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Enter the body of text here I've tried to install DeSeq2. and received the following warnings as shown below
Code should be placed in three backticks as shown below
Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.1 (2022-06-23)
Installing package(s) 'DESeq2'
Warning: unable to access index for repository https://www.stats.ox.ac.uk/pub/RWin/bin/macosx/contrib/4.2:
cannot open URL 'https://www.stats.ox.ac.uk/pub/RWin/bin/macosx/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://R-Forge.R-project.org/bin/macosx/contrib/4.2:
cannot open URL 'https://R-Forge.R-project.org/bin/macosx/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://www.rforge.net/bin/macosx/contrib/4.2:
cannot open URL 'https://www.rforge.net/bin/macosx/contrib/4.2/PACKAGES'
trying URL 'https://bioconductor.org/packages/3.16/bioc/bin/macosx/contrib/4.2/DESeq2_1.38.2.tgz'
Content type 'application/x-gzip' length 2791368 bytes (2.7 MB)
==================================================
downloaded 2.7 MB
The downloaded binary packages are in
/var/folders/cm/k9s8g0s16d1dl2ymp9pp8kf00000gn/T//RtmpseWNQ1/downloaded_package
When I tried to load DeSeq2, it gave the following error:
> library(DESeq2)
Loading required package: GenomicRanges
Error in value[[3L]](cond) :
Package ‘GenomicRanges’ version 1.50.1 cannot be unloaded:
Error in unloadNamespace(package) : namespace ‘GenomicRanges’ is imported by ‘DESeq2’, ‘SummarizedExperiment’, ‘SingleCellExperiment’ so cannot be unloaded
In addition: Warning messages:
1: package ‘DESeq2’ was built under R version 4.2.2
2: package ‘GenomicRanges’ was built under R version 4.2.2
If I try to install GenomicRanges, I got the following errors:
> BiocManager::install("GenomicRange", force = TRUE)
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
BioCsoft: https://bioconductor.org/packages/3.15/bioc
BioCann: https://bioconductor.org/packages/3.15/data/annotation
BioCexp: https://bioconductor.org/packages/3.15/data/experiment
Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.1 (2022-06-23)
Installing package(s) 'GenomicRange'
Warning: unable to access index for repository https://www.stats.ox.ac.uk/pub/RWin/bin/macosx/contrib/4.2:
cannot open URL 'https://www.stats.ox.ac.uk/pub/RWin/bin/macosx/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://R-Forge.R-project.org/bin/macosx/contrib/4.2:
cannot open URL 'https://R-Forge.R-project.org/bin/macosx/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://www.rforge.net/bin/macosx/contrib/4.2:
cannot open URL 'https://www.rforge.net/bin/macosx/contrib/4.2/PACKAGES'
Warning message:
package ‘GenomicRange’ is not available for Bioconductor version '3.16'
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
Thanks for any help.