afni.nimh.nih.gov

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