Unable to install DESeq2, 'getOption("repos") replaces Bioconductor standard repositories, see '?repositories' for details
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Entering edit mode
Yong ▴ 10
@fcafe6a5
Last seen 2.4 years ago
United States

I got a new computer and re-installed Rstudio with R version 4.2.0. I am using BiocManager version 1.30.18. I already had a R code written for DESeq2 in the older computer so I tried using this and found that I cannot seem to install DESeq2 using the BiocManager.

Here is the code I used.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("DESeq2")

Here is the error I get.

'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Warning: unable to access index for repository https://bioconductor.org/packages/3.15/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.15/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.15/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/workflows/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.15/workflows/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/books/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.15/books/src/contrib/PACKAGES'
Warning: unable to access index for repository https://cran.rstudio.com/src/contrib:
  cannot open URL 'https://cran.rstudio.com/src/contrib/PACKAGES'
Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.0 (2022-04-22 ucrt)
Installing package(s) 'DESeq2'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.15/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.15/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/workflows/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.15/workflows/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/books/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.15/books/src/contrib/PACKAGES'
Warning: unable to access index for repository https://cran.rstudio.com/src/contrib:
  cannot open URL 'https://cran.rstudio.com/src/contrib/PACKAGES'
Warning: package ‘DESeq2’ is not available for Bioconductor version '3.15'

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/bioc/bin/windows/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.15/bioc/bin/windows/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/data/annotation/bin/windows/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.15/data/annotation/bin/windows/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/data/experiment/bin/windows/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.15/data/experiment/bin/windows/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/workflows/bin/windows/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.15/workflows/bin/windows/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/books/bin/windows/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.15/books/bin/windows/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://cran.rstudio.com/bin/windows/contrib/4.2:
  cannot open URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.15/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.15/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/workflows/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.15/workflows/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/books/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.15/books/src/contrib/PACKAGES'
Warning: unable to access index for repository https://cran.rstudio.com/src/contrib:
  cannot open URL 'https://cran.rstudio.com/src/contrib/PACKAGES'

I know for sure that DESeq2 package for R 2.4.0 is in bioconductor 3.15. I have also read that bioconductor 3.15 is the correct version for R 2.4.0. So I don't understand why this is not installing.
From reading other posts, it seems I am not the only one having the same issue but there does not seem to be any reply to these posts asking for help on this other than "try again later". Please advise.

Thanks.

sessionInfo( )

R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                           LC_TIME=English_United States.utf8
BiocManager • 4.5k views
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1
Entering edit mode

Sorry I am unable to reproduce this error on Windows with R 4.2 and Bioconductor 3.16 or 3.15.

Please make sure you are not behind a firewall or having connection problems. The errors seem to be related to network connectivity.

FWIW, you should be installing the binaries for Windows instead of source but either way it should work if you have RTools installed.

R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)

Best,

Marcel

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