I have installed AFNI on a Macbook running version 10.14 of OSX and can't get 3dMVM to work. I've reinstalled it a few times using R versions 3.4.1, 3.5.3, 3.6.3, and 4.0.0 with no success.
Here are is the output from the commands listed here [
afni.nimh.nih.gov]
(1)
[L2174:~] kburrows% otool -L `@GetAfniBin`/R_io.so
/Users/kburrows/abin/R_io.so:
R_io.so (compatibility version 0.0.0, current version 0.0.0)
/sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib (compatibility version 3.6.0, current version 3.6.3)
/sw/lib/libjpeg.9.dylib (compatibility version 13.0.0, current version 13.0.0)
/sw/lib/libXt.6.dylib (compatibility version 7.0.0, current version 7.0.0)
/opt/X11/lib/libXft.2.dylib (compatibility version 6.0.0, current version 6.2.0)
/opt/X11/lib/libfontconfig.1.dylib (compatibility version 11.0.0, current version 11.2.0)
/sw/lib/libpng16.16.dylib (compatibility version 54.0.0, current version 54.0.0)
/sw/lib/libiconv.2.dylib (compatibility version 9.0.0, current version 9.1.0)
/opt/X11/lib/libXmu.6.dylib (compatibility version 9.0.0, current version 9.0.0)
/opt/X11/lib/libXp.6.dylib (compatibility version 9.0.0, current version 9.0.0)
/opt/X11/lib/libXpm.4.dylib (compatibility version 16.0.0, current version 16.0.0)
/opt/X11/lib/libXext.6.dylib (compatibility version 11.0.0, current version 11.0.0)
/opt/X11/lib/libX11.6.dylib (compatibility version 10.0.0, current version 10.0.0)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.8)
/sw/lib/libexpat.1.dylib (compatibility version 8.0.0, current version 8.10.0)
/sw/lib/python2.7/config/libpython2.7.dylib (compatibility version 2.7.0, current version 2.7.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1238.60.2)
/sw/lib/libintl.8.dylib (compatibility version 10.0.0, current version 10.6.0)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1349.8.0)
/sw/lib/gcc7/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
(2)
> first.in.path <- function(file)
{ + ff <- paste(strsplit(Sys.getenv('PATH'),':')[[1]],'/', file, sep='') + ff<-ff[lapply(ff,file.exists)==TRUE]; + #cat('Using ', ff[1],'\n'); + return(gsub('//','/',ff[1], fixed=TRUE)) + }
> source(first.in.path('AFNIio.R'))
oo Warning:
Failed to load R_io.so with this error message:
Error in dyn.load(ll) :
unable to load shared object '/Users/kburrows/abin/R_io.so':
dlopen(/Users/kburrows/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
Referenced from: /Users/kburrows/abin/R_io.so
Reason: image not found
>
> (ll <- find.in.path('R_io.so'))
[1] "/Users/kburrows/abin/R_io.so"
> dyn.load(ll)
Error in dyn.load(ll) :
unable to load shared object '/Users/kburrows/abin/R_io.so':
dlopen(/Users/kburrows/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
Referenced from: /Users/kburrows/abin/R_io.so
Reason: image not found
(3)
MacOS Mojave 10.14.6, 64-bit
(4)
Precompiled binary macos_10.12_local: Jun 3 2020 (Version AFNI_20.1.13 'Otho')
(5)
R version 4.0.0 (2020-04-24) – "Arbor Day"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
Additionally, here is the output from afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 18.7.0
version: Darwin Kernel Version 18.7.0: Mon Apr 27 20:09:39 PDT 2020; root:xnu-4903.278.35~1/RELEASE_X86_64
distribution: unknown Darwin
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/kburrows/abin/afni
afni version : Precompiled binary macos_10.12_local: Jun 3 2020
: AFNI_20.1.13 'Otho'
AFNI_version.txt : AFNI_20.1.13, macos_10.12_local, Jun 03 2020
which python : /usr/bin/python
python version : 2.7.16
which R : /usr/local/bin/R
R version : R version 4.0.0 (2020-04-24) -- "Arbor Day"
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/Users/kburrows/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/4.0/Resources/bin/R)
python : 1 (/usr/bin/python)
python2 : 0
python3 : 0
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/kburrows/abin/R_io.so':
dlopen(/Users/kburrows/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
Referenced from: /Users/kburrows/abin/R_io.so
Reason: image not found
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
Execution halted
checking for R packages...
rPkgsInstall -pkgs ALL -check : success
R RHOME : /Library/Frameworks/R.framework/Resources
checking for $HOME files...
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
** failed to load module PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp
++ module loaded: matplotlib.pyplot
module file : /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/pyplot.pyc
-------------------------------- env vars --------------------------------
PATH = /usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/kburrows/abin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /Users/kburrows/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11
which brew : /usr/local/bin/brew
brew version : Homebrew 2.3.0
-- for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
++ found 1 dylib files under '/opt/X11/lib/flat_namespace'
-- found 'libXt' dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
** env var DYLD_LIBRARY_PATH is not set to contain /opt/X11/lib/flat_namespace
(so afni and suma may fail)
========================= summary, please fix: =========================
* login shell 'bash', trusting user to translate code examples from 'tcsh'
* AFNI programs show FAILURE
* insufficient data for AFNI bootcamp
* OS X version might be old
* consider setting DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace
I'm not sure why DYLD_LIBRARY_PATH doesn't show anything in the system check. Here is what's printed when I echo that variable:
L2174:~ kburrows$ echo $DYLD_LIBRARY_PATH
:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace
