AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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Cesar Caballero Gaudes
September 28, 2022 01:00PM
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


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Subject Author Posted

error loading R_io.so

Cesar Caballero Gaudes September 28, 2022 01:00PM

Re: error loading R_io.so

rick reynolds September 28, 2022 08:25PM

Re: error loading R_io.so

Cesar Caballero Gaudes September 29, 2022 06:54PM