Hi AFNI Gurus,
I recently updated my AFNI binaries, and now can no longer run 3dMVM. When I run afni_system_check.py -check_all I get the following error for the 3dMVM check:
3dMVM : FAILURE
Error in dyn.load(ll) :
unable to load shared object '/Users/laurenlebois/abin/R_io.so':
dlopen(/Users/laurenlebois/abin/R_io.so, 6): Library not loaded: /sw/lib/libjpeg.9.dylib
Referenced from: /Users/laurenlebois/abin/R_io.so
Reason: Incompatible library version: R_io.so requires version 12.0.0 or later, but libjpeg.9.dylib provides version 11.0.0
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
Execution halted
Any advice on how to address this? I've checked several other threads about this, but my error seems slightly different.
In case it is helpful, here is the rest of the afni_system_check.py output:
~ % afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 18.7.0
version: Darwin Kernel Version 18.7.0: Tue Aug 20 16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64
distribution: 10.14.6 x86_64
number of CPUs: 8
apparent login shell: csh
shell RC file: .cshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/laurenlebois/abin/afni
afni version : Precompiled binary macos_10.12_local: Mar 30 2020
: AFNI_20.0.24 'Galba'
AFNI_version.txt : AFNI_20.0.24, macos_10.12_local, Mar 30 2020
which python : /sw/bin/python
python version : 2.7.11
which R : /usr/local/bin/R
R version : R version 3.5.3 (2019-03-11) -- "Great Truth"
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/Users/laurenlebois/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.5/Resources/bin/R)
python : 2
/sw/bin/python2.7
/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/laurenlebois/abin/R_io.so':
dlopen(/Users/laurenlebois/abin/R_io.so, 6): Library not loaded: /sw/lib/libjpeg.9.dylib
Referenced from: /Users/laurenlebois/abin/R_io.so
Reason: Incompatible library version: R_io.so requires version 12.0.0 or later, but libjpeg.9.dylib provides version 11.0.0
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 -------------------------------
++ module loaded: PyQt4
module file : /usr/local/lib/python2.7/site-packages/PyQt4/__init__.pyc
** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is not required, but is desirable
-- python binaries under /sw/bin:
/sw/bin/python (sym link to /sw/bin/python2.7)
/sw/bin/python2.7
-------------------------------- env vars --------------------------------
PATH = /opt/local/bin:/opt/local/sbin:/usr/local/fsl/bin:/opt/local/bin:/opt/local/sbin:/sw/bin:/sw/sbin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/sw/bin:/opt/local/bin:/opt/local/sbin:/usr/local/fsl/bin:/opt/local/bin:/opt/local/sbin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/sw/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/laurenlebois/abin:/Users/laurenlebois/Programs_Misc:/Users/laurenlebois/scripts:/opt/local/bin:opt/local/sbin:/bin:/Applications/gedit.app/Contents/MacOS:/opt/local/bin:/opt/local/sbin:/Users/laurenlebois/osx:/usr/local/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/laurenlebois/abin:/Applications/mricron:/Applications/mricron/dcm2niix:/Applications/freesurfer:/Applications/R:/opt/X11/bin:/Users/laurenlebois/abin:/Users/laurenlebois/Programs_Misc:/Users/laurenlebois/scripts:/opt/local/bin:opt/local/sbin:/bin:/Applications/gedit.app/Contents/MacOS:/opt/local/bin:/opt/local/sbin:/Users/laurenlebois/osx:/usr/local/bin:/opt/local/bin:/opt/local/sbin:/usr/local/fsl/bin:/opt/local/bin:/opt/local/sbin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/sw/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/laurenlebois/abin:/Users/laurenlebois/Programs_Misc:/Users/laurenlebois/scripts:/opt/local/bin:opt/local/sbin:/bin:/Applications/gedit.app/Contents/MacOS:/opt/local/bin:/opt/local/sbin:/Users/laurenlebois/osx:/usr/local/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/laurenlebois/abin:/Applications/mricron:/Applications/mricron/dcm2niix:/Applications/freesurfer:/Applications/R:/opt/X11/bin:/Users/laurenlebois/abin:/Applications/mricron:/Applications/mricron/dcm2niix:/Applications/freesurfer:/Applications/R
PYTHONPATH = /usr/local/lib/python2.7/site-packages
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = /opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) = FSL_DIR /usr/local/fsl
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: ... [rickr]: updated FT_white.nii w/out 16 (brain stem)
data dir : found AFNI_demos under $HOME
top history: ... [pault]: remove rank from FATCAT_DEMO, FAT_MVM_DEMO
data dir : found suma_demo under $HOME
top history: .../SUMA_data/Build_tmp on Wed Aug 20 10:04:23 EDT 2014
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under .
------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11
which fink : /sw/bin/fink
fink version : Package manager version: 0.39.2
which brew : /usr/local/bin/brew
brew version : Homebrew 2.2.11
which port : /opt/local/bin/port
port version : Error: Current platform "darwin 18" does not match expected platform "darwin 14"
++ found 'brew' at /usr/local/bin/brew
++ 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 'csh'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace
========================= summary, please fix: =========================
* AFNI programs show FAILURE
* insufficient data for AFNI bootcamp
Thanks for your time and guidance!
