Problems in AFNI installation

AFNI Message Board
1

Hello,

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/com.apple.launchd.fKSb86E06h/org.macosforge.xquartz:0”

            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

Thanks!
Swati

2

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
3

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.

Swati

4

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

afni_system_check.py -check_all

  • rick
5

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
/Users/swatirane/anaconda/bin/R
/Library/Frameworks/R.framework/Versions/3.5/Resources/bin/R
python : 2
/Users/swatirane/anaconda/bin/python3.5
/usr/bin/python
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
uber_subject.py : 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/GPI.app/Contents/Resources/miniconda/bin:/Users/swatirane/anaconda/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Applications/VMware Fusion.app/Contents/Public:/Library/TeX/texbin:/opt/X11/bin:/Users/swatirane/abin:/Users/swatirane/abin:/Users/swatirane/abin

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = /opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =

------------------------------ 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:
/opt/X11/lib/flat_namespace/libXt.6.dylib
– 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.

Swati

6

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
7

Will, keep that in mind, Rick.

Thanks!
Swati