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 bioconductor.org/packages/3.13/bioc/src/contrib:
cannot open URL ‘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?
Read more here: Source link
