Crash during installation

Dear AFNI experts,

I am completely new to AFNI and tried to install it on Mac OS following the described steps. However, when evaluating the setup, it crashes.

I copied the crash log below and afni_system_check.py output. I have never worked with Python or Shell scripts before, so I do not really understand what I need to do to address the error messages.

Last login: Tue Aug 7 19:17:03 on ttys002
Stefanies-iMac:~ stefaniemeliss$ afni
Precompiled binary macos_10.12_local: Jul 31 2018 (Version AFNI_18.2.06)

Thanks go to J Gonzalez-Castillo for useful feedback

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].
Fatal Signal 11 (SIGSEGV) received
ISQ_record_button
open_MCW_imseq
SPLASH_popup_image
AFNI_splashup
MAIN_workprocess
AFNI:main
Bottom of Debug Stack
** AFNI version = AFNI_18.2.06 Compile date = Jul 31 2018
** [[Precompiled binary macos_10.12_local: Jul 31 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/stefaniemeliss/.afni.crashlog
++ AFNI is detached from terminal.

-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 17.7.0
version: Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64
distribution: 10.13.6 x86_64
number of CPUs: 4
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/stefaniemeliss/abin/afni
afni version : Precompiled binary macos_10.12_local: Jul 31 2018
: AFNI_18.2.06
AFNI_version.txt : AFNI_18.2.06, macos_10.12_local, Jul 31 2018
which python : /sw/bin/python
python version : 2.7.15
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/stefaniemeliss/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.5/Resources/bin/R)
python : 3
/sw/bin/python2.7
/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
/usr/bin/python
python2 : 1 (/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
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 -------------------------------
++ module ‘PyQt4’ found at /sw/lib/python2.7/site-packages/PyQt4
++ module loaded: PyQt4

python binaries under /sw/bin:
/sw/bin/python (sym link to /sw/bin/python2.7)
/sw/bin/python2.7

-------------------------------- env vars --------------------------------
PATH = /sw/bin:/sw/sbin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/usr/local/fsl/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/stefaniemeliss/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/stefaniemeliss/abin

------------------------------ OS specific -------------------------------
which fink : /sw/bin/fink
fink version : Package manager version: 0.43.1
which brew : /usr/local/bin/brew
brew version : Homebrew 1.7.1

++ found ‘brew’ at /usr/local/bin/brew
++ 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’
  • shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile

Please let me know whether I can provide more information. Any help is highly appreciated!

Many thanks,
Stef

Hi Stef,

Just to be sure, what happens when you open a new window and run ‘afni’?
And what happens if you first run ‘source ~/.bashrc’ and then ‘afni’?

  • rick

Hi Rick,

When I type afni, that is the output:

Last login: Tue Aug 7 19:19:02 on ttys001
webvpn-19:~ stefaniemeliss$ afni
Precompiled binary macos_10.12_local: Jul 31 2018 (Version AFNI_18.2.06)

Thanks go to DA Jacobson for inspiration

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.

++ AFNI is detached from terminal.
webvpn-19:~ stefaniemeliss$ [The X.Org Foundation v 11804000].
Fatal Signal 11 (SIGSEGV) received
ISQ_record_button
open_MCW_imseq
SPLASH_popup_image
AFNI_splashup
MAIN_workprocess
AFNI:main
Bottom of Debug Stack
** AFNI version = AFNI_18.2.06 Compile date = Jul 31 2018
** [[Precompiled binary macos_10.12_local: Jul 31 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/stefaniemeliss/.afni.crashlog

However, if I type in source ~/.bashrc first, it works!! Thank you!
Stef

Hi Stef,

The issue is surely getting that DYLD_LIBRARY_PATH set in the shell.
At some point try logging out completely, and see if opening a new
window works.

If not, please let us know.

To be sure, you did not mention opening a new window before running
‘afni’ this time. Does it still fail when opening a new window?

If so, I can tell you how to send your init files to me via email.

  • rick