Mac Sierra build problem


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 is below. Any suggestions would be welcome.



-------------------------------- 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 
    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      : 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


------------------------------ 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

This is strange in that we should either see this with everyone,
or there was just a very recent change. Try:

ln -s /usr/local/lib/libglib-2.0.dylib /usr/local/lib/libglib-2.0.0.dylib

  • rick

Thanks! This seems to correct the problem.