Installing DESEq2 Error: unable to access index for repository https://bioconductor.org
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ladypurrsia ▴ 10
@ladypurrsia-11377
Last seen 4 weeks ago
United States

Recently I have updated my mac, R, and R studio and the new versions are as follows:

sessionInfo()

R version 4.1.1 (2021-08-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 11.6

I have used DESEQ2without issue prior to the update. After the update, I need to re-install DESEQ2. For this I followed the directions posted here: Bioconductor: DESeq2. However, when I run the following command for install, I now get the following error (multiple lines of this):

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DESeq2")

Warning: unable to access index for repository https://bioconductor.org/packages/3.13/bioc/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.13/bioc/src/contrib/PACKAGES'

When I navigate to the web-page included in the error: Packages, and after doing a global search for DESEQ2, I see that it is there:

Package: DESeq2 Version: 1.32.0 Depends: S4Vectors (>= 0.23.18), IRanges, GenomicRanges, SummarizedExperiment (>= 1.1.6) Imports: BiocGenerics (>= 0.7.5), Biobase, BiocParallel, genefilter, methods, stats4, locfit, geneplotter, ggplot2, Rcpp (>= 0.11.0) LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, apeglm, ashr, tximport, tximeta, tximportData, readr, pbapply, airway, pasilla (>= 0.2.10), glmGamPoi, BiocManager License: LGPL (>= 3) MD5sum: cf6f5468280b2282d587bec61fc9cb5c NeedsCompilation: yes

I am confused as to why the installation cannot access this web-site.

For context, I have been able to download other packages without issue using the BiocManager::install() command after the updates. So far, it's only been DESEQ2 that I have run into issues with.

Is there a work-around to this?

Install Bioconductor DESeq2 • 133 views
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Am I correct in that you are running under Apple M1 BigSur from your sessionInfo()? If yes, could you please see this related post: Warning messages on Apple M1 BigSur

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ladypurrsia ▴ 10
@ladypurrsia-11377
Last seen 4 weeks ago
United States

I have figured out this error from my end: I had a firewall activated that was running in the background of my computer that was not allowing access to the Bioconductor index repository DESEQ2 needed for download. Once I turned that off, I was able to download DESEQ2 without issue. I think this is why, when I navigated toward the posted link via my web-browser, I was able to access the page w/out issue, but for some reason, the firewall was actively blocking it during the R download? Either way, firewall off, DESEQ2 loaded.

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