Fail to install BSgenome and library
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Entering edit mode
Tsung-Han • 0
@9cc7f98a
Last seen 2.6 years ago
United States

I have problems installing BSgenome and sequence library (BSgenome.Celegans.UCSC.ce11). I appreciate any help! Thank you.

-TY

# run
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("BSgenome")

# Result
Warning messages:
1: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
2: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
3: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
4: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/workflows/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/workflows/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
5: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/books/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
6: In .inet_warning(msg) :
  installation of package ‘Rhtslib’ had non-zero exit status
7: In .inet_warning(msg) :
  installation of package ‘Rsamtools’ had non-zero exit status
8: In .inet_warning(msg) :
  installation of package ‘GenomicAlignments’ had non-zero exit status
9: In .inet_warning(msg) :
  installation of package ‘rtracklayer’ had non-zero exit status
10: In .inet_warning(msg) :
  installation of package ‘BSgenome’ had non-zero exit status

sessionInfo( )
R version 4.1.2 (2021-11-01)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.3
BSgenome Celegans • 1.2k views
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