I have problems installing DESeq2 using R4.1.2. It tells me that it is not available for my version of R and I need to upgrade my R version. but I cant install new version in Ubuntu(22.04 LTS)
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yari.hadi • 0
@1552d6f8
Last seen 7 weeks ago
United States

several time I tried to install DESeq2 but I had problem and it didn't work. An error tells me I need to upgrade my R version. but unfortunately every time I reinstall R it was 4.1.2 version, not 4.2.1. my operation system is Ubuntu 22.04 LTS.

Please tell me how I can solve my problem.

DESeq2 • 316 views
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Please show the command and the output.

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using this command I tried to install R version 4.2 but after installation it was 4.1.2

sudo apt install -y --no-install-recommends software-properties-common dirmngr

wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc

sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"

sudo apt install --no-install-recommends r-base

and

using this command I tried to install DESeq2 but it didt install the package

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

BiocManager::install("DESeq2")

Error Installing package into ‘/home/hadi/R/x86_64-pc-linux-gnu-library/4.1’ (as ‘lib’ is unspecified) Warning: unable to access index for repository https://cloud.r-project.org/src/contrib: cannot open URL 'https://cloud.r-project.org/src/contrib/PACKAGES' Warning message: package ‘BiocManager’ is not available for this version of R

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 Error in loadNamespace(x) : there is no package called ‘BiocManager’

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Maybe it is trivial but did you restart R after upgrading ?

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@james-w-macdonald-5106
Last seen 47 minutes ago
United States

You did everything except the actual installation of R! The next step is

sudo apt install --no-install-recommends r-base

Which is what actually installs R

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