brainhack/MY_SYSTEM_CHECK.txt at master · debyee/brainhack · GitHub

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-------------------------------- general ---------------------------------
architecture:         64bit
system:               Darwin
release:              15.6.0
version:              Darwin Kernel Version 15.6.0: Thu Jun 23 18:25:34 PDT 2016; root:xnu-3248.60.10~1/RELEASE_X86_64
distribution:         10.11.6 x86_64
number of CPUs:       8
apparent login shell: bash  (current shell is csh)
shell RC file:        .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /Users/debbieyee/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         : /Library/Frameworks/Python.framework/Versions/2.7/bin/python
python version       : 2.7.12
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/debbieyee/abin/afni)
    R       : 1   (/Library/Frameworks/R.framework/Versions/3.3/Resources/bin/R)
    python  : 5
      /Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
      /anaconda/bin/python2.7
      /Users/debbieyee/anaconda/bin/python2.7
      /usr/bin/python
      /usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/bin/python2.7
    python2 : 4
      /Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
      /anaconda/bin/python2.7
      /Users/debbieyee/anaconda/bin/python2.7
      /usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/bin/python2.7
    python3 : 0


testing ability to start various programs...
    afni                 : success
    suma                 : success
    3dSkullStrip         : success
    uber_subject.py      : success
    3dAllineate          : FAILURE
        dyld: Library not loaded: /usr/local/lib/libgomp.1.dylib
          Referenced from: /Users/debbieyee/abin/3dAllineate
          Reason: image not found
    3dRSFC               : success
    SurfMesh             : success

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 -------------------------------
++ module 'PyQt4' found at /usr/local/lib/python2.7/site-packages/PyQt4
++ module loaded: PyQt4

-------------------------------- env vars --------------------------------
PATH = /Library/Frameworks/Python.framework/Versions/2.7/bin:/opt/local/bin:/opt/local/sbin:/usr/local/fsl/bin:/sw/bin:/sw/sbin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/opt/local/bin:/opt/local/sbin:/usr/local/fsl/bin:/Users/debbieyee/afni:/opt/local/bin:/opt/local/sbin://anaconda/bin:/Users/debbieyee/anaconda/bin:/Users/debbieyee/anaconda/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Library/TeX/texbin:/Users/debbieyee/abin:/Users/debbieyee/abin:/usr/X11R6/bin:/Users/debbieyee/abin:/Users/debbieyee/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 : found AFNI_data6   under $HOME
           top history: 30 Dec 2016 [rickr]: applied updated FS reordering
data dir : found suma_demo    under $HOME
           top history: .../SUMA_data/Build_tmp on Wed Aug 20 10:04:23 EDT 2014
data dir : found FATCAT_DEMO  under $HOME/AFNI_demos
           top history: ...CAT/FATCAT_DEMO.Distro, Wed Apr  8 12:41:00 EDT 2015
data dir : found afni_handouts under $HOME
atlas    : found TT_N27+tlrc  under /Users/debbieyee/abin

------------------------------ OS specific -------------------------------
which brew           : /usr/local/bin/brew
brew version         : Homebrew 1.1.6
which port           : /opt/local/bin/port
port version         : Usage: port
which fink           : /sw/bin/fink
fink version         : Package manager version: 0.38.3

++ found valid link /usr/local/lib/libglib-2.0.dylib
   to ../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: consider sourcing (non-login) .bashrc from (login) .bash_profile
*  AFNI programs show FAILURE
*  consider linking /usr/local/Cellar/gcc/6.3.0_1/lib/gcc/6/libgomp.1.dylib under /usr/local/lib
*  cannot tell if DYLD_LIBRARY_PATH includes /opt/X11/lib/flat_namespace