Problems in AFNI installation


I am getting ready for the AFNI bootcamp on July 9th.

Here is my installation check file. Everything seem ok there but

When I type afni, the gui comes up. If I close any of the image windows, it crashes. Here is the error:
XIO: fatal IO error 35 (Resource temporarily unavailable) on X server “/private/tmp/”

            Based on the FAQ, I have already added:
   setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace

When I type suma, it says,
Error: attempt to add non-widget child “dsm” to parent “[A] SUMA” which supports only widgets

Can you help me fix this?

My OS: MAC OS 10.13.5 High Sierra
XQuartx: 2.7.11, since the FAQ seems to suggest that this could be a problem


Hi Swati,

You are probably using bash, is that correct? That variable should
be set in your .bashrc and .bash_profile, as well (we often source
the ~/.bashrc from .bash_profile).

What does “echo $0” show?

  • rick

Hi Rick,

Thanks for replying to me.

echo $0 says bash.

I did set the variable in my .bashrc and .bash_profile using export DYLD_LIBRARY_PATH=/opt/X11/lib/flat_namespace.
I also source the .bashrc from .bash_profile to get rid of the warning that the afni check showed.


Does this mean it is working now? If not, would you please
send me email (click on my name) with the output from: -check_all

  • rick

Hi Rick,

No it did not work.

But I saw an old thread that said to type the command for setting the variable in the terminal itself for a temporary fix. For some reason, it has permanently fixed my problem. afni and suma both seem to be working even if I open a fresh terminal window without having to set the variable again!

Thanks for your help. I have attached the new output of the check here.
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 17.6.0
version: Darwin Kernel Version 17.6.0: Tue May 8 15:22:16 PDT 2018; root:xnu-4570.61.1~1/RELEASE_X86_64
distribution: 10.13.5 x86_64
number of CPUs: 4
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/swatirane/abin/afni
afni version : Precompiled binary macosx_10.7_local: May 30 2018
: AFNI_18.1.23
AFNI_version.txt : AFNI_18.1.23, macosx_10.7_local, May 30 2018
which python : /Users/swatirane/anaconda/bin/python
python version : 3.5.4
which R : /Users/swatirane/anaconda/bin/R
R version : R version 3.4.3 (2017-11-30) – “Kite-Eating Tree”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/swatirane/abin/afni)
R : 2
python : 2
python2 : 0
python3 : 1 (/Users/swatirane/anaconda/bin/python3.5)

** have python3 but not python2

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : 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 /Users/swatirane/anaconda/lib/python3.5/site-packages/PyQt4
++ module loaded: PyQt4

-------------------------------- env vars --------------------------------
PATH = /Applications/

DYLD_LIBRARY_PATH (sub-shell) = /opt/X11/lib/flat_namespace

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: … Jun 2018 [gangc]: added 0.BGA and updated 2.3groups
data dir : found AFNI_demos under $HOME
top history: … [pault]: remove rank from FATCAT_DEMO, FAT_MVM_DEMO
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 afni_handouts under $HOME
atlas : found TT_N27+tlrc under /Users/swatirane/abin

------------------------------ OS specific -------------------------------

** no package manager found (okay for bootcamp)
++ found 1 dylib files under ‘/opt/X11/lib/flat_namespace’
– found ‘libXt’ dylib files:
– recent OS X, cheating to check DYLD_LIBRARY_PATH in cur shell ‘bash’…
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace
– recent OS X, cheating to check DYLD_LIBRARY_PATH in shell ‘tcsh’…
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace

========================= summary, please fix: =========================

  • login shell ‘bash’, trusting user to translate from ‘tcsh’
  • have python version 3.5.4, some programs need 2.7.x

For the python, I am just going to activate the python 2.7 version. I have that installed as well.


Okay, great! Note that editing those files does
not do anything for the current shell. So you
would either have to set them in the current
shell, too, or open a new window.

  • rick

Will, keep that in mind, Rick.