It checks the status of the configured or supplied repositories, for the specified platforms and R versions.
repo_status(
platforms = default_platforms(),
r_version = getRversion(),
bioc = TRUE,
cran_mirror = default_cran_mirror()
)Platforms to use, default is default_platforms().
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. See bioc_version() for the details about
how pkgcache handles Bioconductor repositories.
The CRAN mirror to use, see
default_cran_mirror().
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 pkgcache. It is typically CRAN for CRAN, and the
current Bioconductor repositories are BioCsoft, BioCann,
BioCexp, BioCworkflows, BioCbooks.
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, see default_platforms() for possible values.
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.
The returned data frame has a summary() method, which shows
the same information is a concise table. See examples below.
Other repository functions:
repo_get()
repo_status()
#> # A data frame: 8 × 10
#> name url type bioc_version platform path r_version ok ping error
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <lgl> <dbl> <list>
#> 1 RSPM http… cran… NA source src/… 4.4 TRUE 0.416 <NULL>
#> 2 gh-pkg-m… http… cran… NA source src/… 4.4 TRUE 0.190 <NULL>
#> 3 CRAN http… cran NA source src/… 4.4 TRUE 0.194 <NULL>
#> 4 BioCsoft http… bioc 3.20 source src/… 4.4 TRUE 0.699 <NULL>
#> 5 BioCann http… bioc 3.20 source src/… 4.4 TRUE 0.818 <NULL>
#> 6 BioCexp http… bioc 3.20 source src/… 4.4 TRUE 0.822 <NULL>
#> 7 BioCwork… http… bioc 3.20 source src/… 4.4 TRUE 0.848 <NULL>
#> 8 BioCbooks http… bioc 3.20 source src/… 4.4 TRUE 0.436 <NULL>
rst <- repo_status(
platforms = c("windows", "macos"),
r_version = c("4.0", "4.1")
)
summary(rst)
#> Repository summary: i386+x86_64-w64-mingw32 x86_64-apple-darwin17.0
#> RSPM @ packagemanager.posit.co (R 4.0) ✔ ✔ (1s )
#> gh-pkg-mirror @ a2-ai.github.io (R 4.0) ✖ ✖
#> CRAN @ cloud.r-project.org (R 4.0) ✔ ✔ (369ms)
#> RSPM @ packagemanager.posit.co (R 4.1) ✔ ✔ (1.4s )
#> gh-pkg-mirror @ a2-ai.github.io (R 4.1) ✖ ✖
#> CRAN @ cloud.r-project.org (R 4.1) ✔ ✔ (395ms)
#> BioCsoft @ bioconductor.org (R 4.0) ✔ ✔ (716ms)
#> BioCann @ bioconductor.org (R 4.0) ✔ ✔ (940ms)
#> BioCexp @ bioconductor.org (R 4.0) ✔ ✔ (897ms)
#> BioCworkflows @ bioconductor.org (R 4.0) ✔ ✔ (854ms)
#> BioCbooks @ bioconductor.org (R 4.0) ✔ ✔ (816ms)
#> BioCsoft @ bioconductor.org (R 4.1) ✔ ✔ (807ms)
#> BioCann @ bioconductor.org (R 4.1) ✔ ✔ (847ms)
#> BioCexp @ bioconductor.org (R 4.1) ✔ ✔ (885ms)
#> BioCworkflows @ bioconductor.org (R 4.1) ✔ ✔ (971ms)
#> BioCbooks @ bioconductor.org (R 4.1) ✔ ✔ (673ms)