OK, I stepped through step 2 again bit by bit and I uncovered some of the issues (although I am still unsure how to fix):

Lines that do not work include:

sudo apt-get install -y xfonts-base python-qt4
sudo apt-get install -y python-matplotlib
sudo apt-get install -y libssl-dev libgfortran3

The rest seem to have worked once I went line by line. suma -update_env is now working. I realize now I need to find a way to install R differently since it looks like the instructions are specific to Ubuntu 18 (will look more into that later today).

There does not appear to be a python-qt4 available? Neither is there a python-matplotlib or libgfortran3.

Thank you!!

Here is the updated output from the system check:

-------------------------------- general ---------------------------------
architecture:         64bit 
system:               Linux
release:              5.4.0-31-generic
version:              #35-Ubuntu SMP Thu May 7 20:20:34 UTC 2020
distribution:         debian bullseye/sid 
number of CPUs:       8
apparent login shell: bash
shell RC file:        .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /home/keith/abin/afni
afni version         : Precompiled binary linux_ubuntu_16_64: Jun  3 2020 
                     : AFNI_20.1.13 'Otho'
AFNI_version.txt     : AFNI_20.1.13, linux_ubuntu_16_64, Jun 03 2020
which python         : /home/keith/miniconda3/bin/python
python version       : 3.7.6
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   (/home/keith/abin/afni)
    R       : 1   (/usr/bin/R)
    python  : 1   (/home/keith/miniconda3/bin/python3.7)
    python2 : 1   (/usr/bin/python2.7)
    python3 : 2 
      /home/keith/miniconda3/bin/python3.7
      /usr/bin/python3.8


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: afex!
        These packages are not installed on the computer: phia!
        These packages are not installed on the computer: snow!
        These packages are not installed on the computer: lmerTest!
        These packages are not installed on the computer: paran!
        These packages are not installed on the computer: psych!
        These packages are not installed on the computer: brms!
        These packages are not installed on the computer: corrplot!
        These packages are not installed on the computer: metafor!
        

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

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

-------------------------------- env vars --------------------------------
PATH = /home/keith/miniconda3/bin:/home/keith/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/keith/abin:/home/keith/abin

PYTHONPATH = 
R_LIBS = /home/keith/R

LD_LIBRARY_PATH = 
DYLD_LIBRARY_PATH = 
DYLD_FALLBACK_LIBRARY_PATH = 

------------------------------ data checks -------------------------------
data dir : found AFNI_data6   under $HOME
           top history: 20 Feb 2020 [rickr]: updated FT_analysis examples
data dir : found AFNI_demos   under $HOME
           top history: 22 Oct 2019 [discoraj]: added Cluster Explorer Demo
data dir : found suma_demo    under $HOME
           top history: ...s_New/data/Build_tmp on Mon Mar  4 11:56:45 EST 2013
data dir : found afni_handouts under $HOME
atlas    : found TT_N27+tlrc  under /home/keith/abin

------------------------------ OS specific -------------------------------
which apt-get        : /usr/bin/apt-get
apt-get version      : apt 2.0.2ubuntu0.1 (amd64)


=========================  summary, please fix:  =========================
*  login shell 'bash', trusting user to translate code examples from 'tcsh'
*  have python version 3.7.6, some programs need 2.7.x
*  missing R packages (see rPkgsInstall)