lib_status {pak}

Status of packages in a library

Description

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 …      

See Also

Other package functions: pak(), pkg_deps_tree(), pkg_deps(), pkg_download(), pkg_install(), pkg_remove(), pkg_status(), pkg_sysreqs()