Hello,
I'm having this error too after upgrading to Catalina and also updating R, which won't let me run MVM and other commands requiring R packages. I cannot install these packages because I get an error (see below).
All was working prior o these updates...
Any idea how to fix this?
Thanks!!
Pascale
Here is the output of afni_system_check.py -check_all
[Echinacee:IRM/Scripts/fMRI] pascaletremblay% afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.6.0
version: Darwin Kernel Version 19.6.0: Sun Jul 5 00:43:10 PDT 2020; root:xnu-6153.141.1~9/RELEASE_X86_64
distribution: 10.15.6 x86_64
number of CPUs: 8
apparent login shell: tcsh
shell RC file: .cshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/pascaletremblay/abin/afni
afni version : Precompiled binary macosx_10.7_local: Aug 28 2018
: AFNI_18.2.15
AFNI_version.txt : AFNI_18.2.15, macosx_10.7_local, Aug 28 2018
which python : /usr/bin/python
python version : 2.7.16
which R : /usr/local/bin/R
R version : R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/Users/pascaletremblay/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R)
python : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python2 : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python3 : 1 (/usr/bin/python3)
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 : FAILURE
*** caught segfault ***
address 0x0, cause 'memory not mapped'
Traceback:
1: .Call("R_SUMA_HistString", ExecName, args, ohist)
2: AFNI.command.history(ExecName, args, NULL)
3: read.rPkgsInstall.opts.batch(args, verb = 0)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
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 = /Users/pascaletremblay/processing:/usr/local/fsl/bin:/sw/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/pascaletremblay/abin:/Users/pascaletremblay/abin
PYTHONPATH = /sw/lib/qt4-x11/lib/python2.7/site-packages
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH = /Users/pascaletremblay/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 /Users/pascaletremblay/abin
------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 0.9.5 (git revision 8109; last commit 2016-03-01)
++ found PyQt4 under /usr/local/lib/python2.7/site-packages
++ found valid link /usr/local/lib/libgomp.1.dylib
to /Users/pascaletremblay/abin/libgomp.1.dylib
++ found valid link /usr/local/lib/libglib-2.0.dylib
to ../Cellar/glib/2.46.2/lib/libglib-2.0.dylib
++ found 1 dylib files under '/opt/X11/lib/flat_namespace'
-- found 'libXt' dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
++ yay, env var DYLD_LIBRARY_PATH contains /opt/X11/lib/flat_namespace
========================= summary, please fix: =========================
* missing R packages (see rPkgsInstall)
* insufficient data for AFNI bootcamp
* consider adding /usr/local/lib/python2.7/site-packages to PYTHONPATH
########### R install error ####################
[Echinacee:IRM/Scripts/fMRI] pascaletremblay% sudo rPkgsInstall -pkgs ALL
Password:
*** caught segfault ***
address 0x0, cause 'memory not mapped'
Traceback:
1: .Call("R_SUMA_HistString", ExecName, args, ohist)
2: AFNI.command.history(ExecName, args, NULL)
3: read.rPkgsInstall.opts.batch(args, verb = 0)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
