Migrating packages between R installations

migrate_packages.R

### Open old version of R and type:

packages.file <- "Rpackages.RData"
a <- installed.packages()
my.packages <- a[,"Package"]
save(my.packages, file = packages.file)


### Open new version of R and type:

packages.file <- "Rpackages.RData"
load(packages.file)  # my.packages
new.packages <- installed.packages()
new.packages <- new.packages[,"Package"]

need.to.install <- my.packages[!(my.packages %in% new.packages)]

# Install packages from CRAN
# you might be prompted that you don't have the permissions to install into the default (admin) library and asked whether you want to install the packages into your local library instead --> confirm with yes

install.packages(pkgs = unique(need.to.install), repos = "http://cran.r-project.org")

# Some packages will not be found because they are from Bioconductor
# Install remaining packages from Bioconductor:

new.packages <- installed.packages()
new.packages <- new.packages[,"Package"]
need.to.install <-  my.packages[!(my.packages %in% new.packages)]

if (!requireNamespace("BiocManager", quietly = TRUE)){
    install.packages("BiocManager")
}
BiocManager::install(unique(need.to.install))


# Some packages might still not be installed because they are not available for the new version of R, their dependency is not available, or something went wrong during the installation
# Check which packages were not installed

new.packages <- installed.packages()
new.packages <- new.packages[,"Package"]
not.installed <-  my.packages[!(my.packages %in% new.packages)]