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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'
I get the above error when I try to install packages using BiocManager. I am not sure why it is happening. I am on a Mac M1 and my Rprofile is blank, if that matters. I am running R 4.2.0. I tried to change my CRAN Mirror (to "0"), but I haven't tried anything else. My entire code and error message is as follows:
> BiocManager::install(c('BiocGenerics', 'DelayedArray', 'DelayedMatrixStats',
+ 'limma', 'lme4', 'S4Vectors', 'SingleCellExperiment',
+ 'SummarizedExperiment', 'batchelor', 'Matrix.utils',
+ 'HDF5Array', 'terra', 'ggrastr'))
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: http://cran.rstudio.com/
Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.0 (2022-04-22)
Installing package(s) 'BiocGenerics', 'DelayedArray', 'DelayedMatrixStats', 'S4Vectors',
'SingleCellExperiment', 'SummarizedExperiment', 'batchelor', 'HDF5Array'
also installing the dependencies ‘XVector’, ‘IRanges’, ‘GenomicRanges’, ‘Biobase’, ‘GenomeInfoDb’, ‘BiocNeighbors’, ‘BiocSingular’, ‘scuttle’, ‘ResidualMatrix’, ‘ScaledMatrix’, ‘beachmat’, ‘rhdf5’, ‘rhdf5filters’
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: ‘XVector’ ‘IRanges’ ‘GenomicRanges’ ‘Biobase’ ‘BiocNeighbors’
‘BiocSingular’ ‘scuttle’ ‘beachmat’ ‘rhdf5’ ‘rhdf5filters’ ‘DelayedArray’ ‘S4Vectors’
‘batchelor’ ‘HDF5Array’
Yes! After much searching of the issue, using
type = "source"worked for me! Thank you so so much!! You have saved me so much time my friend!! :)I think you are right that Bioconductor not providing big-sur-arm64 binaries yet because I am using a Mac computer with an M1 chip and big-sur-arm64 and none of the other troubleshooting methods I tried solved the issue for me.
Thank you again!
Glad it helped! I think soon, this or next release, bioconductor will be able to provide binaries.
I have the same problem on Mac with an Apple M1 chip. Using type = "source" worked for me for only some of the packages above, such as 'BiocGenerics'. However, most others failed, such as 'DelayedArray', 'SingleCellExperiment', 'SummarizedExperiment'
I also tried to install other packages (Biobase, IRanges, GenomicRanges) in this way but failed. I think we have to wait until next Bioconductor release for the complete resolution of this problem. Currently, I am switching back to an Intel based Mac now.