Having just updated the afni binaries (and also updated xquartz to 2.7.11), afni GUI now crashes on startup, without even opening a window. I cannot work out why. because the afni system check doesn't find a problem, as far as I can tell.
The Terminal output is as follows:
Precompiled binary macos_10.12_local: Feb 15 2019 (Version AFNI_19.0.14 'Tiberius')
Thanks go to J Kummer 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.
[The X.Org Foundation v 11804000].
++++++++ IMAGE SAVE SETUP WARNINGS ++++++++
++ Can't find program ppmtogif AND/OR ppmquant for Save to GIF
++ 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 [fink.sourceforge.net]
++ is a way to get the netpbm programs for OS X; *OR*
++ Netpbm can be found at [netpbm.sourceforge.net]
++ To disable these warnings, set environment
++ variable AFNI_IMSAVE_WARNINGS to 'NO'.
+++++++++++++++++++++++++++++++++++++++++++
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_19.0.14 Compile date = Feb 15 2019
** [[Precompiled binary macos_10.12_local: Feb 15 2019]]
** 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/hb435/.afni.crashlog
++ AFNI is detached from terminal.
The crashlog is as follows:
*********------ CRASH LOG ------------------------------***********
Fatal Signal 11 (SIGSEGV) received
.......... recent internal history .........................................
-------THD_find_executable [7]: EXIT} (file=thd_getpathprogs.c line=39) to open_MCW_imseq
+++++++THD_find_executable [7]: {ENTRY (file=thd_getpathprogs.c line=27) from open_MCW_imseq
-------THD_find_executable [7]: EXIT} (file=thd_getpathprogs.c line=39) to open_MCW_imseq
+++++++THD_find_executable [7]: {ENTRY (file=thd_getpathprogs.c line=27) from open_MCW_imseq
-------THD_find_executable [7]: EXIT} (file=thd_getpathprogs.c line=36) to open_MCW_imseq
+++++++THD_find_executable [7]: {ENTRY (file=thd_getpathprogs.c line=27) from open_MCW_imseq
-------THD_find_executable [7]: EXIT} (file=thd_getpathprogs.c line=39) to open_MCW_imseq
+++++++THD_find_executable [7]: {ENTRY (file=thd_getpathprogs.c line=27) from open_MCW_imseq
-------THD_find_executable [7]: EXIT} (file=thd_getpathprogs.c line=39) to open_MCW_imseq
+++++++THD_find_executable [7]: {ENTRY (file=thd_getpathprogs.c line=27) from open_MCW_imseq
-------THD_find_executable [7]: EXIT} (file=thd_getpathprogs.c line=39) to open_MCW_imseq
+++++++SPLASH_imseq_getim [7]: {ENTRY (file=afni_splash.c line=442) from open_MCW_imseq
-------SPLASH_imseq_getim [7]: EXIT} (file=afni_splash.c line=464) to open_MCW_imseq
+++++++SPLASH_imseq_getim [7]: {ENTRY (file=afni_splash.c line=442) from open_MCW_imseq
++++++++mri_valpad_2D [8]: {ENTRY (file=mri_zeropad.c line=28) from SPLASH_imseq_getim
+++++++++mri_new_7D_generic [9]: {ENTRY (file=mri_new.c line=48) from mri_valpad_2D
---------mri_new_7D_generic [9]: EXIT} (file=mri_new.c line=142) to mri_valpad_2D
+++++++++mri_add_name [9]: {ENTRY (file=mri_add_name.c line=19) from mri_valpad_2D
---------mri_add_name [9]: EXIT} (file=mri_add_name.c line=24) to mri_valpad_2D
--------mri_valpad_2D [8]: EXIT} (file=mri_zeropad.c line=138) to SPLASH_imseq_getim
-------SPLASH_imseq_getim [7]: EXIT} (file=afni_splash.c line=484) to open_MCW_imseq
+++++++mri_free [7]: {ENTRY (file=mri_free.c line=49) from open_MCW_imseq
mri_free -- call killpurge
++++++++mri_killpurge [8]: {ENTRY (file=mri_purger.c line=259) from mri_free
mri_killpurge -- check if im==NULL ptr=0x7fc72e802cc0
mri_killpurge -- can't killpurge NULL fname!
--------mri_killpurge [8]: EXIT} (file=mri_purger.c line=270) to mri_free
mri_free -- free ptr
mri_free -- free im
-------mri_free [7]: EXIT} (file=mri_free.c line=67) to open_MCW_imseq
+++++++ISQ_record_button [7]: {ENTRY (file=imseq.c line=10947) from open_MCW_imseq
............................................................................
ISQ_record_button
open_MCW_imseq
SPLASH_popup_image
AFNI_splashup
MAIN_workprocess
AFNI:main
** AFNI compile date = Feb 15 2019
** [[Precompiled binary macos_10.12_local: Feb 15 2019]]
** Program Crash **
And checking the system check gives the following:
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 16.6.0
version: Darwin Kernel Version 16.6.0: Fri Apr 14 16:21:16 PDT 2017; root:xnu-3789.60.24~6/RELEASE_X86_64
distribution: 10.12.5 x86_64
number of CPUs: 12
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /usr/local/abin/afni
afni version : Precompiled binary macos_10.12_local: Feb 15 2019
: AFNI_19.0.14 'Tiberius'
AFNI_version.txt : AFNI_19.0.14, macos_10.12_local, Feb 15 2019
which python : /usr/bin/python
python version : 2.7.10
which R : /usr/local/bin/R
R version : R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/usr/local/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.4/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/xcede/bin:/usr/local/dicomtools:/usr/local/fsl/bin:/usr/local/abin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = :/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH = /opt/X11/lib:/usr/local/abin
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /usr/local/abin
------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : 0.9.5
-- 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) .profile
* insufficient data for AFNI bootcamp
Edited 2 time(s). Last edit at 02/20/2019 03:05PM by henrybrice.
