Hello everyone -
A few weeks ago, I installed a few modules for Freesurfer, and now all of a sudden all of my afni libraries are messed up. I'm running Mac OS Sierra.
After running afni_system_check, the output is below. Does anyone know how to update these libraries without completely uninstalling and re-installing afni? Some of afni is still intact, but clearly without these functions below, I cannot preprocess.
Thank you in advance!
Steffie
afni version : Precompiled binary macosx_10.7_Intel_64: Jan 3 2017
AFNI_version.txt : AFNI_17.0.00, macosx_10.7_Intel_64, Jan 03 2017
which python : /usr/bin/python
python version : 2.7.10
which R : /usr/local/bin/R
R version : R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/Users/steffie/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.3/Resources/bin/R)
python : 1 (/usr/bin/python)
python2 : 0
python3 : 1 (/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/bin/python3.6)
testing ability to start various programs...
afni : success
suma : FAILURE
dyld: Library not loaded: /sw/lib/libglib-2.0.0.dylib
Referenced from: /Users/steffie/abin/suma
Reason: image not found
3dSkullStrip : FAILURE
dyld: Library not loaded: /sw/lib/libglib-2.0.0.dylib
Referenced from: /Users/steffie/abin/3dSkullStrip
Reason: image not found
uber_subject.py : success
3dAllineate : FAILURE
dyld: Library not loaded: /usr/local/lib/libgomp.1.dylib
Referenced from: /Users/steffie/abin/3dAllineate
Reason: image not found
3dRSFC : success
SurfMesh : FAILURE
dyld: Library not loaded: /sw/lib/libglib-2.0.0.dylib
Referenced from: /Users/steffie/abin/SurfMesh
Reason: image not found
checking for R packages...
rPkgsInstall -pkgs ALL -check : success
checking for $HOME files...
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
** python module not found: PyQt4
-------------------------------- env vars --------------------------------
PATH = /usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/steffie/abin
PYTHONPATH = /usr/local/lib/python2.7/site-packages
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing suma_demo
data dir : missing FATCAT_DEMO
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /Users/steffie/abin
------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 1.1.7
++ found 1 dylib files under '/opt/X11/lib/flat_namespace'
-- found 'libXt' dylib files, e.g. /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 comments ============================
* have python3 but not python2
* AFNI programs show FAILURE
* insufficient data for AFNI bootcamp
* consider running: brew install pyqt
* consider linking /usr/local/Cellar/gcc/6.3.0_1/lib/gcc/6/libgomp.1.dylib under /usr/local/lib
* consider linking /usr/local/Cellar/glib/2.50.2/lib/libglib-2.0.dylib under /usr/local/lib
* cannot tell if DYLD_LIBRARY_PATH includes /opt/X11/lib/flat_namespace
