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repo_status.Rd
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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/repo.R
\name{repo_status}
\alias{repo_status}
\alias{repo_ping}
\title{Show the status of CRAN-like 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{
\item{platforms}{Platforms to use, default is the current platform,
plus source packages, via the \code{\link[=pak-config]{pkg.platforms}} option.}
\item{r_version}{R version(s) to use, the default is the current
R version, via \code{\link[=getRversion]{getRversion()}}.}
\item{bioc}{Whether to add the Bioconductor repositories. If you
already configured them via \code{options(repos)}, then you can
set this to \code{FALSE}. Defaults to the \code{\link[=pak-config]{pkg.use_bioconductor}}
option.}
\item{cran_mirror}{The CRAN mirror to use. Defaults to the
\code{\link[=pak-config]{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:
\itemize{
\item \code{name}: the name of the repository. This comes from the names
of the configured repositories in \code{options("repos")}, or
added by pak. It is typically \code{CRAN} for CRAN, and the
current Bioconductor repositories are \code{BioCsoft}, \code{BioCann},
\code{BioCexp}, \code{BioCworkflows}.
\item \code{url}: base URL of the repository.
\item \code{bioc_version}: Bioconductor version, or \code{NA} for
non-Bioconductor repositories.
\item \code{username}: Included if at least one repository is authenticated.
\code{NA_character_} for repositories without authentication. See
\code{\link[=repo_auth]{repo_auth()}}.
\item \code{has_password}: \code{TRUE} is the function could retrieve the password
for the authenticated repository. It is \code{NA} for repositories without
authentication. This column is included only if at least one
repository has authentication. See \code{\link[=repo_auth]{repo_auth()}}.
\item \code{platform}: platform, possible values are \code{source}, \code{macos} and
\code{windows} currently.
\item \code{path}: the path to the packages within the base URL, for a
given platform and R version.
\item \code{r_version}: R version, one of the specified R versions.
\item \code{ok}: Logical flag, whether the repository contains a metadata
file for the given platform and R version.
\item \code{ping}: HTTP response time of the repository in seconds. If
the \code{ok} column is \code{FALSE}, then this columns in \code{NA}.
\item \code{error}: the error object if the HTTP query failed for this
repository, platform and R version.
}
}
\description{
It checks the status of the configured or supplied repositories.
}
\details{
\code{repo_ping()} is similar to \code{repo_status()} but also prints a short
summary of the data, and it returns its result invisibly.
}
\section{Examples}{
\if{html}{\out{<div class="sourceCode r">}}\preformatted{repo_status()
}\if{html}{\out{</div>}}\if{html}{\out{
<div class="asciicast" style="color: #172431;font-family: 'Fira Code',Monaco,Consolas,Menlo,'Bitstream Vera Sans Mono','Powerline Symbols',monospace;line-height: 1.300000"><pre>
#> <span style="color: #999999;"># A data frame: 12 × 10</span>
#> name url type bioc_version platform path r_version ok ping
#> <span style="font-style: italic;color: #999999;"><chr></span> <span style="font-style: italic;color: #999999;"><chr></span> <span style="font-style: italic;color: #999999;"><chr></span> <span style="font-style: italic;color: #999999;"><chr></span> <span style="font-style: italic;color: #999999;"><chr></span> <span style="font-style: italic;color: #999999;"><chr></span> <span style="font-style: italic;color: #999999;"><chr></span> <span style="font-style: italic;color: #999999;"><lgl></span> <span style="font-style: italic;color: #999999;"><dbl></span>
#> <span style="color: #c2c2c2;"> 1</span> CRAN http… cran <span style="color: #DC322F;">NA</span> source src/… 4.4 TRUE 0.246
#> <span style="color: #c2c2c2;"> 2</span> CRAN http… cran <span style="color: #DC322F;">NA</span> aarch64… bin/… 4.4 TRUE 0.298
#> <span style="color: #c2c2c2;"> 3</span> BioCso… http… bioc 3.20 source src/… 4.4 TRUE 0.298
#> <span style="color: #c2c2c2;"> 4</span> BioCso… http… bioc 3.20 aarch64… bin/… 4.4 TRUE 0.322
#> <span style="color: #c2c2c2;"> 5</span> BioCann http… bioc 3.20 source src/… 4.4 TRUE 0.530
#> <span style="color: #c2c2c2;"> 6</span> BioCann http… bioc 3.20 aarch64… bin/… 4.4 TRUE 0.643
#> <span style="color: #c2c2c2;"> 7</span> BioCexp http… bioc 3.20 source src/… 4.4 TRUE 0.498
#> <span style="color: #c2c2c2;"> 8</span> BioCexp http… bioc 3.20 aarch64… bin/… 4.4 TRUE 0.707
#> <span style="color: #c2c2c2;"> 9</span> BioCwo… http… bioc 3.20 source src/… 4.4 TRUE 0.569
#> <span style="color: #c2c2c2;">10</span> BioCwo… http… bioc 3.20 aarch64… bin/… 4.4 TRUE 0.724
#> <span style="color: #c2c2c2;">11</span> BioCbo… http… bioc 3.20 source src/… 4.4 TRUE 0.662
