The BioCmirrors package provides functions to check the health status
of Bioconductor mirrors. The package is useful for users who want to
ensure that the mirror they are using is up-to-date and has all the
packages available. The package also provides a list of all available
mirrors and their statistics. The capital C in BioCmirrors is
intentional to be consistent with the chooseBioCmirror function in the
utils package.
Currently, the package can only be found on GitHub. To install it, use the following:
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("Bioconductor/BioCmirrors")
library(BioCmirrors)
The checkBioCmirror function checks the health status of a
Bioconductor mirror including the main Bioconductor URL:
url <- "https://bioconductor.org"
checkBioCmirror(mirror = url)
#> Warning in rep(as.integer(len), length = length(str)): partial argument match of 'length' to 'length.out'
#> https://bioconductor.org/packages/3.21/bioc/src/contrib/PACKAGES
#> TRUE
The function can also be run interactively, where it will display a list of mirrors to choose from:
checkBioCmirror()
#' Secure BioC mirrors
#'
#' 1: 0-Bioconductor (World-wide) [https] 2: USA (Boston) [https]
#' 3: Germany (Gottingen) [https] 4: Japan (Wako) [https]
#' 5: Taiwan (Hsinchu) [https] 6: China (Peking) [https]
#' 7: China (Nanjing) [https] 8: China (Hefei Anhui) [https]
#' 9: Norway (Bergen) [https] 10: Denmark (Aalborg) [https]
#' 11: Sweden (Umea) [https] 12: (other mirrors)
#'
#'
#' Selection: 3
#' https://ftp.gwdg.de/pub/misc/bioconductor/packages/bioc/src/contrib/PACKAGES
#' TRUE
The listBioCmirrors function returns a list of all available
Bioconductor mirrors:
mirrors <- listBioCmirrors()
mirrors
#> # A tibble: 34 × 10
#> Name Country City URL Host Maintainer OK CountryCode Comment Protocol
#> <chr> <chr> <chr> <chr> <chr> <chr> <int> <chr> <chr> <chr>
#> 1 0-Bioconductor (World-wide) [https] 0-Bioc… Worl… http… Bioc… Bioconduc… 1 us "secur… https
#> 2 0-Bioconductor (World-wide) [unsecur… 0-Bioc… Worl… http… Bioc… Bioconduc… 0 us "secur… http
#> 3 USA (Boston) [https] USA Bost… http… Posi… Joshua Sp… 1 us "secur… https
#> 4 USA (Boston) [unsecure] USA Bost… http… Posi… Joshua Sp… 0 us "secur… http
#> 5 Germany (Dortmund) [https] Germany Dort… http… Depa… Uwe Ligge… 1 de "" https
#> 6 Germany (Dortmund) [unsecure] Germany Dort… http… Depa… Uwe Ligge… 1 de "" http
#> 7 Germany (Gottingen) [https] Germany Gott… http… GWDG Tim Ehler… 1 de "secur… https
#> 8 Germany (Gottingen) [unsecure] Germany Gott… http… GWDG Tim Ehler… 1 de "secur… http
#> 9 Japan (Wako) [https] Japan Wako http… RIKE… Itoshi NI… 1 jp "secur… https
#> 10 Japan (Wako) [unsecure] Japan Wako http… RIKE… Itoshi NI… 1 jp "secur… http
#> # ℹ 24 more rows
The tibble output can be used to filter the mirrors by country:
mirrors |>
dplyr::filter(.data[["Country"]] == "USA")
#> # A tibble: 2 × 10
#> Name Country City URL Host Maintainer OK CountryCode Comment Protocol
#> <chr> <chr> <chr> <chr> <chr> <chr> <int> <chr> <chr> <chr>
#> 1 USA (Boston) [https] USA Boston https://bioconduct… Posi… Joshua Sp… 1 us secure… https
#> 2 USA (Boston) [unsecure] USA Boston http://bioconducto… Posi… Joshua Sp… 0 us secure… http
The BioCmirrorStats function returns details about the PACKAGES file
time stamp, the number of packages available, and the number of packages
mirrored. The function can be used to check the status of a specific
mirror. In this example, we reproduce the output of
utils::chooseBioCmirror() by creating a named string with the URL of
the mirror in Germany:
url <- "https://ftp.gwdg.de/pub/misc/bioconductor"
de_mirror <- c("Germany (Gottingen) [https]" = url)
stats <- BioCmirrorStats(mirror = de_mirror)
stats
#> Bioconductor version: 3.21
#> Bioconductor mirror:
#> https://ftp.gwdg.de/pub/misc/bioconductor
#> PACKAGES timestamp:
#> Query timestamp: 2025-02-26 22:57 UTC
#> Bioconductor software packages: 2258
#> Mirror packages: 2258
#> Mirror software packages: 2258
#> Missing mirror software packages: 0
#>
#> Out-of-date mirror software packages: 0
As shown, the packages on the mirror are up-to-date, and there are no missing packages.
Click to expand
sessionInfo()
#> R Under development (unstable) (2025-02-06 r87702)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.2 LTS
#>
#> Matrix products: default
#> BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
#> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> time zone: America/New_York
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] BioCmirrors_0.0.1
#>
#> loaded via a namespace (and not attached):
#> [1] vctrs_0.6.5 httr_1.4.7 cli_3.6.4 knitr_1.49 rlang_1.1.5
#> [6] xfun_0.51 processx_3.8.6 generics_0.1.3 glue_1.8.0 RCurl_1.98-1.16
#> [11] htmltools_0.5.8.1 pkgbuild_1.4.6 ps_1.9.0 rsconnect_1.3.4 rmarkdown_2.29
#> [16] evaluate_1.0.3 tibble_3.2.1 bitops_1.0-9 fastmap_1.2.0 yaml_2.3.10
#> [21] lifecycle_1.0.4 BiocManager_1.30.25 compiler_4.5.0 dplyr_1.1.4 codetools_0.2-20
#> [26] pkgconfig_2.0.3 rstudioapi_0.17.1 digest_0.6.37 R6_2.6.1 tidyselect_1.2.1
#> [31] utf8_1.2.4 curl_6.2.1 pillar_1.10.1 callr_3.7.6 magrittr_2.0.3
#> [36] tools_4.5.0 remotes_2.5.0 desc_1.4.3