Status of packages in a library

Usage

lib_status(lib = .libPaths()[1])

pkg_list(lib = .libPaths()[1])

Arguments

lib: Path to library.

Value

Data frame the contains data about the packages installed in the library. It has always has columns:

biocviews: the corresponding field from DESCRIPTION, it must be present for all Bioconductor packages, other packages typically don't have it.
built: the Built field from DESCRIPTION.
depends, suggests, Imports, linkingto, enhances: the corresponding fields from the DESCRIPTION files.
deps: A list or data frames, the dependencies of the package. It has columns: ref, type (dependency type in lowercase), package (dependent package, or R), op and version, for last two are for version requirement. op can be >=, >, == or <=, although the only the first one is common in practice.
library: path to the package library containing the package.
license: from DESCRIPTION.
md5sum: from DESCTIPTION, typically NA, except on Windows.
needscompilation: from DESCRIPTION, this column is logical.
package: package name.
platform: from the Built field in DESCRIPTION, the current platform if missing from DESCRIPTION.
priority: from DESCRIPTION, usually base, recommended, or missing.
ref: the corresponding installed::* package reference.
repository: from DESCRIPTION. For packages from a CRAN repository this is CRAN, some other repositories, e.g. R-universe adds the repository URL here.
repotype: cran, bioc or missing.
rversion: from the Built field. If no such field, then the current R version.
sysreqs: the SystemRequirements field from DESCRIPTION.
title: package title.
type: always installed.
version: package version (as string).

Most of these columns are unchanged from DESCRIPTION, but pak also adds a couple.

Notes:

In addition, it also has all remote* and config/needs/* entries from the DESCRIPTION files. (Case insensitive.)
All columns are of type character, except for needscompilation, which is logical and deps, which is a list columns.
If an entry is missing for a package, it is set to NA.
Note that column names are lowercase, even if the corresponding entries are not in DESCRIPTION.
The order of the columns is not deterministic, so don't assume any order.
Additional columns might be present, these are internal for pak and should not be used in user code.

Examples

lib_status(.Library)

#> # A data frame: 31 × 31
#>    library   package version prior…¹ title license sugge…² built depends
#>    <chr>     <chr>   <chr>   <chr>   <chr> <chr>   <chr>   <chr> <chr>
#>  1 /Library… base    4.2.2   base    "The… Part o… methods R 4.… NA
#>  2 /Library… boot    1.3-28  recomm… "Boo… Unlimi… MASS, … R 4.… R (>= …
#>  3 /Library… class   7.3-20  recomm… "Fun… GPL-2 … NA      R 4.… R (>= …
#>  4 /Library… cluster 2.1.4   recomm… "\"F… GPL (>… MASS, … R 4.… R (>= …
#>  5 /Library… codeto… 0.2-18  recomm… "Cod… GPL     NA      R 4.… R (>= …
#>  6 /Library… compil… 4.2.2   base    "The… Part o… NA      R 4.… NA
#>  7 /Library… datase… 4.2.2   base    "The… Part o… NA      R 4.… NA
#>  8 /Library… filelo… 1.0.2   NA      "Por… MIT + … callr … R 4.… NA
#>  9 /Library… foreign 0.8-83  recomm… "Rea… GPL (>… NA      R 4.… R (>= …
#> 10 /Library… graphi… 4.2.2   base    "The… Part o… NA      R 4.… NA
#> # … with 21 more rows, 22 more variables: needscompilation <lgl>,
#> #   repository <chr>, imports <chr>, remotetype <chr>,
#> #   remotepkgref <chr>, remoteref <chr>, remoterepos <chr>,
#> #   remotepkgplatform <chr>, remotesha <chr>, enhances <chr>,
#> #   linkingto <chr>, md5sum <chr>, platform <chr>, biocviews <chr>,
#> #   sysreqs <chr>, ref <chr>, type <chr>, status <chr>, rversion <chr>,
#> #   sources <list>, repotype <chr>, deps <list>, and abbreviated …

Status of packages in a library

Usage

Arguments

Value

Notes:

Examples

See also