Hi-
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 17.2.0
version: Darwin Kernel Version 17.2.0: Fri Sep 29 18:27:05 PDT 2017; root:xnu-4570.20.62~3/RELEASE_X86_64
distribution: 10.13.1 x86_64
number of CPUs: 4
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/xyz/abin/afni
afni version : Precompiled binary macos_10.12_local: Nov 27 2017
: AFNI_17.3.05
AFNI_version.txt : AFNI_17.3.05, macos_10.12_local, Nov 27 2017
which python : /usr/bin/python
python version : 2.7.10
which R : /usr/local/bin/R
R version : R version 3.4.2 (2017-09-28) -- "Short Summer"
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/Users/xyz/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.4/Resources/bin/R)
python : 1 (/usr/bin/python)
python2 : 1 (/usr/local/Cellar/python/2.7.14/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python3 : 1 (/usr/local/Cellar/python3/3.6.3/Frameworks/Python.framework/Versions/3.6/bin/python3.6)
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
Error in dyn.load(ll) :
unable to load shared object '/Users/xyz/abin/R_io.so':
dlopen(/Users/xyz/abin/R_io.so, 6): Library not loaded: /sw/lib/libXm.4.dylib
Referenced from: /Users/xyz/abin/R_io.so
Reason: image not found
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
Execution halted
checking for $HOME files...
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
** python module not found: PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp
-------------------------------- env vars --------------------------------
PATH = /usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/xyz/abin
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) = /Users/xyz/abin
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME/CD
top history: ...PPI scripts are now based on FT_analysis/s05.ap.uber
data dir : found AFNI_demos under $HOME/CD
top history: ... [pault]: remove rank from FATCAT_DEMO, FAT_MVM_DEMO
data dir : found suma_demo under $HOME/CD
top history: .../SUMA_data/Build_tmp on Wed Aug 20 10:04:23 EDT 2014
data dir : found afni_handouts under $HOME/Documents/AFNI
atlas : found TT_N27+tlrc under /Users/xyz/abin
------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 1.3.9
-- for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
++ found valid link /usr/local/lib/libgomp.1.dylib
to /usr/local/Cellar/gcc/7.2.0/lib/gcc/7/libgomp.1.dylib
++ found valid link /usr/local/lib/libglib-2.0.dylib
to ../Cellar/glib/2.54.2/lib/libglib-2.0.dylib
++ 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 'bash'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in shell 'tcsh'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace
========================= summary, please fix: =========================
* login shell 'bash', trusting user to translate from 'tcsh'
* shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
* missing R packages (see rPkgsInstall)
Thanks.
