afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 15.5.0
version: Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64
distribution: 10.11.5 x86_64
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (does not exist)
--------------------- AFNI and related program tests ---------------------
which afni : /usr/local/afni/afni
afni version : Precompiled binary macosx_10.10_icc: May 25 2016
AFNI_version.txt : AFNI_16.1.16, macosx_10.10_icc, May 25 2016
which python : /Users/piero/anaconda/bin/python
python version : 2.7.11
which R : /usr/local/bin/R
R version : R version 3.3.0 (2016-05-03) -- "Supposedly Educational"
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/usr/local/afni/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.3/Resources/bin/R)
python : 2
/Users/piero/anaconda/bin/python2.7
/usr/bin/python
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
Error in dyn.load(ll) :
unable to load shared object '/usr/local/afni/R_io.so':
dlopen(/usr/local/afni/R_io.so, 6): Symbol not found: ___intel_sse2_strcat
Referenced from: /usr/local/afni/R_io.so
Expected in: flat namespace
in /usr/local/afni/R_io.so
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
Execution halted
checking for $HOME files...
.afnirc : missing
.sumarc : missing
.afni/help/all_progs.COMP : missing
------------------------------ python libs -------------------------------
++ module 'PyQt4' found at /Users/piero/anaconda/lib/python2.7/site-packages/PyQt4
++ module loaded: PyQt4
-------------------------------- env vars --------------------------------
PATH = /Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/fsl/bin:/Users/piero/anaconda/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Library/TeX/texbin:/usr/local/bin:/usr/local/afni:/Users/piero/Documents/dev/ITAB/codes:/Users/piero/Documents/dev/ITAB/codes/ANTs/bin
PYTHONPATH =
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 /usr/local/afni
------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 0.9.9 (git revision 5768; last commit 2016-07-19)
============================ summary comments ============================
* login shell 'bash', trusting user to translate from 'tcsh'
* shell bash: MISSING non-login setup file .bashrc
* shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
* missing R packages (see rPkgsInstall)
* consider running: cp /usr/local/afni/AFNI.afnirc ~/.afnirc
* consider running "suma -update_env" for .sumarc
* consider running: apsearch -update_all_afni_help
* insufficient data for AFNI bootcamp
