unable to access bioconductor packages - qvalue installation failed...
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gabry.scata ▴ 10
@372e99bd
Last seen 19 days ago
Australia

Hi, I am having issues installing BiocManager R packages (i.e. qvalue), in a new computer and R version. Had no problems in the previous PC and R version, so no idea of what is happening here but would love some help as this is obstructing my work.

See error messages below. Thanks Gabriella


BiocManager::install("qvalue")

    ```r

This is the error message I get:

'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Warning: unable to access index for repository https://bioconductor.org/packages/3.18/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.18/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.18/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.18/workflows/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.18/workflows/src/contrib/PACKAGES'
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.3 (2024-02-29 ucrt)
Installing package(s) 'qvalue'
Warning: unable to access index for repository https://bioconductor.org/packages/3.18/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/PACKAGES'


sessionInfo( )

R version 4.3.3 (2024-02-29 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale: [1] LC_COLLATE=English_Australia.utf8 LC_CTYPE=English_Australia.utf8 LC_MONETARY=English_Australia.utf8 LC_NUMERIC=C
[5] LC_TIME=English_Australia.utf8

time zone: Australia/Brisbane tzcode source: internal

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] BiocManager_1.30.23

loaded via a namespace (and not attached): [1] gtable_0.3.4 miniUI_0.1.1.1 dplyr_1.1.4 compiler_4.3.3 promises_1.2.1 tidyselect_1.2.1 Rcpp_1.0.12 stringr_1.5.1
[9] later_1.3.2 scales_1.3.0 fastmap_1.1.1 mime_0.12 ggplot2_3.5.0 R6_2.5.1 generics_0.1.3 patchwork_1.2.0
[17] htmlwidgets_1.6.4 tibble_3.2.1 profvis_0.3.8 munsell_0.5.1 shiny_1.8.1.1 pillar_1.9.0 rlang_1.1.3 utf8_1.2.4
[25] stringi_1.8.3 cachem_1.0.8 httpuv_1.6.15 fs_1.6.3 pkgload_1.3.4 memoise_2.0.1 cli_3.6.2 magrittr_2.0.3
[33] digest_0.6.35 grid_4.3.3 xtable_1.8-4 rstudioapi_0.16.0 remotes_2.5.0 devtools_2.4.5 lifecycle_1.0.4 vctrs_0.6.5
[41] glue_1.7.0 urlchecker_1.0.1 sessioninfo_1.2.2 pkgbuild_1.4.4 fansi_1.0.6 colorspace_2.1-0 purrr_1.0.2 usethis_2.2.3
[49] tools_4.3.3 pkgconfig_2.0.3 ellipsis_0.3.2 htmltools_0.5.8

Install • 201 views
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Seems to be a general problem at the moment, can reproduce. The the mirror suggestion here: can't open mghp.osn.xsede.org that works for me (for now).

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shepherl 3.9k
@lshep
Last seen 13 hours ago
United States

An outage was reported at the location we store the Bioconductor archives. We are in process of temporarily activating a different backup location to resolve the issue. We are sorry for any inconvenience this has caused. Access should be restored

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