Suma error after update Xquarts

Dear AFNI experts,

I updated XQuartz today and now SUMA won’t work. This is the error I get:

Error: attempt to add non-widget child “dsm” to parent “[A] SUMA” which supports only widgets.

This is the output of the system_check:

[isabellemacbook:~] Isa% -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 14.5.0
version: Darwin Kernel Version 14.5.0: Sun Sep 25 22:07:15 PDT 2016; root:xnu-2782.50.9~1/RELEASE_X86_64
distribution: 10.10.5 x86_64
number of CPUs: 4
apparent login shell: tcsh
shell RC file: .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/Isa/abin/afni
afni version : Precompiled binary macosx_10.7_Intel_64: Nov 4 2016
AFNI_version.txt : AFNI_16.3.08, macosx_10.7_Intel_64, Nov 04 2016
which python : /usr/bin/python
python version : 2.7.10
which R : /usr/bin/R
R version : R version 3.1.2 (2014-10-31) – “Pumpkin Helmet”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/Isa/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.1/Resources/bin/R)
python : 2

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success : success
3dAllineate : success
3dRSFC : success
SurfMesh : success

checking for R packages…
rPkgsInstall -pkgs ALL -check : FAILURE

    oo Warning: 
       These packages are not installed on the computer: afex!
    These packages are not installed on the computer: snow!
    These packages are not installed on the computer: paran!
    These packages are not installed on the computer: psych!

checking for $HOME files…
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found

------------------------------ python libs -------------------------------
** python module not found: PyQt4

-------------------------------- env vars --------------------------------
PATH = /usr/local/fsl/bin:/Library/Frameworks/Python.framework/Versions/3.5/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/Isa/abin:/Users/Isa/abin:/Applications/anaconda/bin:/Applications/scilpy/scripts:/Users/Isa/mrtrix2/bin:/Users/Isa/antsbin/bin:/Users/Isa/tract_querier/scripts:/Applications/anaconda/lib/python2.7/site-packages/

PYTHONPATH = /Applications/scilpy/


------------------------------ 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 /Users/Isa/abin

------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : 0.9.5

++ found PyQt4 under /usr/local/lib/python2.7/site-packages

============================ summary comments ============================

  • missing R packages (see rPkgsInstall)
  • insufficient data for AFNI bootcamp
  • consider adding /usr/local/lib/python2.7/site-packages to PYTHONPATH

Any idea what I can do to fix this issue?

Thank you!


The workaround is to set environment variable DYLD_LIBRARY_PATH to be /opt/X11/lib/flat_namespace

This is best done in the login script for your shell. If you use tcsh (as I do), that file is .cshrc in your home directory, and you would add the command
setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace
to that file. By itself, this will have no effect – until you start a new shell (command window). To make it work in the shell you are using NOW NOW NOW, you can just manually execute the command (e.g., copy+paste into the shell).