AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

|
January 10, 2017 01:39PM
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

Subject Author Posted

Mac Sierra build problem

dftatephd January 10, 2017 01:39PM

Re: Mac Sierra build problem

rick reynolds January 10, 2017 02:21PM

Re: Mac Sierra build problem

dftatephd January 10, 2017 04:13PM