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.. _ahelp_afni_system_check.py:

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afni_system_check.py
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.. contents:: :local:


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.. code-block:: none

    
    =============================================================================
    afni_system_check.py    - perform various system checks
    
    This program is intended to be helpful for figuring out AFNI installation
    issues.
    
    examples
    
       1.  afni_system_check.py -check_all
       2a. afni_system_check.py -find_prog python
       2b. afni_system_check.py -find_prog python -exact yes
       3a. afni_system_check.py -disp_R_ver_for_lib $R_LIBS
       3b. afni_system_check.py -disp_abin
    
    -----------------------------------------------------------------------------
    terminal options:
    
       -help                : show this help
       -help_dot_files      : show help on shell setup files
       -help_rc_files       : SAME
       -hist                : show program history
       -show_valid_opts     : show valid options for program
       -todo                : show current todo list
       -ver                 : show current version
    
       NOTE: either a terminal or an action option is required
    
    action options:
    
       -check_all           : perform all system checks
                              - see section, "details displayed via -check_all"
       -disp_num_cpu        : display number of CPUs available
       -disp_R_ver_for_lib  : display the R version used when building an R library
                              - this refers to those installed by rPkgsInstall,
                                most likely under $R_LIBS
       -disp_abin           : display directory containing 'afni' (or this)
       -disp_ver_afni       : display AFNI package version (else "None")
       -disp_ver_matplotlib : display matplotlib version (else "None")
       -disp_ver_pylibs LIB LIB ... :
                              display versions of given python libraries (else NONE)
                              - use 'ALL' to include the default test list
       -dot_file_list       : list all found dot files (startup files)
       -dot_file_show       : display contents of all found dot files
       -dot_file_pack NAME  : create a NAME.tgz package containing dot files
       -find_prog PROG      : search PATH for PROG
                              - default is *PROG*, case-insensitive
                              - see also -casematch, -exact
    
    other options:
    
       -casematch yes/no    : match case in -find_prog
       -data_root DDIR      : search for class data under DDIR
       -exact yes/no        : search for PROG without wildcards in -find_prog
       -use_asc_path        : prepend ASC dir to PATH
                              (to test programs in same directory as ASC.py)
       -verb LEVEL          : set the verbosity level
    
    -----------------------------------------------------------------------------
    details displayed via -check_all (just run to see):
    
       general information:
          - CPU, operating system and version, # CPUs, login shell
    
       AFNI and related tests:
          - which afni, python, R and tcsh, along with versions
          - check for multiple afni packages in PATH
          - check that various AFNI programs run
          - check for AFNI $HOME dot files (.afnirc, .sumarc, etc.)
    
       python libs:
          - check that various python libraries are found and loaded
    
       environment vars:
          - show PATH, PYTHONPATH, R_LIBS, LD_LIBRARY_PATH, DYLD_LIBRARY_PATH, etc.
    
       evaluation of dot files:
          - show the output of "init_user_dotfiles -test", restricted
            to shells of interest (user shells plus tcsh)
    
       data checks:
          - check for AFNI bootcamp data directories and atlases
    
       OS specific:
          - on linux, check for programs and version of dnf, yum
          - on macs, check for homebrew, fink, flat_namespace, etc.
    
       final overview:
          - report anything that seems to need fixing for a bootcamp
            (details shown earlier)
    
    -----------------------------------------------------------------------------
    R Reynolds    July, 2013
    =============================================================================