Problems installing methylumi package
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Entering edit mode
Alison • 0
@abef403e
Last seen 8 weeks ago
United States

Hello,

I am new to R and having trouble installing the methylumi package. When I enter the suggested code, it seems to be trying to load an earlier version of methylumi (Bioconductor 3.15) which is not compatible with my version of R (4.2.1).

I entered the code below, as described on the bioconductor website: https://bioconductor.org/packages/release/bioc/html/methylumi.html

 if (!require("BiocManager", quietly = TRUE))
+     install.packages("BiocManager")
> 
> BiocManager::install("methylumi")

And then I receive the following warning messages: 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

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

Bioconductor version 3.15 (BiocManager 1.30.19), R 4.2.1 (2022-06-23) Installing package(s) 'methylumi' also installing the dependencies ‘Rhtslib’, ‘multtest’, ‘sparseMatrixStats’, ‘rhdf5’, ‘rhdf5filters’, ‘Rhdf5lib’, ‘zlibbioc’, ‘Rsamtools’, ‘GenomicAlignments’, ‘TxDb.Hsapiens.UCSC.hg19.knownGene’, ‘org.Hs.eg.db’, ‘Biostrings’, ‘bumphunter’, ‘siggenes’, ‘limma’, ‘preprocessCore’, ‘DelayedMatrixStats’, ‘GEOquery’, ‘DelayedArray’, ‘HDF5Array’, ‘BiocParallel’, ‘XVector’, ‘KEGGREST’, ‘BiocIO’, ‘rtracklayer’, ‘biomaRt’, ‘Biobase’, ‘FDb.InfiniumMethylation.hg19’, ‘minfi’, ‘S4Vectors’, ‘IRanges’, ‘GenomeInfoDb’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘annotate’, ‘genefilter’, ‘AnnotationDbi’, ‘illuminaio’, ‘GenomicFeatures’

Warning: unable to access index for repository https://bioconductor.org/packages/3.15/bioc/bin/macosx/big-sur-arm64/contrib/4.2: cannot open URL 'https://bioconductor.org/packages/3.15/bioc/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.15/data/annotation/bin/macosx/big-sur-arm64/contrib/4.2: cannot open URL 'https://bioconductor.org/packages/3.15/data/annotation/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.15/data/experiment/bin/macosx/big-sur-arm64/contrib/4.2: cannot open URL 'https://bioconductor.org/packages/3.15/data/experiment/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.15/workflows/bin/macosx/big-sur-arm64/contrib/4.2: cannot open URL 'https://bioconductor.org/packages/3.15/workflows/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.15/books/bin/macosx/big-sur-arm64/contrib/4.2: cannot open URL 'https://bioconductor.org/packages/3.15/books/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES' Packages which are only available in source form, and may need compilation of C/C++/Fortran: ‘Rhtslib’ ‘multtest’ ‘sparseMatrixStats’ ‘rhdf5’ ‘rhdf5filters’ ‘Rhdf5lib’ ‘zlibbioc’ ‘Rsamtools’ ‘GenomicAlignments’ ‘Biostrings’ ‘limma’ ‘preprocessCore’ ‘DelayedArray’ ‘HDF5Array’ ‘BiocParallel’ ‘XVector’ ‘rtracklayer’ ‘Biobase’ ‘S4Vectors’ ‘IRanges’ ‘GenomicRanges’ ‘genefilter’ ‘illuminaio’

Any help would be appreciated. Thank you!

Alison

methylumi • 109 views
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1
Entering edit mode

I think something has ended up a bit confused about which version of Bioconductor should be used. It looks likes it's trying to download versions of the packages for an M1 Mac that didn't exist in Bioconductor version 3.15 (they're really new!).

What happens if you run BiocManager::install(version = "3.16") ? That should update to the latest version, and hopefully get the packages you need.

It might take a while if you have some packages already installed, and you'll probably have to run BiocManager::install("methylumi") again once it's finished.

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