Hi-
I am trying to install AFNI and its dependencies on a new Mac 10.12, and I can’t get around some errors with libglib. I haven’t had fink on this computer, but there seems to be some link to /sw/… pathways getting in the way. My afni_system_check.py is below. Any suggestions would be welcome.
Thanks,
David
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 16.3.0
version: Darwin Kernel Version 16.3.0: Thu Nov 17 20:23:58 PST 2016; root:xnu-3789.31.2~1/RELEASE_X86_64
distribution: 10.12.2 x86_64
number of CPUs: 4
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/davidtate/abin/afni
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/local/bin/python
python version : 2.7.13
which R : /usr/local/bin/R
R version : R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/Users/davidtate/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.3/Resources/bin/R)
python : 2
/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
/usr/bin/python
python2 : 1 (/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
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/davidtate/abin/suma
Reason: image not found
3dSkullStrip : FAILURE
dyld: Library not loaded: /sw/lib/libglib-2.0.0.dylib
Referenced from: /Users/davidtate/abin/3dSkullStrip
Reason: image not found
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : FAILURE
dyld: Library not loaded: /sw/lib/libglib-2.0.0.dylib
Referenced from: /Users/davidtate/abin/SurfMesh
Reason: image not found
checking for R packages...
rPkgsInstall -pkgs ALL -check : success
checking for $HOME files...
.afnirc : found
.sumarc : missing
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
** python module not found: PyQt4
-------------------------------- env vars --------------------------------
PATH = /usr/local/bin:/Users/davidtate/abin:/Users/davidtate/antsbin/bin/:/usr/local/bin:/Users/davidtate/abin:/Users/davidtate/antsbin/bin/:/usr/local/bin:/Users/davidtate/abin:/Users/davidtate/antsbin/bin/:/usr/local/bin:/Users/davidtate/abin:/Users/davidtate/antsbin/bin/:/usr/local/bin:/Users/davidtate/antsbin/bin/:/usr/local/bin:/Users/davidtate/antsbin/bin/:/usr/local/bin:/Users/davidtate/antsbin/bin/:/Library/Frameworks/Python.framework/Versions/2.7/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
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 ./
------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 1.1.6
++ found valid link /usr/local/lib/libgomp.1.dylib
to /usr/local/Cellar/gcc/6.3.0_1/lib/gcc/6/libgomp.1.dylib
++ found valid link /usr/local/lib/libglib-2.0.dylib
to /usr/local/Cellar/glib/2.50.2/lib/libglib-2.0.dylib
++ 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 ============================
* login shell 'bash', trusting user to translate from 'tcsh'
* shell bash: MISSING login setup file, e.g. .bash_profile
* shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
* AFNI programs show FAILURE
* consider running "suma -update_env" for .sumarc
* insufficient data for AFNI bootcamp
* consider running: brew install pyqt
* cannot tell if DYLD_LIBRARY_PATH includes /opt/X11/lib/flat_namespace