afni crash after building binaries

Installation Issues
1

Hi All,

I built afni binaries however afni is crashing when I try to open afni.

Please see error below -

Any suggestions on how I can fix it ?

Many thanks

Ri

(base) WITSH4TFM1NEPN7:FR10003002 rdatta4$ afni
Precompiled binary macosx_10.7_Intel_64: Jun 15 2023 (Version AFNI_23.1.05 'Publius Helvius Pertinax')

** Version check disabled: AFNI_VERSION_CHECK forbids
Thanks go to EA DeYoe for advice and help

Initializing: X11[The X.Org Foundation v 12101006].
++++++++ IMAGE SAVE SETUP WARNINGS ++++++++
++ Can't find program ffmpeg for Save to MPEG-1
++ To disable these warnings, set environment
++ variable AFNI_IMSAVE_WARNINGS to 'NO'.
+++++++++++++++++++++++++++++++++++++++++++++
. Widgets...... Input files:++ AFNI is detached from terminal.
(base) WITSH4TFM1NEPN7:FR10003002 rdatta4$ +/Volumes/ns2/NSImagingBiomarker/taumab/IA1/Proc/FR10003002
session # 1 = Proc/FR10003002/ ==> 53 datasets
dataset count = 53
Timeseries.1D = 13 files read
.[tc]sv data = 0 files read
Path(s) to be searched for plugins:
/Users/rdatta4/abin /Users/rdatta4/abin/../lib

Plugins = 49 libraries read
Fatal Signal 11 (SIGSEGV) received
Last STATUS: geometrization
PLUG_setup_widgets
AFNI_misc_CB
AFNI_setup_viewing
AFNI_initialize_view
MAIN_workprocess
AFNI:main
Bottom of Debug Stack
** AFNI version = AFNI_23.1.05 Compile date = Jun 15 2023
** [[Precompiled binary macosx_10.7_Intel_64: Jun 15 2023]]
** 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/rdatta4/.afni.crashlog

*********------ CRASH LOG ------------------------------*********** Fatal Signal 11 (SIGSEGV) received .......... recent internal history ......................................... ----------AV_assign_ival [10]: EXIT} (file=bbox.c line=1984) to new_MCW_optmenu_orig {3531 ms} ++++++++++AV_assign_ival [10]: {ENTRY (file=bbox.c line=1928) from new_MCW_optmenu_orig {3531 ms} AV_assign_ival -- adjust text {3531 ms} ----------AV_assign_ival [10]: EXIT} (file=bbox.c line=1984) to new_MCW_optmenu_orig {3531 ms} ++++++++++AV_assign_ival [10]: {ENTRY (file=bbox.c line=1928) from new_MCW_optmenu_orig {3531 ms} AV_assign_ival -- adjust text {3531 ms} AV_assign_ival -- adjust optmenu history {3531 ms} ----------AV_assign_ival [10]: EXIT} (file=bbox.c line=1984) to new_MCW_optmenu_orig {3531 ms} ---------new_MCW_optmenu_orig [9]: EXIT} (file=bbox.c line=1121) to new_MCW_arrowval {3531 ms} --------new_MCW_arrowval [8]: EXIT} (file=bbox.c line=556) to PLUG_setup_widgets {3531 ms} PLUG_setup_widgets -- create PLUGIN_NUMBER_TYPE {3532 ms} ++++++++new_MCW_arrowval [8]: {ENTRY (file=bbox.c line=549) from PLUG_setup_widgets {3532 ms} new_MCW_arrowval -- creating wrowcol {3532 ms} new_MCW_arrowval -- creating wlabel {3532 ms} new_MCW_arrowval -- getting label height {3532 ms} new_MCW_arrowval -- freeing xstr {3532 ms} new_MCW_arrowval -- creating item labels {3532 ms} new_MCW_arrowval -- creating wtext2 {3532 ms} +++++++++AV_assign_ival [9]: {ENTRY (file=bbox.c line=1928) from new_MCW_arrowval {3532 ms} AV_assign_ival -- adjust text {3532 ms} ---------AV_assign_ival [9]: EXIT} (file=bbox.c line=1984) to new_MCW_arrowval {3532 ms} --------new_MCW_arrowval [8]: EXIT} (file=bbox.c line=792) to PLUG_setup_widgets {3532 ms} PLUG_setup_widgets -- create row Separator {3533 ms} PLUG_setup_widgets -- create ToggleButton for row {3533 ms} PLUG_setup_widgets -- create Label for row {3533 ms} PLUG_setup_widgets -- create PLUGIN_DATASET_TYPE {3533 ms} PLUG_setup_widgets -- create row Separator {3534 ms} PLUG_setup_widgets -- create vertical Separators {3534 ms} PLUG_setup_widgets -- management {3534 ms} PLUG_setup_widgets -- realization {3534 ms} PLUG_setup_widgets -- geometrization {3536 ms} ............................................................................ Last STATUS: geometrization PLUG_setup_widgets AFNI_misc_CB AFNI_setup_viewing AFNI_initialize_view MAIN_workprocess AFNI:main ** AFNI compile date = Jun 15 2023 ** [[Precompiled binary macosx_10.7_Intel_64: Jun 15 2023]] ** Program Crash **

2

Did you install XQuartz and restart?
How did you do your build? It seems strange that the Makefile label is set to "macosx_10.7_Intel_64".

3

Thanks for the reply. To answer your questions -

Yes I installed xquartz and restarted.

To do the build, I used the instructions from
https://afni.nimh.nih.gov/pub/dist/HOWTO/howto/ht00_inst/html/mac_comp.html

My Mac is 11.7.7.

Can I use Makefile.macos_11_ARM_clang for the build on a Intel 64 Mac ?

Thank you

Ri

4

Hi Ri,

Please try building with:

build_afni.py -build_root $HOME/afni_build -package macos_12_x86_64

For setup preparation, please see OS_notes.macos_12_x86_64_a_admin.txt and b_user.txt at https://github.com/afni/afni/tree/master/src/other_builds

Please let us know how it goes.

Thanks,

  • rick
1 Like
5

Hi Rick,

The installation worked and I am able to launch afni and also use our local R repos.

Thanks for the instructions.

Rito

6

Glad to hear it, thanks!

  • rick