installation path not writable R, unable to update packages

Question

I am trying to install Bioconductor into R, using the code on their website. When I type in the code (see bellow) I get an error message saying that some packages can\'t be

Answer 1

One solution is to open a terminal and load R using admin rights

sudo R
update.packages()
source("https://bioconductor.org/biocLite.R")
biocLite()

Then you can update. But careful. This can create packages by the admin in a directory supposed to be owned by a user.

In this case, instead of loading R as root (which is solving the problem until the next update), check the .libPaths(). You will have a list of directories.

.libPaths()
"/home/it_s_me/R/x86_64-pc-linux-gnu-library/3.4" "/usr/lib/R/library"

In my case, all packages in "/usr/lib/R/library" are owned by root, and all except one are owned by a normal user (not root) at "/home/itsame/R/x86_64-pc-linux-gnu-library/3.4".

If you have admin rights, an easy solution may be to run chown in all the places: For example, I had trouble updating the curl package. I used:

sudo chown -R it_s_me /home/it_s_me/R/x86_64-pc-linux-gnu-library/3.4/curl/

Answer 2

Since with the version of R 3.6.1 the script http://bioconductor.org/biocLite.R returns this message " Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install " I solved the problem with the following steps:

1. Get the list of directories used by R to install libraries and choose the one with write permissions using: .libPaths()
2. Installing the "BiocManager" library using: install.packages("BiocManager")
3. Installation of the library "bioconductor" by forcing the directory with write permissions using: BiocManager::install("Rgraphviz", lib = "C:/Users/tizbet/Documents/R/win-library/3.6")

I worked on the following R installation:

platform x86_64-w64-mingw32, arch x86_64, os mingw32, system x86_64, mingw32, version.string R version 3.6.1 (2019-07-05)

I was inspired by the Kasper Thystrup Karstensen answer

Answer 3

Correct way to resolve this problem is as followed:

1. Start R as an administrator: sudo R
2. In R console execute this: update.packages()

Summary is, some latest packages are required and updating those on admin mode solve this issue. `

Answer 4

Quit R by typing q() and enter then type again sudo R and hit enter for mew package installation.

Answer 5

I solved it by opening Rstudio as administrator.