Fatal Signal 11 (SIGSEGV) received


While installing AFNI, I got the error when I checked afni command:

Precompiled binary macos_10.12_local: Jul 6 2018 (Version AFNI_18.2.04)

Thanks go to PSF Bellgowan for “quick” questions

Initializing: X11
++ If you are using XQuartz 2.7.10 (or later), and AFNI crashes when

  • opening windows, or you cannot type text into AFNI popup windows,
  • you might need to set an environment variable to solve this problem:
  • setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace
  • This command is best put in your startup ~/.cshrc file, so that
  • it will be invoked for every (t)csh shell you open.

[The X.Org Foundation v 11804000].
++ Can’t find program ppmtogif AND/OR ppmquant for Save to GIF
++ Can’t find program ppm2tiff OR pnmtotiff OR pamtotiff for Save to TIFF
++ Can’t find program ppmtobmp for Save to BMP
++ Can’t find program pnmtopng for Save to PNG
++ Some of the missing image Save programs are in
++ the netpbm software package, which is freeware.
++ The ‘fink’ package at http://fink.sourceforge.net/
++ is a way to get the netpbm programs for OS X; OR
++ Netpbm can be found at http://netpbm.sourceforge.net/
++ To disable these warnings, set environment
++ variable AFNI_IMSAVE_WARNINGS to ‘NO’.

Fatal Signal 11 (SIGSEGV) received
Bottom of Debug Stack
** AFNI version = AFNI_18.2.04 Compile date = Jul 6 2018
** [[Precompiled binary macos_10.12_local: Jul 6 2018]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /Users/yufei/.afni.crashlog
++ AFNI is detached from terminal.

By typing afni_system_check.py -check_all, I got:
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 17.4.0
version: Darwin Kernel Version 17.4.0: Sun Dec 17 09:19:54 PST 2017; root:xnu-4570.41.2~1/RELEASE_X86_64
distribution: 10.13.3 x86_64
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/yufei/abin/afni
afni version : Precompiled binary macos_10.12_local: Jul 6 2018
: AFNI_18.2.04
AFNI_version.txt : AFNI_18.2.04, macos_10.12_local, Jul 06 2018
which python : /usr/bin/python
python version : 2.7.10
which R : /usr/local/bin/R
R version : R version 3.5.0 (2018-04-23) – “Joy in Playing”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/yufei/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.5/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

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 -------------------------------
** python module not found: PyQt4
– PyQt4 is no longer needed for an AFNI bootcamp

-------------------------------- env vars --------------------------------
PATH = /usr/local/fsl/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Library/TeX/texbin:/Users/yufei/abin:/Users/yufei/abin

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/yufei/abin

------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 1.6.15

– 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:
– 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’

I am a newbie in Unix. How can I fix this problem?
thank you!!

To be sure, does this happen if you open a new Terminal window?
What is the output of:


  • rick