Not able to install packages in Bioconductor version '3.16'
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Tonmoya • 0
@a1ef27f0
Last seen 21 days ago
India

I have recently installed Bioconductor 3.16 in my R 4.2. But I am not able to install packages. I typed this

BiocManager::install("DESeq2")

I get this error

Warning: unable to access index for repository https://bioconductor.org/packages/3.16/bioc/src/contrib:
 cannot open URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/PACKAGES'
sessionInfo( )

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

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

Warning: unable to access index for repository https://bioconductor.org/packages/3.16/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/workflows/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/workflows/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/books/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/books/src/contrib/PACKAGES'
Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31 ucrt)
Installing package(s) 'BiocVersion', 'DESeq2'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/workflows/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/workflows/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/books/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/books/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/workflows/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/workflows/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/books/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/books/src/contrib/PACKAGES'
Installation paths not writeable, unable to update packages
  path: C:/Program Files/R/R-4.2.2/library
  packages:
    boot, Matrix
Warning message:
packages ‘BiocVersion’, ‘DESeq2’ are not available for Bioconductor version '3.16'

Versions of these packages 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
Install BiocManager version3.16 • 1.2k views
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1
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Do you have access to the internet? It also looks you are writing to a not writeable directory?

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Yes, internet is working fine. There is no problem when I install packages through CRAN. But Bioconductor is showing such problems

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See this related thread: unable to access index for repository

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