nmuncy/afni_ub24 repository overview

root@8c2c4b00a848:/# afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture:         64bit ELF
cpu type:             x86_64
system:               Linux
release:              5.15.0-107-generic
version:              #117~20.04.1-Ubuntu SMP Tue Apr 30 10:35:57 UTC 2024
distribution:         ubuntu 24.04 Noble Numbat
number of CPUs:       16
apparent login shell: bash
shell RC file:        .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /opt/abin/afni
afni version         : Precompiled binary linux_ubuntu_24_64: Jul 16 2024 
                     : AFNI_24.2.01 'Macrinus'
AFNI_version.txt     : AFNI_24.2.01, linux_ubuntu_24_64, Jul 16 2024, official
which python         : /usr/bin/python
python version       : 3.12.3
which R              : /usr/bin/R
R version            : R version 4.3.3 (x86_64-pc-linux-gnu)

instances of various programs found in PATH:
    afni    : 1   (/opt/abin/afni)
    R       : 1   (/usr/bin/R)
    python  : 1   (/usr/bin/python3.12)
    python2 : 0 
    python3 : 1   (/usr/bin/python3.12)

** 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
tcsh version         : 6.24.10
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 : 3.6.3

++ module loaded: flask
   module file : /usr/lib/python3/dist-packages/flask/__init__.py
   flask version : 3.0.2

++ module loaded: flask_cors
   module file : /usr/lib/python3/dist-packages/flask_cors/__init__.py
   flask_cors version : 4.0.0

-------------------------------- env vars --------------------------------
PATH                       = /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/abin:/opt/R

PYTHONPATH                 = 
R_LIBS                     = /opt/R
LD_LIBRARY_PATH            = 
DYLD_LIBRARY_PATH          = 
DYLD_FALLBACK_LIBRARY_PATH = 
CONDA_SHLVL                = 
CONDA_DEFAULT_ENV          = 
CC                         = 

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

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

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

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

   -- no .tcshrc, will create one as a follower of .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 4 modifications across 3 files:
   
      file             path  flatdir  apsearch        follower
      ---------------  ----  -------  --------        --------
      .cshrc           1     0        1               0     
      .tcshrc          0     0        0               1     
      .bashrc          1     0        1               0     
   
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas    : found TT_N27+tlrc  under /opt/abin

------------------------------ OS specific -------------------------------
which apt-get        : /usr/bin/apt-get
apt-get version      : apt 2.7.14 (amd64)

have Ubuntu system: ubuntu 24.04 Noble Numbat
have Ubuntu afni  : Precompiled binary linux_ubuntu_24_64: Jul 16 2024 

=========================  summary, please fix:  =========================
*  just be aware: login shell 'bash', but our code examples use 'tcsh'
*  please run: cp /opt/abin/AFNI.afnirc ~/.afnirc
*  please run: "suma -update_env" for .sumarc
*  please run: apsearch -update_all_afni_help
*  dot file test : want 4 modifications across 3 files:
*  insufficient data for AFNI bootcamp
   (see "Prepare for Bootcamp" on install pages)