================== Welcome to rPkgsInstall ==================
Install/update/remove R packages for AFNI
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Version 1.0.1, Feb 13, 2024
Author: Gang Chen (gangchen@mail.nih.gov)
Website - https://afni.nimh.nih.gov/gangchen_homepage
SSCC/NIMH, National Institutes of Health, Bethesda MD 20892
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Usage:
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rPkgsInstall is a program for installing, checking, updating, or removing any
R packages. It conveniently runs on the shell terminal instead of the R prompt.
Check out the examples below or the option specifications for usage details.
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Example 1 --- Install all the R packages that are currently required for most
AFNI programs except for RBA, MBA and TRR, which require the R package 'brms':
rPkgsInstall -pkgs ALL
rPkgsInstall -pkgs ALL -site 'http://cloud.r-project.org'
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Example 2 --- Install user-specified R packages:
rPkgsInstall -pkgs 'brms'
rPkgsInstall -pkgs 'afex,phia,paran'
rPkgsInstall -pkgs 'snow,nlme,psych' -site 'http://cloud.r-project.org'
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Example 3 --- check/update/remove R packages:
rPkgsInstall -pkgs ALL -check
rPkgsInstall -pkgs ALL -update
rPkgsInstall -pkgs ALL -remove
rPkgsInstall -pkgs ALL -update -site 'http://cloud.r-project.org/'
rPkgsInstall -pkgs 'lmerTest,pixmap,plotrix' -check
rPkgsInstall -pkgs 'afex,phia,paran' -update
rPkgsInstall -pkgs 'boot' -remove
rPkgsInstall -pkgs 'snow,nlme,vars' -update -site 'http://cloud.r-project.org'
Options in alphabetical order:
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-check: This option verifies whether all or the user-specified R packages
listed in option -pkgs are installed on the computer, but it does not
install/update/remove the packages.
-help: this help message
-pkgs package_list: List all the packages that you would like to install,
update or move. This option is required for installation, update,
or removal. The absence of both options -update and -remove means
installation. The package names should be separated with comma (,)
without any other characters such as spaces, and should be surrounded
within single/double quotes. For example, -pkgs "afex,phia". If
package_list is set as ALL, all the following packages required for
AFNI programs will be installed, updated, or removed:
'afex', 'phia', 'snow', 'nlme', 'lmerTest', 'gamm4', 'data.table',
'paran', 'psych', 'corrplot', 'metafor'.
You can use rPkgsInstall to install, update, or remove any R packages,
and those packages do not have to be in the list above.
***NOTE*** these R packages should be good enough for running all major
programs that use R except for programs such as RBA, MBA and TRR, which
require installing the R package 'brms'. To install 'brms', run the
following command at the terminal:
rPkgsInstall -pkgs 'brms'
Or, type the following in R:
install.packages("brms").
-remove: This option indicates that all or the user-specified R packages in AFNI
will be purged from your computer. The absence of the option (default)
means installing or updating, but no removing.
-show_allowed_options: list of allowed options
-site download_website: You can specify the package repository website within
single/double quotes. The current sites can be found at
http://cran.r-project.org/mirrors.html
The default is 'http://cloud.r-project.org'
University, Houghton, MI.
-update: This option indicates that all or the user-specified R packages in AFNI
will be updated. The absence of the option (default) means no updating.
A package specified in '-pkgs package_list' that has not been installed on
the computer will be installed under this option.
WARNING: Updating some R packages may require that R be upgraded to the
most recent version.
