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Query and set the list of CRAN-like repositories

Source: R/repo-set.R
repo_get.Rd

pkgcache uses the repos option, see options(). It also automatically uses the current Bioconductor repositories, see bioc_version(). These functions help to query and manipulate the repos option.

Usage

repo_get(
  r_version = getRversion(),
  bioc = TRUE,
  cran_mirror = default_cran_mirror()
)

repo_resolve(spec, username = NULL)

repo_add(..., .list = NULL, username = NULL)

with_repo(repos, expr)

Arguments

r_version

R version(s) to use for the Bioconductor repositories, if bioc is TRUE.

bioc

Whether to add Bioconductor repositories, even if they are not configured in the repos option.

cran_mirror

The CRAN mirror to use, see default_cran_mirror().

spec

A single repository specification, a possibly named character scalar. See details below.

username

User name to set, for authenticated repositories, see repo_auth().

...

Repository specifications. See details below.

.list

List or character vector of repository specifications, see details below.

repos

A list or character vector of repository specifications.

expr

R expression to evaluate.

Value

repo_get() returns a data frame with columns:

  • name: repository name. Names are informational only.

  • url: repository URL.

  • type: repository type. This is also informational, currently it can be cran for CRAN, bioc for a Bioconductor repository, and cranlike: for other repositories.

  • r_version: R version that is supposed to be used with this repository. This is only set for Bioconductor repositories. It is * for others. This is also informational, and not used when retrieving the package metadata.

  • bioc_version: Bioconductor version. Only set for Bioconductor repositories, and it is NA for others.

  • username: user name, for authenticated repositories.

  • has_password: whether repo_get() could find the password for this repository. Call repo_auth() for more information if the credential lookup failed.

repo_resolve() returns a named character vector, with the URL(s) of the repository.

repo_add() returns the same data frame as repo_get(), invisibly.

with_repo() returns the value of expr.

Details

repo_get() queries the repositories pkgcache uses. It uses the repos option (see options), and also the default Bioconductor repository.

repo_resolve() resolves a single repository specification to a repository URL.

repo_add() adds a new repository to the repos option. (To remove a repository, call option() directly, with the subset that you want to keep.)

with_repo() temporarily adds the repositories in repos, evaluates expr, and then resets the configured repositories.

Repository specifications

The format of a repository specification is a named or unnamed character scalar. If the name is missing, pkgcache adds a name automatically. The repository named CRAN is the main CRAN repository, but otherwise names are informational.

Currently supported repository specifications:

  • URL pointing to the root of the CRAN-like repository. Example:

    https://cloud.r-project.org

  • PPM@latest, PPM (Posit Package Manager, formerly RStudio Package Manager), the latest snapshot.

  • PPM@<date>, PPM (Posit Package Manager, formerly RStudio Package Manager) snapshot, at the specified date.

  • PPM@<package>-<version> PPM snapshot, for the day after the release of <version> of <package>.

  • PPM@R-<version> PPM snapshot, for the day after R <version> was released.

Still works for dates starting from 2017-10-10, but now deprecated, because MRAN is discontinued:

  • MRAN@<date>, MRAN (Microsoft R Application Network) snapshot, at the specified date.

  • MRAN@<package>-<version> MRAN snapshot, for the day after the release of <version> of <package>.

  • MRAN@R-<version> MRAN snapshot, for the day after R <version> was released.

Notes:

  • See more about PPM at https://packagemanager.posit.co/client/#/.

  • The RSPM@ prefix is still supported and treated the same way as PPM@.

  • The MRAN service is now retired, see https://techcommunity.microsoft.com/blog/azuresqlblog/microsoft-r-application-network-retirement/3707161 for details.

  • MRAN@... repository specifications now resolve to PPM, but note that PPM snapshots are only available from 2017-10-10. See more about this at https://posit.co/blog/migrating-from-mran-to-posit-package-manager/.

  • All dates (or times) can be specified in the ISO 8601 format.

  • If PPM does not have a snapshot available for a date, the next available date is used.

  • Dates that are before the first, or after the last PPM snapshot will trigger an error.

