Hi pt,

Thanks for the quick repsonse.

The output of that command is:

afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 3.10.0-957.12.1.el7.x86_64
version: #1 SMP Mon Apr 29 14:59:59 UTC 2019
distribution: CentOS Linux 7 (Core)
number of CPUs: 4
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /cubric/software/afni.versions/21.2.09/afni
afni version : Precompiled binary linux_openmp_64: Sep 27 2021
: AFNI_21.2.09 'Nerva'
AFNI_version.txt : AFNI_21.2.09, linux_openmp_64, Sep 27 2021
which python : /cubric/data/c1639425/miniconda3/envs/python3.9/bin/python
python version : 3.9.12
which R : /cubric/software/r.versions/3.5.1/bin/R
R version : R version 3.5.1 (2018-07-02) -- "Feather Spray"
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/cubric/software/afni.versions/21.2.09/afni)
R : 2
/cubric/software/r.versions/3.5.1/bin/R
/usr/bin/R
python : 3
/cubric/data/c1639425/miniconda3/envs/python3.9/bin/python3.9
/usr/bin/python2.7
/cubric/data/c1639425/miniconda3/bin/python3.9
python2 : 1 (/usr/bin/python2.7)
python3 : 3
/cubric/data/c1639425/miniconda3/envs/python3.9/bin/python3.9
/usr/bin/python3.6
/cubric/data/c1639425/miniconda3/bin/python3.9


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: brms!
These packages are not installed on the computer: metafor!


R RHOME : /cubric/software/r.versions/3.5.1/lib64/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

** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is not required, but is desirable

-------------------------------- env vars --------------------------------
PATH = /cubric/data/c1639425/miniconda3/envs/python3.9/bin:/cubric/data/c1639425/miniconda3/condabin:/cubric/software/gcc.versions/8.3/bin:/cubric/software/r.versions/3.5.1/bin:/cubric/software/fsl/bin:/cubric/software/freesurfer/bin:/cubric/software/freesurfer/fsfast/bin:/cubric/software/freesurfer/tktools:/cubric/software/fsl/bin:/cubric/software/freesurfer/mni/bin:/cubric/software/gcc.versions/8.3/bin:/cubric/software/r.versions/3.5.1/bin:/cubric/software/fsl/bin:/cubric/software/freesurfer/bin:/cubric/software/freesurfer/fsfast/bin:/cubric/software/freesurfer/tktools:/cubric/software/fsl/bin:/cubric/software/freesurfer/mni/bin:/cubric/software/gcc.versions/8.3/bin:/cubric/software/r.versions/3.5.1/bin:/opt/VirtualGL/bin:/cubric/software/fsl/bin:/cubric/software/freesurfer/bin:/cubric/software/freesurfer/fsfast/bin:/cubric/software/freesurfer/tktools:/cubric/software/fsl/bin:/cubric/software/freesurfer/mni/bin:/cubric/software/gcc.versions/8.3/bin:/cubric/software/r.versions/3.5.1/bin:/opt/VirtualGL/bin:/cubric/software/fsl/bin:/cubric/software/freesurfer/bin:/cubric/software/freesurfer/fsfast/bin:/cubric/software/freesurfer/tktools:/cubric/software/fsl/bin:/cubric/software/freesurfer/mni/bin:/cubric/software/gcc.versions/8.3/bin:/cubric/software/r.versions/3.5.1/bin:/opt/VirtualGL/bin:/usr/lib64/qt-3.3/bin:/cubric/software/fsl/bin:/cubric/software/freesurfer/bin:/cubric/software/freesurfer/fsfast/bin:/cubric/software/freesurfer/tktools:/cubric/software/freesurfer/mni/bin:/usr/local/MATLAB/R2015aSP1/bin:/sbin:/bin:/usr/bin:/usr/local/bin:/usr/local/sbin:/usr/sbin:/opt/matlab/bin:/cubric/software/bin:/opt/MATLAB/R2012b/bin:/opt/MATLAB/R2017b/bin:/cubric/software/afni.versions/21.2.09:/home/c1639425/itksnap/itksnap-3.8.0-20190612-Linux-gcc64/bin:/cubric/software/mrtrix.versions/3_20200227/bin:/cubric/software/ants.versions/2.1.0/Scripts:/cubric/software/ants.versions/2.1.0/bin:/cubric/data/c1639425/miniconda3/bin:/home/c1639425/.local/bin:/home/c1639425/bin:/cubric/software/bin:/opt/MATLAB/R2017b/bin:/opt/MATLAB/R2012b/bin:/cubric/software/afni.versions/21.2.09:/home/c1639425/itksnap/itksnap-3.8.0-20190612-Linux-gcc64/bin:/cubric/software/mrtrix.versions/3_20200227/bin:/cubric/software/ants.versions/2.1.0/Scripts:/cubric/software/ants.versions/2.1.0/bin:/cubric/data/c1639425/miniconda3/bin:/home/c1639425/.local/bin:/home/c1639425/bin:/cubric/software/bin:/opt/MATLAB/R2017b/bin:/opt/MATLAB/R2012b/bin:/cubric/software/afni.versions/21.2.09:/home/c1639425/itksnap/itksnap-3.8.0-20190612-Linux-gcc64/bin:/cubric/software/mrtrix.versions/3_20200227/bin:/cubric/software/ants.versions/2.1.0/Scripts:/cubric/software/ants.versions/2.1.0/bin:/cubric/data/c1639425/miniconda3/bin:/home/c1639425/.local/bin:/home/c1639425/bin:/cubric/software/bin:/opt/MATLAB/R2017b/bin:/opt/MATLAB/R2012b/bin:/cubric/software/afni.versions/21.2.09:/home/c1639425/itksnap/itksnap-3.8.0-20190612-Linux-gcc64/bin:/cubric/software/mrtrix.versions/3_20200227/bin:/cubric/software/ants.versions/2.1.0/Scripts:/cubric/software/ants.versions/2.1.0/bin:/cubric/data/c1639425/miniconda3/bin:/cubric/software/bin:/opt/MATLAB/R2017b/bin:/opt/MATLAB/R2012b/bin:/cubric/software/afni.versions/21.2.09:/home/c1639425/itksnap/itksnap-3.8.0-20190612-Linux-gcc64/bin:/cubric/software/mrtrix.versions/3_20200227/bin:/cubric/software/ants.versions/2.1.0/Scripts:/cubric/software/ants.versions/2.1.0/bin:/cubric/data/c1639425/miniconda3/bin

PYTHONPATH =
R_LIBS = /home/c1639425/R

LD_LIBRARY_PATH = /cubric/software/gcc.versions/8.3/lib64:/cubric/software/gcc.versions/8.3/lib64::/cubric/software/ctf.versions/ctf-libs/:/cubric/software/mrtrix.versions/3_20200227/lib:/cubric/software/ants.versions/2.1.0/lib/:/cubric/software/ctf.versions/ctf-libs/:/cubric/software/mrtrix.versions/3_20200227/lib:/cubric/software/ants.versions/2.1.0/lib/

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 /cubric/software/afni.versions/21.2.09

------------------------------ OS specific -------------------------------
which yum : /bin/yum
yum version : 3.4.3


========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* missing R packages (see rPkgsInstall)
* insufficient data for AFNI bootcamp

Best wishes,
Sam