Question

DESeq2 is not available for R version 4.2.1

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annamariabugaj ▴ 10

@e7994b78

Last seen 21 months ago

Norway

I am trying to install DESeq2 but it is not available for current R version. Did anyone have this problem and have a good solution? The same is in case of WGCNA package. I tried other methods of installing but it did not work.

install.packages("DDESeq2") Warning in install.packages : package ‘DDESeq2’ is not available for this version of R

DESeq2 • 4.8k views

ADD COMMENT • link 2.2 years ago annamariabugaj ▴ 10

score 0 · Answer 1 · 2022-09-13

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shepherl 4.1k

@lshep

Last seen 2 hours ago

United States

Firstly you have a typo with an extra D -- it is DESeq2 not DDESeq2. Secondly, This is a Bioconductor package and needs to be installed with BiocManager not with install.packages as described on the DESeq2 landing page

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DESeq2")

ADD COMMENT • link 2.2 years ago shepherl 4.1k

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All Bioconductor packages should be installed using BiocManager::install and for what its worth BiocManager::install will also install any available CRAN package.

ADD REPLY • link 2.2 years ago shepherl 4.1k

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yes, sorry, I was trying to install so many times I finally have a typo. But the way you suggested is not working either:

Warning messages: 1: In install.packages(...) : installation of package ‘genefilter’ had non-zero exit status 2: In install.packages(...) : installation of package ‘DESeq2’ had non-zero exit status 3: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘Matrix’ had non-zero exit status 4: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘RcppArmadillo’ had non-zero exit status

library("DESeq2") Error in library("DESeq2") : there is no package called ‘DESeq2’

I think it has something to do with Mac M1 silicone (?) or the new R version, I am not able to install EdgeR as well.

My version of BiocManagaer is 3.15

ADD REPLY • link 2.2 years ago annamariabugaj ▴ 10

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Yes. Bioconductor is close to but not yet providing mac m1 binaries. There are several post on the support site here that suggest work arounds.

ADD REPLY • link 2.2 years ago shepherl 4.1k

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However on my other Mac M1 I do have all of this software installed but with lower Rstudio (4.1.2) version. So I am not sure what exactly makes the problem with installation in this case...I wanted to install the 4.1.2 version on the new one but I can not find it anywhere :/

ADD REPLY • link 2.2 years ago annamariabugaj ▴ 10