DESeq2 is not available for R version 4.2.1
1
0
Entering edit mode
@e7994b78
Last seen 15 hours 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 • 132 views
ADD COMMENT
0
Entering edit mode
shepherl 3.3k
@lshep
Last seen 8 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
0
Entering edit mode

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
0
Entering edit mode

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
0
Entering edit mode

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
0
Entering edit mode

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

Login before adding your answer.

Traffic: 347 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6