dot file test : want 1 modifications across 2 files

Hello,

I have just installed AFNI's latest version. Doing a "afni_system_check.py -check_all", I got "got file test : want 1 modification across 2 files:" to be fixed. The whole output is: Gabriels_Laptop:~> afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
cpu type: x86_64
system: Linux
release: 5.10.16.3-microsoft-standard-WSL2
version: #1 SMP Fri Apr 2 22:23:49 UTC 2021
distribution: ubuntu 20.04 focal
number of CPUs: 12
apparent login shell: tcsh
shell RC file: .tcshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /home/gabenorrie/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: Oct 31 2024
: AFNI_24.3.06 'Elagabalus'
AFNI_version.txt : AFNI_24.3.06, linux_ubuntu_16_64, Oct 31 2024, official
which python : /usr/bin/python
python version : 3.8.10
which R : /usr/bin/R
R version : R version 4.4.2 (x86_64-pc-linux-gnu)

instances of various programs found in PATH:
afni : 1 (/home/gabenorrie/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python3.8)
python2 : 0
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
tcsh version : 6.21.00
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 : /home/gabenorrie/.local/lib/python3.8/site-packages/matplotlib/pyplot.py
matplotlib version : 3.7.5

++ module loaded: flask
module file : /usr/lib/python3/dist-packages/flask/init.py
flask version : 1.1.1

++ module loaded: flask_cors
module file : /usr/lib/python3/dist-packages/flask_cors/init.py
flask_cors version : 3.0.8

-------------------------------- env vars --------------------------------
PATH = /home/gabenorrie/abin:/home/gabenorrie/abin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/wsl/lib:/mnt/c/windows/system32:/mnt/c/windows:/mnt/c/windows/System32/Wbem:/mnt/c/windows/System32/WindowsPowerShell/v1.0/:/mnt/c/windows/System32/OpenSSH/:/mnt/c/Program:Files:(x86)/NVIDIA:Corporation/PhysX/Common:/mnt/c/Program:Files/NVIDIA:Corporation/NVIDIA:NvDLISR:/mnt/c/WINDOWS/system32:/mnt/c/WINDOWS:/mnt/c/WINDOWS/System32/Wbem:/mnt/c/WINDOWS/System32/WindowsPowerShell/v1.0/:/mnt/c/WINDOWS/System32/OpenSSH/:/mnt/c/Program:Files/HP/HP:One:Agent:/mnt/c/Users/gabe/AppData/Local/Microsoft/WindowsApps

PYTHONPATH =
R_LIBS = /home/gabenorrie/R
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
CONDA_SHLVL =
CONDA_DEFAULT_ENV =
CC =

----------------------------- 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, apsearch

-- 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 2 files:

  file             path  flatdir  apsearch        follower
  ---------------  ----  -------  --------        --------
  .cshrc           0     0        1               0
  .tcshrc          0     0        0               1

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME (257007M Avail)
top history: 08 Nov 2024 [rickr/ptaylor]: add afni/bad_scripts
data dir : found AFNI_demos under $HOME
top history: 07 Nov 2024 [rickr]: shrank AFNI_pamenc tree
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/gabenorrie/abin

------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 2.0.10 (amd64)

have Ubuntu system: ubuntu 20.04 focal
have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Oct 31 2024

========================= summary, please fix: =========================

  • dot file test : want 1 modifications across 2 files:

Hello,
That requested apsearch update shows your .cshrc file is missing something like:

# set up tab completion for AFNI programs
# (only do this in an interactive shell)
if ( $?prompt ) then
   if ( "$prompt" != "" ) then
      if ( -f $HOME/.afni/help/all_progs.COMP ) then
         source $HOME/.afni/help/all_progs.COMP
      endif
   endif
endif

That sets up tab completion for options in AFNI programs.
You may have already run apsearch -update_all_afni_help, but then .cshrc should source that all_progs.COMP file to actually set up the tab completion.

Does that seem reasonable?

  • rick