Thank you that was helpful, I am closer. I still have a few issues.

First, what I have done since my last post:
(1) I ran the lines you stated.
(2) I installed Miniconda for python 2.7 (I already had for python3 installed). I have confirmed that both python3 and python2 work, although it seems like python3 is the default if I just type "python" into my terminal.
(3) I installed R for ubuntu 20.04 following these instructions
(4) I got a brms error so I tried to run

sudo add-apt-repository -y "ppa:marutter/rrutter3.5"
sudo add-apt-repository -y "ppa:marutter/c2d4u3.5"

sudo apt update

sudo apt install -y r-cran-rstan r-cran-shinystan r-cran-brms

I am still getting errors:
(1) brms is still not installed or working and I am unsure how to fix that. The repositories and from (4) above did not work for me.
(2) AFNI is still saying I have python3 but that I need python2... so it doesn't seem to recognize that I have python2 which makes me worried that if I use anything that needs python2, it will not find my python2.
(3) I still get an error of "login shell 'bash', trusting user to translate code examples from 'tcsh'"

Here is my output of my afni check for reference:

-------------------------------- general ---------------------------------
architecture:         64bit 
system:               Linux
release:              5.4.0-33-generic
version:              #37-Ubuntu SMP Thu May 21 12:53:59 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 4.0.1 (2020-06-06) -- "See Things Now"
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: brms!
        

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

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)

Thank you again!



Edited 1 time(s). Last edit at 06/08/2020 12:45PM by kxd344.