FATCAT_demo issues at Do_06

mozbet · April 3, 2020, 3:16pm

Hello all,

I was going through the FATCAT_demo and at Do_06_VISdti_SUMA_visual_ex1.tcsh I ended up with the error below.
I’m not sure what to do here

thanks

searching for talking afni…
searching for talking 3dGroupInCorr…
searching for talking plugout_drive…
searching for talking suma…
searching for talking DriveSuma…
searching for talking 3dSkullStrip…
searching for talking SurfSmooth…
[1] 89392
++ Notice SUMA_XtWarn_handler (SUMA_display.c:4116 @08:45:54):
X11 Warning 1:Fatal Error:
_XmGetDefaultDisplay cannot be used prior to VendorS.Initialize, returns NULL
Have 1 X11 warnings so far, see Help–>Message Log if curious.
This notice is shown once for each additional 10 warnings.

Fatal Signal 11 (SIGSEGV) received
SUMA_X_SurfaceViewer_Create
suma

ptaylor · April 3, 2020, 6:05pm

Hi, Patrick-

A) What OS are you using?

B) Does your afni_system_check.py show anything that needs fixing?

C) If you just run “suma”, does that open a GUI?

–pt

mozbet · April 3, 2020, 7:40pm

Hi Paul

I have OS 10.14.6

I don’t see anything special missing; well the R packages are missing.
Hard to tell what’s being used for this purpose, so I’ve pasted below the output of afni_system_check.py.

suma works fine on it’s own, I have the gui an can plot some data.

Thanks

p

architecture: 64bit
system: Darwin
release: 18.7.0
version: Darwin Kernel Version 18.7.0: Tue Aug 20 16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64
distribution: 10.14.6 x86_64
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/bedardp2/abin/afni
afni version : Precompiled binary macos_10.12_local: Mar 26 2020
: AFNI_20.0.21 ‘Galba’
AFNI_version.txt : AFNI_20.0.21, macos_10.12_local, Mar 26 2020
which python : /usr/bin/python
python version : 2.7.10
which R : /usr/local/bin/R
R version : R version 3.6.1 (2019-07-05) – “Action of the Toes”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/bedardp2/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R)
python : 1 (/usr/bin/python)
python2 : 0
python3 : 0

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
3dMVM : 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: phia!
    These packages are not installed on the computer: snow!
    These packages are not installed on the computer: lmerTest!
    These packages are not installed on the computer: paran!
    These packages are not installed on the computer: psych!
    These packages are not installed on the computer: brms!
    These packages are not installed on the computer: corrplot!
    These packages are not installed on the computer: metafor!

R RHOME : /Library/Frameworks/R.framework/Resources

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

------------------------------ python libs -------------------------------
** failed to load module PyQt4
– PyQt4 is no longer needed for an AFNI bootcamp

++ module loaded: matplotlib.pyplot
module file : /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/pyplot.pyc

-------------------------------- env vars --------------------------------
PATH = /Users/bedardp2/TORTOISE_V3.1.2/DRTAMASV312/bin:/Users/bedardp2/TORTOISE_V3.1.2/DRBUDDIV312/bin:/Users/bedardp2/TORTOISE_V3.1.2/DIFFCALC/DIFFCALCV312:/Users/bedardp2/TORTOISE_V3.1.2/DIFFPREPV312/bin/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/bedardp2/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: 20 Feb 2020 [rickr]: updated FT_analysis examples
data dir : found AFNI_demos under $HOME
top history: 22 Oct 2019 [discoraj]: added Cluster Explorer Demo
data dir : found suma_demo under $HOME
top history: …s_New/data/Build_tmp on Mon Mar 4 11:56:45 EST 2013
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /Users/bedardp2/abin

------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11

which brew : /usr/local/bin/brew
brew version : Homebrew 2.1.15

– for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
– consider installing gcc under homebrew
– consider installing glib under homebrew
++ 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 code examples from ‘tcsh’
shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
missing R packages (see rPkgsInstall)

ptaylor · April 4, 2020, 3:28am

Hi, Patrick-

I assume that means that the $DYLD_LIBRARY_PATH isn’t being set in one shell. That has been the case in previous MB questions about that kind of message, like here:
https://afni.nimh.nih.gov/afni/community/board/read.php?1,153612,153612#msg-153612
https://afni.nimh.nih.gov/afni/community/board/read.php?1,156192,156192#msg-156192

From your system check outputs, it seems like that variable is set in your login (bash) shell. Can you just verify what the output of:


echo $DYLD_LIBRARY_PATH

is from your terminal?

Can you copy+paste this in a terminal:


touch ~/.cshrc
echo "" >> ~/.cshrc
echo 'setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace' >> ~/.cshrc 
echo "" >> ~/.cshrc

And also, to address the 2nd line of your “please fix” message in the system check, can you copy+paste this in a terminal:


echo "" >> ~/.bash_profile
echo "source ~/.bashrc" >> ~/.bash_profile
echo "" >> ~/.bash_profile

If you do that and open a new terminal, and then you try running the Do_06*.tcsh command, does that work, by any chance?

–pt

mozbet · May 10, 2020, 11:46am

Hi Paul

All seems t be working fine now

thanks a lot