  • Unknown R or package versions will trigger an error.

See also

Other repository functions: repo_status()

Examples

repo_get()
#> # A data frame: 7 × 5
#>   name            url                               type  r_version bioc_version
#> * <chr>           <chr>                             <chr> <chr>     <chr>       
#> 1 ""              https://prism.dev.a2-ai.cloud/rp… cran… *         NA          
#> 2 "CRAN"          https://cloud.r-project.org       cran  *         NA          
#> 3 "BioCsoft"      https://bioconductor.org/package… bioc  4.5.1     3.22        
#> 4 "BioCann"       https://bioconductor.org/package… bioc  4.5.1     3.22        
#> 5 "BioCexp"       https://bioconductor.org/package… bioc  4.5.1     3.22        
#> 6 "BioCworkflows" https://bioconductor.org/package… bioc  4.5.1     3.22        
#> 7 "BioCbooks"     https://bioconductor.org/package… bioc  4.5.1     3.22        
repo_resolve("PPM@2021-01-21")
#>                                                              CRAN 
#> "https://packagemanager.posit.co/cran/__linux__/noble/2021-01-21" 
#' repo_resolve("[email protected]")
#' repo_resolve("[email protected]")
with_repo(c(CRAN = "[email protected]"), repo_get())
#> # A data frame: 7 × 5
#>   name            url                               type  r_version bioc_version
#> * <chr>           <chr>                             <chr> <chr>     <chr>       
#> 1 ""              https://prism.dev.a2-ai.cloud/rp… cran… *         NA          
#> 2 "CRAN"          https://packagemanager.posit.co/… cran  *         NA          
#> 3 "BioCsoft"      https://bioconductor.org/package… bioc  4.5.1     3.22        
#> 4 "BioCann"       https://bioconductor.org/package… bioc  4.5.1     3.22        
#> 5 "BioCexp"       https://bioconductor.org/package… bioc  4.5.1     3.22        
#> 6 "BioCworkflows" https://bioconductor.org/package… bioc  4.5.1     3.22        
#> 7 "BioCbooks"     https://bioconductor.org/package… bioc  4.5.1     3.22        
with_repo(c(CRAN = "[email protected]"), meta_cache_list(package = "dplyr"))
#> 
#> ✔ Updated metadata database: 2.31 MB in 4 files.
#> 
#> ℹ Updating metadata database
#> ✔ Updating metadata database ... done
#> 
#> # A data frame: 2 × 32
#>   package version depends      imports  suggests license md5sum needscompilation
#> * <chr>   <chr>   <chr>        <chr>    <chr>    <chr>   <chr>  <chr>           
#> 1 dplyr   1.2.1   R (>= 4.1.0) "cli (>… "broom,… MIT + … 8b7c8… yes             
#> 2 dplyr   0.8.5   R (>= 3.2.0) "ellips… "bit64,… MIT + … NA     yes             
#> # ℹ 24 more variables: enhances <chr>, linkingto <chr>, license_is_foss <chr>,
#> #   os_type <chr>, repodir <chr>, rversion <chr>, platform <chr>,
#> #   priority <chr>, ref <chr>, type <chr>, direct <lgl>, status <chr>,
#> #   target <chr>, mirror <chr>, sources <list>, filesize <int>, sha256 <chr>,
#> #   sysreqs <chr>, built <chr>, published <chr>, deps <list>,
#> #   license_restricts_use <chr>, path <chr>, archs <chr>

with_repo(c(CRAN = "MRAN@2018-06-30"), summary(repo_status()))
#> Repository summary:                       source          
#>               @ prism.dev.a2-ai.cloud       ✔      (69ms )
#> CRAN          @ packagemanager.posit.co     ✔      (160ms)
#> BioCsoft      @ bioconductor.org            ✔      (160ms)
#> BioCann       @ bioconductor.org            ✔      (169ms)
#> BioCexp       @ bioconductor.org            ✔      (214ms)
#> BioCworkflows @ bioconductor.org            ✔      (254ms)
#> BioCbooks     @ bioconductor.org            ✔      (174ms)