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