After update to R 4.1

# update indices

sudo apt update -qq

# install two helper packages we need

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

# import the signing key (by Michael Rutter) for these repo

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9

# add the R 4.0 repo from CRAN -- adjust 'focal' to 'groovy' or 'bionic' as needed

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

Here we use lsb_release -cs to access which Ubuntu flavor you run: one of “hirsuite”, “groovy”, “focal”, “bionic”, …

Then run

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

See: https://cran.r-project.org/bin/linux/ubuntu/

pkgs <- as.data.frame(installed.packages(), stringsAsFactors = FALSE, row.names = FALSE)

pkgs[, c("Package", "Version", "Built")]

Will list the packages with their built version.

Then you can do:

update.packages(ask = FALSE, checkBuilt = TRUE)

See: https://shiny.rstudio.com/articles/upgrade-R.html

You can also remove duplicated packages:

library("HelpersMG")

li <- duplicated_packages()

if (nrow(li) != 0) 

for (i in 1:nrow(li))

remove.packages(rownames(li)[i], lib=li[i, "Lib1"])

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