#> <span style="color: #c2c2c2;">12</span> BioCbo… http… bioc 3.20 aarch64… bin/… 4.4 TRUE 0.754
#> <span style="color: #999999;"># ℹ 1 more variable: error <list></span>
</pre></div>
}}
\if{html}{\out{<div class="sourceCode r">}}\preformatted{repo_status(
platforms = c("windows", "macos"),
r_version = c("4.0", "4.1")
)
}\if{html}{\out{</div>}}\if{html}{\out{
<div class="asciicast" style="color: #172431;font-family: 'Fira Code',Monaco,Consolas,Menlo,'Bitstream Vera Sans Mono','Powerline Symbols',monospace;line-height: 1.300000"><pre>
#> <span style="color: #999999;"># A data frame: 18 × 10</span>
#> name url type bioc_version platform r_version path ok ping
#> <span style="font-style: italic;color: #999999;"><chr></span> <span style="font-style: italic;color: #999999;"><chr></span> <span style="font-style: italic;color: #999999;"><chr></span> <span style="font-style: italic;color: #999999;"><chr></span> <span style="font-style: italic;color: #999999;"><chr></span> <span style="font-style: italic;color: #999999;"><chr></span> <span style="font-style: italic;color: #999999;"><chr></span> <span style="font-style: italic;color: #999999;"><lgl></span> <span style="font-style: italic;color: #999999;"><dbl></span>
#> <span style="color: #c2c2c2;"> 1</span> CRAN http… cran <span style="color: #DC322F;">NA</span> i386+x8… 4.0 bin/… TRUE 0.175
#> <span style="color: #c2c2c2;"> 2</span> CRAN http… cran <span style="color: #DC322F;">NA</span> i386+x8… 4.1 bin/… TRUE 0.180
#> <span style="color: #c2c2c2;"> 3</span> CRAN http… cran <span style="color: #DC322F;">NA</span> aarch64… 4.1 bin/… FALSE <span style="color: #DC322F;">NA</span>
#> <span style="color: #c2c2c2;"> 4</span> BioCs… http… bioc 3.12 i386+x8… 4.0 bin/… TRUE 0.539
#> <span style="color: #c2c2c2;"> 5</span> BioCa… http… bioc 3.12 i386+x8… 4.0 bin/… TRUE 0.538
#> <span style="color: #c2c2c2;"> 6</span> BioCe… http… bioc 3.12 i386+x8… 4.0 bin/… TRUE 1.04
#> <span style="color: #c2c2c2;"> 7</span> BioCw… http… bioc 3.12 i386+x8… 4.0 bin/… TRUE 0.809
#> <span style="color: #c2c2c2;"> 8</span> BioCb… http… bioc 3.12 i386+x8… 4.0 bin/… TRUE 0.610
#> <span style="color: #c2c2c2;"> 9</span> BioCs… http… bioc 3.14 i386+x8… 4.1 bin/… TRUE 1.16
#> <span style="color: #c2c2c2;">10</span> BioCs… http… bioc 3.14 aarch64… 4.1 bin/… FALSE <span style="color: #DC322F;">NA</span>
#> <span style="color: #c2c2c2;">11</span> BioCa… http… bioc 3.14 i386+x8… 4.1 bin/… TRUE 0.659
#> <span style="color: #c2c2c2;">12</span> BioCa… http… bioc 3.14 aarch64… 4.1 bin/… FALSE <span style="color: #DC322F;">NA</span>
#> <span style="color: #c2c2c2;">13</span> BioCe… http… bioc 3.14 i386+x8… 4.1 bin/… TRUE 0.913
#> <span style="color: #c2c2c2;">14</span> BioCe… http… bioc 3.14 aarch64… 4.1 bin/… FALSE <span style="color: #DC322F;">NA</span>
#> <span style="color: #c2c2c2;">15</span> BioCw… http… bioc 3.14 i386+x8… 4.1 bin/… TRUE 0.811
#> <span style="color: #c2c2c2;">16</span> BioCw… http… bioc 3.14 aarch64… 4.1 bin/… FALSE <span style="color: #DC322F;">NA</span>
#> <span style="color: #c2c2c2;">17</span> BioCb… http… bioc 3.14 i386+x8… 4.1 bin/… TRUE 1.04
#> <span style="color: #c2c2c2;">18</span> BioCb… http… bioc 3.14 aarch64… 4.1 bin/… FALSE <span style="color: #DC322F;">NA</span>
#> <span style="color: #999999;"># ℹ 1 more variable: error <list></span>
</pre></div>
}}
\if{html}{\out{<div class="sourceCode r">}}\preformatted{repo_ping()
}\if{html}{\out{</div>}}\if{html}{\out{
<div class="asciicast" style="color: #172431;font-family: 'Fira Code',Monaco,Consolas,Menlo,'Bitstream Vera Sans Mono','Powerline Symbols',monospace;line-height: 1.300000"><pre>
#> Repository summary: source aarch64-apple-darwin20<span style="color: #2AA198;"> </span>
#> CRAN @ cloud.r-project.org <span style="color: #859900;"> ✔ </span> <span style="color: #859900;"> ✔ </span><span style="color: #2AA198;"> (63ms )</span>
#> BioCsoft @ bioconductor.org <span style="color: #859900;"> ✔ </span> <span style="color: #859900;"> ✔ </span><span style="color: #2AA198;"> (68ms )</span>
#> BioCann @ bioconductor.org <span style="color: #859900;"> ✔ </span> <span style="color: #859900;"> ✔ </span><span style="color: #2AA198;"> (153ms)</span>
#> BioCexp @ bioconductor.org <span style="color: #859900;"> ✔ </span> <span style="color: #859900;"> ✔ </span><span style="color: #2AA198;"> (186ms)</span>
#> BioCworkflows @ bioconductor.org <span style="color: #859900;"> ✔ </span> <span style="color: #859900;"> ✔ </span><span style="color: #2AA198;"> (112ms)</span>
#> BioCbooks @ bioconductor.org <span style="color: #859900;"> ✔ </span> <span style="color: #859900;"> ✔ </span><span style="color: #2AA198;"> (193ms)</span>
</pre></div>
}}
}
\seealso{
Other repository functions:
\code{\link{repo_add}()},
\code{\link{repo_get}()}
}
\concept{repository functions}