Defined Type: r_lang::bioc
- Defined in:
- modules/r_lang/manifests/bioc.pp
Overview
Define: r_lang::bioc
Facilitates installation of R packages from bioconductor.org
Parameters
- timeout
-
default 300 (seconds) but may need to be larger for R packages with a lot of dependencies that take time to build (e.g. tidyverse)
- ensure
-
default 'present' but also accepts 'absent' hoping to support 'latest' eventually
- library
-
default '/usr/local/lib/R/site-library', used for specifying the path of the library for installing the R package
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# File 'modules/r_lang/manifests/bioc.pp', line 20
define r_lang::bioc (
$timeout = 300,
$ensure = 'present',
$library = '/usr/local/lib/R/site-library'
) {
$pkg_path = "${library}/${title}"
case $ensure {
'absent': {
# Since r_lang can be used on machines that don't have shiny_server,
# we only want a package removal to restart the Shiny Server service
# if the service actually exists:
$remove_notify = defined(Service['shiny-server']) ? {
true => Service['shiny-server'],
default => Undef,
}
exec { "remove-${title}":
command => "/usr/bin/R -e \"remove.packages('${title}', lib = '${library}')\"",
notify => $remove_notify,
onlyif => "test -d ${pkg_path}",
}
}
default: {
exec { "package-${title}":
require => [
File['/etc/R/biocLite.R']
],
timeout => $timeout,
command => "/usr/bin/R -e \"source('/etc/R/biocLite.R'); biocLite('${title}', lib = '${library}', suppressUpdates = TRUE, ask = FALSE)\"",
creates => $pkg_path,
}
}
}
}
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