Show the status of CRAN-like repositories

It checks the status of the configured or supplied repositories.

Usage

repo_status(
  platforms = NULL,
  r_version = getRversion(),
  bioc = NULL,
  cran_mirror = NULL
)

repo_ping(
  platforms = NULL,
  r_version = getRversion(),
  bioc = NULL,
  cran_mirror = NULL
)

Arguments

platforms: Platforms to use, default is the current platform, plus source packages, via the pkg.platforms option.
r_version: R version(s) to use, the default is the current R version, via getRversion().
bioc: Whether to add the Bioconductor repositories. If you already configured them via options(repos), then you can set this to FALSE. Defaults to the pkg.use_bioconductor option.
cran_mirror: The CRAN mirror to use. Defaults to the pkg.cran_mirror option.

Value

A data frame that has a row for every repository, on every queried platform and R version. It has these columns:

name: the name of the repository. This comes from the names of the configured repositories in options("repos"), or added by pak. It is typically CRAN for CRAN, and the current Bioconductor repositories are BioCsoft, BioCann, BioCexp, BioCworkflows.
url: base URL of the repository.
bioc_version: Bioconductor version, or NA for non-Bioconductor repositories.
username: Included if at least one repository is authenticated. NA_character_ for repositories without authentication. See repo_auth().
has_password: TRUE is the function could retrieve the password for the authenticated repository. It is NA for repositories without authentication. This column is included only if at least one repository has authentication. See repo_auth().
platform: platform, possible values are source, macos and windows currently.
path: the path to the packages within the base URL, for a given platform and R version.
r_version: R version, one of the specified R versions.
ok: Logical flag, whether the repository contains a metadata file for the given platform and R version.
ping: HTTP response time of the repository in seconds. If the ok column is FALSE, then this columns in NA.
error: the error object if the HTTP query failed for this repository, platform and R version.

Details

repo_ping() is similar to repo_status() but also prints a short summary of the data, and it returns its result invisibly.

Examples

repo_status()

#> # A data frame: 12 × 10
#>    name    url   type  bioc_version platform path  r_version ok     ping
#>    <chr>   <chr> <chr> <chr>        <chr>    <chr> <chr>     <lgl> <dbl>
#>  1 CRAN    http… cran  NA           source   src/… 4.4       TRUE  0.246
#>  2 CRAN    http… cran  NA           aarch64… bin/… 4.4       TRUE  0.298
#>  3 BioCso… http… bioc  3.20         source   src/… 4.4       TRUE  0.298
#>  4 BioCso… http… bioc  3.20         aarch64… bin/… 4.4       TRUE  0.322
#>  5 BioCann http… bioc  3.20         source   src/… 4.4       TRUE  0.530
#>  6 BioCann http… bioc  3.20         aarch64… bin/… 4.4       TRUE  0.643
#>  7 BioCexp http… bioc  3.20         source   src/… 4.4       TRUE  0.498
#>  8 BioCexp http… bioc  3.20         aarch64… bin/… 4.4       TRUE  0.707
#>  9 BioCwo… http… bioc  3.20         source   src/… 4.4       TRUE  0.569
#> 10 BioCwo… http… bioc  3.20         aarch64… bin/… 4.4       TRUE  0.724
#> 11 BioCbo… http… bioc  3.20         source   src/… 4.4       TRUE  0.662
#> 12 BioCbo… http… bioc  3.20         aarch64… bin/… 4.4       TRUE  0.754
#> # ℹ 1 more variable: error <list>

repo_status(
  platforms = c("windows", "macos"),
  r_version = c("4.0", "4.1")
)

#> # A data frame: 18 × 10
#>    name   url   type  bioc_version platform r_version path  ok      ping
#>    <chr>  <chr> <chr> <chr>        <chr>    <chr>     <chr> <lgl>  <dbl>
#>  1 CRAN   http… cran  NA           i386+x8… 4.0       bin/… TRUE   0.175
#>  2 CRAN   http… cran  NA           i386+x8… 4.1       bin/… TRUE   0.180
#>  3 CRAN   http… cran  NA           aarch64… 4.1       bin/… FALSE NA
#>  4 BioCs… http… bioc  3.12         i386+x8… 4.0       bin/… TRUE   0.539
#>  5 BioCa… http… bioc  3.12         i386+x8… 4.0       bin/… TRUE   0.538
#>  6 BioCe… http… bioc  3.12         i386+x8… 4.0       bin/… TRUE   1.04
#>  7 BioCw… http… bioc  3.12         i386+x8… 4.0       bin/… TRUE   0.809
#>  8 BioCb… http… bioc  3.12         i386+x8… 4.0       bin/… TRUE   0.610
#>  9 BioCs… http… bioc  3.14         i386+x8… 4.1       bin/… TRUE   1.16
#> 10 BioCs… http… bioc  3.14         aarch64… 4.1       bin/… FALSE NA
#> 11 BioCa… http… bioc  3.14         i386+x8… 4.1       bin/… TRUE   0.659
#> 12 BioCa… http… bioc  3.14         aarch64… 4.1       bin/… FALSE NA
#> 13 BioCe… http… bioc  3.14         i386+x8… 4.1       bin/… TRUE   0.913
#> 14 BioCe… http… bioc  3.14         aarch64… 4.1       bin/… FALSE NA
#> 15 BioCw… http… bioc  3.14         i386+x8… 4.1       bin/… TRUE   0.811
#> 16 BioCw… http… bioc  3.14         aarch64… 4.1       bin/… FALSE NA
#> 17 BioCb… http… bioc  3.14         i386+x8… 4.1       bin/… TRUE   1.04
#> 18 BioCb… http… bioc  3.14         aarch64… 4.1       bin/… FALSE NA
#> # ℹ 1 more variable: error <list>

repo_ping()

#> Repository summary:                   source aarch64-apple-darwin20          
#> CRAN          @ cloud.r-project.org     ✔              ✔              (63ms )
#> BioCsoft      @ bioconductor.org        ✔              ✔              (68ms )
#> BioCann       @ bioconductor.org        ✔              ✔              (153ms)
#> BioCexp       @ bioconductor.org        ✔              ✔              (186ms)
#> BioCworkflows @ bioconductor.org        ✔              ✔              (112ms)
#> BioCbooks     @ bioconductor.org        ✔              ✔              (193ms)