Hello everyone,
I’m having trouble running 3dNetCorr. It appears to run completely until it attemps to write out the results, only to crash with this message:
*** Error in `3dNetCorr’: munmap_chunk(): invalid pointer: 0x00000000008a67d7 ***
Here is the output from afni_system_check.py:
-------------------------------- general ---------------------------------
architecture: 64bit
system: Linux
release: 3.13.0-147-generic
version: #196-Ubuntu SMP Wed May 2 15:51:34 UTC 2018
distribution: debian jessie/sid
number of CPUs: 64
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/prantik/bin/afni/afni
afni version : Precompiled binary linux_openmp_64: Jul 6 2018
: AFNI_18.2.04
AFNI_version.txt : AFNI_18.2.04, linux_openmp_64, Jul 06 2018
which python : /home/dbrennan/anaconda2/bin/python
python version : 2.7.14
which R : /usr/bin/R
R version : R version 3.4.4 (2018-03-15) – “Someone to Lean On”
which tcsh : /usr/bin/tcsh
instances of various programs found in PATH:
afni : 2
/home/prantik/bin/linux_openmp_64/afni
/usr/lib/afni/bin/afni_wrapper
R : 1 (/usr/bin/R)
python : 2
/home/dbrennan/anaconda2/bin/python2.7
/usr/bin/python2.7
python2 : 2
/home/dbrennan/anaconda2/bin/python2.7
/usr/bin/python2.7
python3 : 1 (/usr/bin/python3.4)
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
oo Warning:
These packages are not installed on the computer: brms!
checking for $HOME files…
.afnirc : missing
.sumarc : missing
.afni/help/all_progs.COMP : missing
------------------------------ python libs -------------------------------
** python module not found: PyQt4
– PyQt4 is no longer needed for an AFNI bootcamp
-------------------------------- env vars --------------------------------
PATH = /home/dbrennan/anaconda2/bin:/home/dbrennan/anaconda3/bin:/home/dbrennan/freesurfer/bin:/home/dbrennan/freesurfer/fsfast/bin:/home/dbrennan/freesurfer/tktools:/usr/share/fsl/5.0/bin:/usr/lib/fsl/5.0:/home/dbrennan/freesurfer/mni/bin:/home/prantik/bin/afni:/home/dbrennan/bin:/usr/local/bin:/usr/bin:/bin
PYTHONPATH =
R_LIBS = /home/kuang/R
LD_LIBRARY_PATH = /usr/lib/fsl/5.0:/usr/lib/nx/X11/Xinerama:/usr/lib/nx/X11
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ 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 /home/prantik/bin/afni
atlas : found TT_N27+tlrc under /usr/share/afni/atlases
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 1.0.1ubuntu2 for amd64 compiled on Dec 8 2016 16:23:38
========================= summary, please fix: =========================
- login shell ‘bash’, trusting user to translate from ‘tcsh’
- shell bash: consider sourcing (non-login) .bashrc from (login) .profile
- have multiple versions of AFNI in PATH
- missing R packages (see rPkgsInstall)
- consider running: cp /home/prantik/bin/afni/AFNI.afnirc ~/.afnirc
- consider running “suma -update_env” for .sumarc
- consider running: apsearch -update_all_afni_help
- insufficient data for AFNI bootcamp
- consider running: apt-get install python-qt4
Thank you
Dan