Question

BioCann repository index warning on Apple Silicon (Bioc 3.17 / R 4.3)

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Entering edit mode

Michael Steinbaugh ▴ 90

@mjsteinbaugh

Last seen 12 months ago

Cambridge, MA

Hi Bioconductor team,

I'm seeing a warning pop up during BiocManager::install calls on Apple Silicon related to the current BioCann repository index configuration.

BiocManager::repositories()

                                                BioCsoft
           "https://bioconductor.org/packages/3.17/bioc"
                                                 BioCann
"https://bioconductor.org/packages/3.17/data/annotation"
                                                 BioCexp
"https://bioconductor.org/packages/3.17/data/experiment"
                                           BioCworkflows
      "https://bioconductor.org/packages/3.17/workflows"
                                               BioCbooks
          "https://bioconductor.org/packages/3.17/books"
                                                    CRAN
                           "https://cloud.r-project.org"
                                            AcidGenomics
                            "https://r.acidgenomics.com"

BiocManager::install("S4Vectors")

Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3:
  cannot open URL 'https://bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES'

sessionInfo()

R version 4.3.0 (2023-04-21)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.3.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

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

other attached packages:
[1] AcidDevTools_0.6.6

loaded via a namespace (and not attached):
[1] compiler_4.3.0 parallel_4.3.0

Best, Mike

Annotation • 1.6k views

ADD COMMENT • link 18 months ago Michael Steinbaugh ▴ 90

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Hi Michael. I have the same problem trying to install 'DMRcate' today.

Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3: cannot open URL 'https://bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES' trying URL 'https://bioconductor.org/packages/3.17/bioc/bin/macosx/big-sur-arm64/contrib/4.3/edgeR_3.41.8.tgz' Content type 'application/x-gzip' length 2751057 bytes (2.6 MB)

sessionInfo() R version 4.3.0 (2023-04-21) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Ventura 13.3.1

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Oslo tzcode source: internal

Kind regards, Jonelle

ADD REPLY • link 18 months ago jonellevillar • 0

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Following up, I'm also seeing this issue on an Intel Mac:

Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/bin/macosx/big-sur-x86_64/contrib/4.3:
  cannot open URL 'https://bioconductor.org/packages/3.17/data/experiment/bin/macosx/big-sur-x86_64/contrib/4.3/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/workflows/bin/macosx/big-sur-x86_64/contrib/4.3:
  cannot open URL 'https://bioconductor.org/packages/3.17/workflows/bin/macosx/big-sur-x86_64/contrib/4.3/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/books/bin/macosx/big-sur-x86_64/contrib/4.3:
  cannot open URL 'https://bioconductor.org/packages/3.17/books/bin/macosx/big-sur-x86_64/contrib/4.3/PACKAGES'

ADD REPLY • link 18 months ago Michael Steinbaugh ▴ 90

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Entering edit mode

Here's some followup with additional warnings:

BiocManager::valid(type = "binary")

Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/bin/macosx/big-sur-x86_64/contrib/4.3:
  cannot open URL 'https://bioconductor.org/packages/3.17/data/experiment/bin/macosx/big-sur-x86_64/contrib/4.3/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/workflows/bin/macosx/big-sur-x86_64/contrib/4.3:
  cannot open URL 'https://bioconductor.org/packages/3.17/workflows/bin/macosx/big-sur-x86_64/contrib/4.3/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/books/bin/macosx/big-sur-x86_64/contrib/4.3:
  cannot open URL 'https://bioconductor.org/packages/3.17/books/bin/macosx/big-sur-x86_64/contrib/4.3/PACKAGES'

ADD REPLY • link 18 months ago Michael Steinbaugh ▴ 90

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Entering edit mode

Also I noticed that GenomeInfoDbData currently isn't available as a binary package. Can we fix this to enable easier binary installs?

BiocManager::install("GenomeInfoDbData", type = "binary")

ADD REPLY • link 18 months ago Michael Steinbaugh ▴ 90