The Beautiful science

updating R and packages

Hola!

A quick note on updating R.

Updating is always important as few bugs are fixed or the code is more efficient than the previous versions.

Though everything will be working as good as in old versions as in new, but some new features might be good to have.

Updating all R packages :

# open R with privileges 

sudo R

# updating all packages, enter ‘y’ when asked

update.packages(,dep=T)

This will update all packages in the library.

The R itself is updated regularly as a part of the Linux suite updates.

sudo apt-get update

sudo apt-get dist upgrade

** when R updates example from 2.12 to 2.13 , you wouldn’t be able to load the packages which you installed locally on 2.12 into 2.13.

Best way is to copy those packages to the new directory of 2.13 as:

# shell commands

cp -r ~/R/x86_64-pc-linux-gnu-library/2.12 ~/R/x86_64-pc-linux-gnu-library/2.13

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

rm -rf ~/R/x86_64-pc-linux-gnu-library/2.12/

UPDATE : You might get an error installing Bio-conductor packages, most likely two libs are missing. Install them by

sudo apt-get install  libcurl4-openssl-dev libxml2-dev

This removed my error of installing ‘rtracklayer’ package from Bioconductor.


Have Fun Coding,

Sukhdeep Singh

Max Planck

Germany

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