt’ dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
** env var DYLD_LIBRARY_PATH is not set to contain /opt/X11/lib/flat_namespace
(so afni and suma may fail)
========================= summary, please fix: =========================
- just be aware: login shell ‘zsh’, but our code examples use ‘tcsh’
- AFNI programs show FAILURE
- insufficient data for AFNI bootcamp
(see “Prepare for Bootcamp” on install pages) - OS X version might be old
- consider setting DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace
~ took 2s