AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

Previous Message Next Message
Message List New Topic Print View
|
krisknut
December 05, 2019 10:34AM
I'm getting a Segmentation fault: 11 when I run afni_system_check.py -check_all. Here is the output:

~: afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 18.7.0
version: Darwin Kernel Version 18.7.0: Sat Oct 12 00:02:19 PDT 2019; root:xnu-4903.278.12~1/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/knutsonk/abin/afni
afni version : Precompiled binary macos_10.12_local: Nov 22 2019
: AFNI_19.3.14 'Nero'
AFNI_version.txt : AFNI_19.3.14, macos_10.12_local, Nov 22 2019
which python : /usr/local/bin/python
python version : 2.7.14
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/knutsonk/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.5/Resources/bin/R)
python : 2
/usr/local/Cellar/python@2/2.7.14_3/Frameworks/Python.framework/Versions/2.7/bin/python2.7
/usr/bin/python
python2 : 1 (/usr/local/Cellar/python@2/2.7.14_3/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python3 : 1 (/usr/local/Cellar/python/3.6.4_4/Frameworks/Python.framework/Versions/3.6/bin/python3.6)


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: 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 -------------------------------
++ module loaded: PyQt4
module file : /usr/local/lib/python2.7/site-packages/PyQt4/__init__.pyc
Segmentation fault: 11
Reply Quote
RSS
Subject Author Posted

Segmentation fault: 11 when running afni_system_check.py -check_all

krisknut December 05, 2019 10:34AM