workflow_updating_r.R

# Based on this blog post: https://www.r-bloggers.com/updating-r/

### 1
## Change accordingly
list_dir <- "/Library/Frameworks/R.framework/Resources/library"

## Get the list of installed packages
installed <- dir(.libPaths())

## Save the list for later use
save(installed, file = file.path(list_dir, paste0(Sys.Date(), '-installed.Rdata')))

## Explore the list
head(installed)

length(installed)

### 2
## Change accordingly
list_dir <- "/Library/Frameworks/R.framework/Resources/library"

## Find the corresponding Rdata files
previous <- dir(path = list_dir, pattern = 'installed.Rdata')

## Load the latest one
load(file.path(list_dir, previous[length(previous)]))

## Just checking it
head(installed)

current <- dir(.libPaths())

## For Bioconductor and CRAN packages
source('http://bioconductor.org/biocLite.R')
biocLite(installed[!installed %in% current])

## Check which packages are missing
current_post_installation <- dir(.libPaths())
installed[!installed %in% current_post_installation]