Update R in Ubuntu

If you installed R from the Ubuntu repository with

sudo apt-get install r-base

you most likely got an out of date version. In February 2018, that method still gave me R version 3.2.3 (2015-12-10). To get the latest versions of R and its packages, you need to add CRAN to the apt-get repositories. Do this with the code below. Enter one line at a time. Cut and paste to prevent errors.

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
sudo add-apt-repository 'deb [arch=amd64,i386] https://cran.rstudio.com/bin/linux/ubuntu xenial/'
sudo apt-get update

Now if you open Synaptic Package Manager and search for r-base, you should see the installed versions and the latest versions of several packages (e.g.  r-base, r-base-core, r-base-core-dbg, r-base-dev, r-base.html). Mark the packages for upgrade and click on apply. This will most likely result in a major update of R so that the next time you run R only the base packages will be available. You will have to re-install any additional R packages that you use to match the updated version of R.

Adapted from https://www.digitalocean.com/community/tutorials/how-to-install-r-on-ubuntu-16-04-2

Get Execution Time for a Shell Script

If you need to know the execution time for a bash script, you can place it inside the script below. The the total run time will be printed to the screen after the script finishes.

res1=$(date +%s.%N)

<your script here>

res2=$(date +%s.%N)
dt=$(echo "$res2 - $res1" | bc)
dd=$(echo "$dt/86400" | bc)
dt2=$(echo "$dt-86400*$dd" | bc)
dh=$(echo "$dt2/3600" | bc)
dt3=$(echo "$dt2-3600*$dh" | bc)
dm=$(echo "$dt3/60" | bc)
ds=$(echo "$dt3-60*$dm" | bc)
printf "Total runtime: %d:%02d:%02d:%02.4f\n" $dd $dh $dm $ds

Shamelessly copied from a post on unix.stackexchange.com by jwchew on August 30, 2013 .

Commenting Code in gedit

Gedit is the basic editor that is included in Ubuntu and other Linux distributions. Its functionality can be extended with plugins as explained in the post below. I installed the plugin initially because it allows one to comment or un-comment selected lines of text. I find this useful when I want to include two configuration blocks in a script, say one for a local installation of a program and another for a remote installation on a cluster. If you do this, just make sure the appropriate blocks are commented and un-commented when you run the script.

Source: Code Comment – gedit Plugin | Delightly Linux