It checks the status of the configured or supplied repositories.
repo_status(
platforms = NULL,
r_version = getRversion(),
bioc = NULL,
cran_mirror = NULL
)
repo_ping(
platforms = NULL,
r_version = getRversion(),
bioc = NULL,
cran_mirror = NULL
)Platforms to use, default is the current platform,
plus source packages, via the pkg.platforms option.
R version(s) to use, the default is the current
R version, via getRversion().
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.
The CRAN mirror to use. Defaults to the
pkg.cran_mirror option.
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.
repo_ping() is similar to repo_status() but also prints a short
summary of the data, and it returns its result invisibly.
#> # 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>
#> Repository summary: source aarch64-apple-darwin20 #> CRAN @ cloud.r-project.org v v (63ms ) #> BioCsoft @ bioconductor.org v v (68ms ) #> BioCann @ bioconductor.org v v (153ms) #> BioCexp @ bioconductor.org v v (186ms) #> BioCworkflows @ bioconductor.org v v (112ms) #> BioCbooks @ bioconductor.org v v (193ms)