I know... it's quite upsetting and I have very little sway in our cluster administration...
Here's that output:
afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 3.10.0-1160.24.1.el7.x86_64
version: #1 SMP Thu Apr 8 19:51:47 UTC 2021
distribution: CentOS Linux 7.9.2009 Core
number of CPUs: 16
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /sharedapps/LS/psych_imaging/afni/07.17.2019/afni
afni version : Precompiled binary linux_openmp_64: Jul 3 2019
: AFNI_19.2.01 'Claudius'
AFNI_version.txt : AFNI_19.2.01, linux_openmp_64, Jul 03 2019
which python : /usr/bin/python
python version : 2.7.15
which R : which: no R in (/sharedapps/LS/psych_imaging/afni/07.17.2019/:/usr/pkg/bin:/usr/pkg/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/cnweis/.local/bin:/home/cnweis/bin)
which tcsh : /usr/pkg/bin/tcsh
instances of various programs found in PATH:
afni : 1 (/raid-07/sharedapps/LS/psych_imaging/afni/07.17.2019/afni)
R : 0
python : 1 (/usr/bin/python2.7)
python2 : 1 (/usr/bin/python2.7)
python3 : 1 (/usr/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
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
R: Command not found.
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 = /sharedapps/LS/psych_imaging/afni/07.17.2019/:/usr/pkg/bin:/usr/pkg/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/cnweis/.local/bin:/home/cnweis/bin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH = /sharedapps/LS/psych_imaging/afni/07.17.2019/lib:/sharedapps/pkg-2018Q2/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 /sharedapps/LS/psych_imaging/afni/07.17.2019/
------------------------------ OS specific -------------------------------
which yum : /usr/bin/yum
yum version : There was a problem importing one of the Python modules
========================= summary, please fix: =========================
* login shell 'bash', trusting user to translate code examples from 'tcsh'
* shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
* failure under initial "AFNI and related program tests"
* missing R packages (see rPkgsInstall)
* please run: cp /sharedapps/LS/psych_imaging/afni/07.17.2019/AFNI.afnirc ~/.afnirc
* please run: "suma -update_env" for .sumarc
* please run: apsearch -update_all_afni_help
* insufficient data for AFNI bootcamp
* consider running: yum install PyQt4
