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duttashi / learnr

Exploratory, Inferential and Predictive data analysis. Feel free to show your :heart: by giving a star :star:
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Set up library path location for installed packages, remove installed packages (clean up) and install only required packages #14

Closed duttashi closed 6 years ago

duttashi commented 6 years ago

Last evening I decided to update the installed packages. During the update process, a prompt came up, do you want to install from sources the packages which need compilation r. I chose the option, yes and boy, this messed up everything in RStudio.

Lesson learnt: if such a message pop's up, choose No. See this post for reference.

Another problem was I had never set up the library path for the installed packages. So, I needed to set the library path. And finally, I needed to tweak the .Rprofile.site file. For windows OS it is located in, C:\Program Files\R\R-3.5.0\etc

duttashi commented 6 years ago

Solution

# Objective 1: Set the library path for installed packages
# Objective 2: To uninstall all packages and then install only the relevant ones

# create a list of all installed packages
ip <- as.data.frame(installed.packages())
head(ip)
# we don't want to remove base or recommended packages either\
ip <- ip[!(ip[,"Priority"] %in% c("base", "recommended")),]
# determine the library where the packages are installed
path.lib <- unique(ip$LibPath)
# create a vector with all the names of the packages you want to remove
pkgs.to.remove <- ip[,1]
head(pkgs.to.remove)
# remove the packages
sapply(pkgs.to.remove, remove.packages, lib = path.lib)

# check the R library path
.libPaths()
# set the library path for R
.libPaths("C:/Program Files/R/R-3.5.0/library") 
# set the library path for Rstudio
assign(".lib.loc", "C:/Program Files/R/R-3.5.0/library", envir = environment(.libPaths))
# check the R library path again
.libPaths()

# Now, installing multiple packages required for analysis
pkgs_to_install<- c("caret","cluster","tidyverse","grid",
                    "RColorBrewer","factoextra","ggpubr","FactoMineR")
install.packages(pkgs_to_install, dependencies = TRUE)

References

duttashi commented 6 years ago

I was still getting error when loading a library in RStudio. My mistake was that earlier, I had set up the library path but it was set for R and not RStudio. So, I had to include the following line in the .RProfile site as well as whenever I would want to install a package in Rstudio, I've to use the following command, assign(".lib.loc", "C:/Program Files/R/R-3.5.0/library", envir = environment(.libPaths))

Reference