standard_args: Standard Template Arguments

Description

Standard Template Arguments

Arguments

at: Date from which to take the version. Default: NULL
attr: logical if a package and its version should be added as an attribute of data.frame or for FALSE as an additional record. Default: TRUE
base: logical if to add base packages too. If TRUE then pacs::pacs_base() are taken into account. Default: FALSE
built: logical if to add an R version under which each package was installed. Useful mainly for a local usage. Packages installed with a previous version of R could not work correctly with the new version of R. Default: FALSE
checkred: list with two named fields, scope and flavor. scope of R CRAN check pages statuses to consider, any of c("ERROR", "FAIL", "WARN", "NOTE"). flavor is a vector of CRAN machines to consider, which might be retrieved with pacs::cran_flavors()$Flavor. By default an empty scope field deactivated assessment for checkred column, and NULL flavor will results in checking all machines. Default: list(scope = character(0), flavor = NULL)
description_v: logical if the dependencies version should be taken from description files, minimal required. By default installed versions are taken. Default: FALSE
exclude_joint: integer exclude packages which are dependencies of at least N other packages, not count main package dependencies. Default: 0
file: character file name to read. Possible values are DESCRIPTION, NEWS and NAMESPACE.
fields: character vector listing the types of dependencies, a subset of c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances"). Character string "all" is shorthand for that vector, character string "most" for the same vector without "Enhances", character string "strong" (default) for the first three elements of that vector. Default: c("Depends", "Imports", "LinkingTo")
flavors: character vector of CRAN server names to consider, possible names could be get with pacs::cran_flavors()$Flavor. The pacs::match_flavors() function could be used to get CRAN server names matched for your local OS. By default all CRAN machines are considered NULL value. Default: NULL
from: Date the lower limit. Default: NULL
lib.loc: character vector of search paths with local packages. Default: .libPaths()
lifeduration: logical if to assess life duration for each package in the library. For installed newest releases of packages, a local evaluation is used. MEATCRAN CRANDB is used for libraries with less than 500 packages. Otherwise the direct web page download from CRAN is used. Default: `FALSE``
limit: numeric at least days to treat as healthy, ">=limit". Default: 14
local: logical if to use local repository (or newest remote packages). Default: FALSE
na.rm: logical if to remove NA values.
new: character a new version of package, default newest version. Default: NULL
old: character an old version of package, default local version. Default: NULL
pac: character a package name.
pacs: character vector of packages names.
path: character path to the shiny app. Default: "."
repos: character vector of repositories URLs to use. By default checking CRAN and newest Bioconductor per R version. Default pacs::biocran_repos()
recursive: logical if to assess the dependencies recursively. Default: TRUE
scope: character vector scope of the check, accepted values c("ERROR", "FAIL", "WARN", "NOTE"). Default: c("ERROR", "FAIL")
source: character one of c("cran", "crandb"). Using the MEATCRAN CRANDB or the direct web page download from CRAN. When "crandb" is set then options(pacs.crandb_ntry = 3) and options(pacs.crandb_nsleep = 0.001) can be used to control the fetch. "pacs.crandb_ntry" can be used to set the maximum number of try outs, by default 3. "pacs.crandb_nsleep" can be used to set the sleep duration between fetch try outs, by default 0.001. Default: "cran"
startup: logical include only startup packages. Default: FALSE
to: Date the upper limit. Default: NULL
vec: character vector.
version: character version of a package. Default: NULL
versions: character vector of packages versions.