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