DeSeq2 and GenomicRange installation possible conflict with bioconductor version 3.16?
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Entering edit mode
hong • 0
@8fe55427
Last seen 4 weeks ago
United States

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.

DESeq2 version3.16 installation bioconductor GenomicRange • 120 views
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Entering edit mode
@james-w-macdonald-5106
Last seen 8 hours ago
United States

You should not try to install packages when you already have packages loaded. Instead, start R, then load the BiocManager package, and then install.

That said, you should simply be able to restart R and it should work. And also, the package is GenomicRanges, not GenomicRange.

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