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May 30, 2022 10:12AM
Thanks so much Rick!

Here's my output from cat /etc/os-release

tue50988@cla19097:~$ cat /etc/os-release
NAME="Ubuntu"
VERSION="20.04.4 LTS (Focal Fossa)"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 20.04.4 LTS"
VERSION_ID="20.04"
HOME_URL="[www.ubuntu.com];
SUPPORT_URL="[help.ubuntu.com];
BUG_REPORT_URL="[bugs.launchpad.net];
PRIVACY_POLICY_URL="[www.ubuntu.com];
VERSION_CODENAME=focal
UBUNTU_CODENAME=focal

and here's the output from: afni_system_check.py -check_all

tue50988@cla19097:~$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 5.13.0-44-generic
version: #49~20.04.1-Ubuntu SMP Wed May 18 18:44:28 UTC 2022
distribution: ubuntu 20.04 focal
number of CPUs: 48
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /usr/local/abin/afni
afni version : /bin/sh: 1: afni: Exec format error
:
AFNI_version.txt : AFNI_22.1.10, macos_10.12_local, May 20 2022
which python : /usr/bin/python
python version : 3.8.10
which R : /usr/bin/R
R version : R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
which tcsh : /usr/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/usr/local/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python3.8)
python2 : 1 (/usr/bin/python2.7)
python3 : 1 (/usr/bin/python3.8)


testing ability to start various programs...
afni : FAILURE
/bin/sh: 1: afni: Exec format error
suma : FAILURE
/bin/sh: 1: suma: Exec format error
3dSkullStrip : FAILURE
/bin/sh: 1: 3dSkullStrip: Exec format error
uber_subject.py : success
3dAllineate : FAILURE
/bin/sh: 1: 3dAllineate: Exec format error
3dRSFC : FAILURE
/bin/sh: 1: 3dRSFC: Exec format error
SurfMesh : FAILURE
/bin/sh: 1: SurfMesh: Exec format error
3dClustSim : FAILURE
/bin/sh: 1: 3dClustSim: Exec format error
3dMVM : FAILURE
Error in dyn.load(ll) :
unable to load shared object '/usr/local/abin/R_io.so':
/usr/local/abin/R_io.so: invalid ELF header
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
Execution halted

checking for R packages...
rPkgsInstall -pkgs ALL -check : success

R RHOME : /usr/lib/R

checking for $HOME files...
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found

------------------------------ python libs -------------------------------
** failed to load module PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp

++ module loaded: matplotlib.pyplot
module file : /usr/lib/python3/dist-packages/matplotlib/pyplot.py
matplotlib version : 3.1.2

-------------------------------- env vars --------------------------------
PATH = /home/local/TU/tue50988/.local/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/freesurfer/mni/bin:/usr/local/fsl/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/abin:/usr/local/abin

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH = :/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace

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 /usr/local/abin

------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 2.0.8 (amd64)

have Ubuntu system: ubuntu 20.04 focal

========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* AFNI programs show FAILURE
* insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)
Subject Author Posted

AFNI Install for Multiple users

MeganQ May 30, 2022 09:14AM

Re: AFNI Install for Multiple users

rick reynolds May 30, 2022 10:05AM

Re: AFNI Install for Multiple users

MeganQ May 30, 2022 10:12AM

Re: AFNI Install for Multiple users

rick reynolds May 30, 2022 08:36PM

Re: AFNI Install for Multiple users

MeganQ May 31, 2022 08:22AM



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