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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
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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
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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)
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R Reynolds July, 2013
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