Setup error or warning?

Installation Issues
1

Hi,

I started installing the AFNI on a Ubuntu 20.04 system and was able to open AFNI and SUMA GUI. However, there was a bug/warning reported in summary section saying that "dot file test : want 1 modifications across 3 files:" after I run afni_system_check.py -check_all.

I wonder if this is actually a bug or just a warning and will affect software experience in the future. I am new to AFNI and happy to listen to any suggestions.

Here is the check summary:

-------------------------------- general ---------------------------------
architecture:         64bit ELF
cpu type:             x86_64
system:               Linux
release:              5.15.0-79-generic
version:              #86~20.04.2-Ubuntu SMP Mon Jul 17 23:27:17 UTC 2023
distribution:         ubuntu 20.04 focal
number of CPUs:       32
apparent login shell: bash
shell RC file:        .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /home/vu/abin/afni
afni version         : Precompiled binary linux_ubuntu_16_64: Aug  9 2023 
                     : AFNI_23.2.04 'Marcus Didius Severus Julianus'
AFNI_version.txt     : AFNI_23.2.04, linux_ubuntu_16_64, Aug 09 2023, official
which python         : /usr/bin/python
python version       : 3.8.10
which R              : /usr/bin/R
R version            : R version 4.3.1 (2023-06-16) -- "Beagle Scouts"

instances of various programs found in PATH:
    afni    : 1   (/home/vu/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                 : success
    suma                 : success
    3dSkullStrip         : success
    3dAllineate          : success
    3dRSFC               : success
    SurfMesh             : success
    3dClustSim           : success
    uber_subject.py      : success
    3dMVM                : success

------------------------ dependent program tests -------------------------
checking for dependent programs...

which tcsh           : /usr/bin/tcsh
which Xvfb           : /usr/bin/Xvfb

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

R RHOME : /usr/lib/R

------------------------------ python libs -------------------------------

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

-------------------------------- env vars --------------------------------
PATH = /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/vu/abin

PYTHONPATH = 
R_LIBS = /home/vu/R

LD_LIBRARY_PATH = 
DYLD_LIBRARY_PATH = 
DYLD_FALLBACK_LIBRARY_PATH = 

----------------------------- eval dot files -----------------------------

----------- AFNI $HOME files -----------

    .afnirc                   : found
    .sumarc                   : found
    .afni/help/all_progs.COMP : found

--------- shell startup files ----------

   -- good: .tcshrc seems to contain 'source .cshrc'
   -- considered operations: path, flatdir, apsearch
      (not on a mac, should skip flatdir)
   
   -- note: followers should not need edits, so edit flags should be 0
      (have 1 follower(s), which can be ignored)
   
   dot file test : want 1 modifications across 3 files:
   
      file             path  flatdir  apsearch        follower
      ---------------  ----  -------  --------        --------
      .cshrc           0     0        1               0     
      .tcshrc          0     0        0               1     
      .bashrc          0     0        0               0     
   
------------------------------ data checks -------------------------------
data dir : found AFNI_data6   under $HOME (1876181M Avail)
           top history: ...3 [rickr]: renamed GroupAna_cases scripts and output
data dir : found AFNI_demos   under $HOME
           top history: ...ct 2020 [taylorp]: updated scripts under FATCAT_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/vu/abin

------------------------------ OS specific -------------------------------
which apt-get        : /usr/bin/apt-get
apt-get version      : apt 2.0.9 (amd64)

have Ubuntu system: ubuntu 20.04 focal
have Ubuntu afni  : Precompiled binary linux_ubuntu_16_64: Aug  9 2023 

=========================  summary, please fix:  =========================
*  just be aware: login shell 'bash', but our code examples use 'tcsh'
*  dot file test : want 1 modifications across 3 files:
2

The "dot files" are the startup files for the shell you are using. You will want to be sure that the path variable set there includes the directory path to AFNI programs. Here's an example with zsh on my Mac (similar to bash notation)

# auto-inserted by @update.afni.binaries :
export PATH=$PATH:/Users/glend/abin

# only for Macs- commented out for this Ubuntu post
# auto-inserted by @update.afni.binaries :
#export DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:/opt/X11/lib/flat_namespace

# auto-inserted by @update.afni.binaries :
#    set up tab completion for AFNI programs
if [ -f $HOME/.afni/help/all_progs.COMP.zsh ]
then
   autoload -U +X bashcompinit && bashcompinit
   autoload -U +X compinit && compinit \
      && source $HOME/.afni/help/all_progs.COMP.zsh
fi

You can see more about the startup scripts each shell uses with

afni_system_check.py -help_dot_files
3

Hi, I have the same issue. I tried pasting the code you wrote (I have a mac so I added also the commented part), but the problem still persists.

4

On a Mac, the default shell is zsh, so you would want to edit the .zshrc file in your home directory. The excerpt I included above was from that file via this command:

cat ~/.zshrc
5

Thank you! My .zshrc file seems to contain all the folders that were included in the .zshrc file you displayed (and more). Do you have any idea why I still get a comment in about dot file in the 'please fix'?

Attached is my .zshrc file:

export PATH=$PATH:/opt/homebrew/opt/python/libexec/bin

export PATH=$PATH:/Library/Frameworks/R.framework/Resources

export PATH=$PATH:/usr/local/gfortran/bin



# auto-inserted by @update.afni.binaries :

export PATH=$PATH:/Users/ramotlab/abin



# auto-inserted by @update.afni.binaries :

export DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:/opt/X11/lib/flat_namespace



# auto-inserted by @update.afni.binaries :

#    set up tab completion for AFNI programs

if [ -f $HOME/.afni/help/all_progs.COMP.zsh ]

then

   autoload -U +X bashcompinit && bashcompinit

   autoload -U +X compinit && compinit \

      && source $HOME/.afni/help/all_progs.COMP.zsh

fi



export PATH=${PATH}:/usr/local/opt/python/libexec/bin