standard_args: Standard Template Arguments
In pacs: Supplementary Tools for R Packages Developers

standard_args

R Documentation

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()$Flavor`. By default an empty scope field deactivated assessment for `checkred` column, and NULL flavor will results in checking all machines. Default: `list(scope = character(0), flavor = NULL)`
`description_v`	`logical` if the dependencies version should be taken from description files, minimal required. By default installed versions are taken. Default: `FALSE`
`exclude_joint`	`integer` exclude packages which are dependencies of at least N other packages, not count main package dependencies. Default: `0`
`fields`	`character` vector listing the types of dependencies, a subset of `c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")`. Character string "all" is shorthand for that vector, character string "most" for the same vector without "Enhances", character string "strong" (default) for the first three elements of that vector. Default: `c("Depends", "Imports", "LinkingTo")`
`flavors`	`character` vector of CRAN server names to consider, possible names could be get with `pacs::cran_flavors()$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.