dot file test : want 3 modifications across 4 files

Installation Issues
1

Hello,

I have just installed AFNI's latest version. Doing a "afni_system_check.py -check_all", I got "got file test : want 3 modifications across 4 files:" to be fixed. The whole output is:

-------------------------------- general ---------------------------------
architecture:         64bit ELF
cpu type:             x86_64
system:               Linux
release:              6.1.0-1033-oem
version:              #33-Ubuntu SMP PREEMPT_DYNAMIC Thu Feb  1 19:38:49 UTC 2024
distribution:         Ubuntu 22.04.4 LTS
number of CPUs:       24
apparent login shell: sh  (current shell is bash)
shell RC file:        .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /home/azman_cbdl/abin/afni
afni version         : Precompiled binary linux_ubuntu_16_64: Feb 15 2024 
                     : AFNI_24.0.07 'Caracalla'
AFNI_version.txt     : AFNI_24.0.07, linux_ubuntu_16_64, Feb 15 2024, official
which python         : /home/azman_cbdl/anaconda3/bin/python
python version       : 3.11.5
which R              : /usr/bin/R
R version            : R version 4.3.2 (x86_64-pc-linux-gnu)

instances of various programs found in PATH:
    afni    : 1   (/home/azman_cbdl/abin/afni)
    R       : 1   (/usr/bin/R)
    python  : 2 
      /home/azman_cbdl/anaconda3/bin/python3.11
      /usr/bin/python3.10
    python2 : 0 
    python3 : 2 
      /home/azman_cbdl/anaconda3/bin/python3.11
      /usr/bin/python3.10

** have python3 but not python2

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 : /home/azman_cbdl/anaconda3/lib/python3.11/site-packages/matplotlib/pyplot.py
   matplotlib version : 3.7.2

++ module loaded: flask
   module file : /home/azman_cbdl/anaconda3/lib/python3.11/site-packages/flask/__init__.py
   flask version : 2.2.2

** failed to load module flask_cors
-- flask_cors is not required, but is desirable

-------------------------------- env vars --------------------------------
PATH = /home/azman_cbdl/anaconda3/bin:/home/azman_cbdl/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/snap/bin:/home/azman_cbdl/abin

PYTHONPATH = 
R_LIBS = /home/azman_cbdl/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, 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 3 modifications across 4 files:
   
      file             path  flatdir  apsearch        follower
      ---------------  ----  -------  --------        --------
      .cshrc           0     0        1               0     
      .tcshrc          0     0        0               1     
      .bashrc          0     0        0               0     
      .profile         1     0        1               0     
   
------------------------------ data checks -------------------------------
data dir : found AFNI_data6   under $HOME (959827M Avail)
           top history: ... [gangc]: redo 0.BGA as 1.bga and update run.MSS.txt
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/azman_cbdl/abin

------------------------------ OS specific -------------------------------
which apt-get        : /usr/bin/apt-get
apt-get version      : apt 2.4.11 (amd64)

have Ubuntu system: Ubuntu 22.04.4 LTS
have Ubuntu afni  : Precompiled binary linux_ubuntu_16_64: Feb 15 2024 

=========================  summary, please fix:  =========================
*  just be aware: login shell 'sh', but our code examples use 'tcsh'
*  dot file test : want 3 modifications across 4 files:

What can be done to fix it?

Thank you!

2

It is surprising to see .cshrc - apsearch in the fix list. What is the output from:

which afni
which init_user_dotfiles.py
init_user_dotfiles.py -test -shell_list tcsh sh -do_updates path apsearch -verb 2
init_user_dotfiles.py -ver

Thanks,

  • rick
3

Thanks for the response, rick.

The outputs you asked for:

which afni

/home/azman_cbdl/abin/afni

which init_user_dotfiles.py

/home/azman_cbdl/abin/init_user_dotfiles.py

init_user_dotfiles.py -test -shell_list tcsh sh -do_updates path apsearch -verb 2

-- processing...
++ have original abin /home/azman_cbdl/abin
-- setting dir_bin to ABIN /home/azman_cbdl/abin
-- setting dir_dot to $HOME
++    .cshrc               :  19 lines
++    .tcshrc              :   6 lines
++    .profile             :  27 lines
-- good: .tcshrc seems to contain 'source .cshrc'
-- skipping file shell tcsh: 1
-- skipping file shell tcsh: 1
-- skipping file shell sh: 1
-- 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 3 files:

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

init_user_dotfiles.py -ver

init_user_dotfiles.py, version 1.5, January 2, 2024

Somehow, now it is "dot file test : want 1 modifications across 3 files:"

This happened after restarted the system once. What does it mean?

Thanks,
Azman

4

Okay, this looks much better, .cshrc is no longer in the list. You are now using a newer version of that init_user_dotfiles.py program, which was in turn run by afni_system_check.py to make the report. The newer version does not require apsearch for the non-login/current shells. For you it tests against sh and bash, since sh is your login shell, and bash is the shell you are currently running.

Anyway, I think things are fine for you. But I need to see why .profile is not being recognized as a follower file. Or maybe it shouldn't be. What is in your .profile?

cat ~/.profile

You can send it via a private message if you prefer.

But either way, this looks fine for you.

  • rick