Ubuntu – R 3.5.0 not working on Ubuntu 18.04

18.04gnomer

I just installed Ubuntu 18.04 on my testbed laptop. Total fresh install (chose the 'minimal' option). The first two things I did were install R 3.5 and R Studio 1.1.453. If I open up a fresh install of R and just let it sit idle for 30 minutes or so I eventually get the error "Error: Unable to establish connection with R session".

At this point in time I can't do anything in R Studio and I have to xkill it and reload everything to continue programming. An internet search reveals that this issue has been popping up repeatedly since people have been installing R/R Studio on Ubuntu machines that use GNOME. Am not sure if GNOME is the root cause but it's interesting.

Anybody solved this? Or maybe you run R 3.5 fine on Ubuntu 18.04 without issue. Please let me know. I can only run for 30 minutes or so before this issue brings my system down. And my system is a fresh install of Bionic Beaver with just R on it. Weird.

—— and for those wondering ——

installation for R was via

sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/"
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
sudo apt-get update
sudo apt-get install r-base r-base-dev

and R Studio was installed via this link through the Ubuntu software center
https://download1.rstudio.org/rstudio-xenial-1.1.453-amd64.deb

and it is speculated that the preview release of R Studio may fix this (TBD)
https://s3.amazonaws.com/rstudio-ide-build/desktop/trusty/amd64/rstudio-1.2.792-amd64.deb

Best Answer

Currently CRAN mirror provides R 3.6 by default.

To get R 3.5 on Ubuntu 18.04 LTS we need to add CRAN repository with:

sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/"
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
sudo apt-get update

and then adjust APT to the highest priority of R 3.5.x versions for the CRAN repository with long single command:

cat <<EOF | sudo tee /etc/apt/preferences.d/pin-r35
Package: r-*
Pin: release a=bionic-cran35
Pin: version 3.5*
Pin-Priority: 800

Package: r-cran-nlme
Pin: release a=bionic-cran35
Pin: version 3.1.139-1bionic0
Pin-Priority: 800

Package: r-cran-cluster
Pin: release a=bionic-cran35
Pin: version 2.0.8-1bionic0
Pin-Priority: 800
EOF

Then install R 3.5 with the command below:

sudo apt-get install r-base r-base-dev

And finally check that R version is 3.5:

$ R

R version 3.5.3 (2019-03-11) -- "Great Truth"

Notes:

I have checked this method on clean Ubuntu 18.04 LTS VM with two essential R packages installed - r-base and r-base-dev (and their dependencies).
If you want to revert to R 3.6 - then simply remove pin/lock file with sudo rm /etc/apt/preferences.d/pin-r35 and run sudo apt-get dist-upgrade to get the newest dependencies.
For Ubuntu 16.04 LTS the method is very similar - see my other answer.

Proceed at your own risk.

The procedure that worked for me is:

Remove all r-cran-* packages from your system (YMMV, I'm usually installing packages from source and have very few of these)
- Search with dpkg -l | grep r-cran-

Add Michael Rutter's PPA:

sudo add-apt-repository ppa:marutter/rrutter3.5
sudo apt-get update

Upgrade R
```
sudo apt install r-api-3.5
```
Install all packages you need from source (to a personal or site library via install.packages()) or by installing the corresponding r-cran-* Ubuntu package.

I use the following script to reinstall all packages my packages from my personal site library for R 3.4:
```
installed <- rownames(installed.packages())
pkgs <- dir("~/R/x86_64-pc-linux-gnu-library/3.4")
new <- setdiff(pkgs, installed)
new
install.packages(new)
```
If you have a machine with multiple CPUs, you can speed up the process, for example:
```
install.packages(new, Ncpus = 6)
```

References

Reply by Dirk Eddelbuettel to a similar inquiry on the R-SIG-Debian mailing list
Related SO question

Ubuntu – Unable to install R 3.5.0 in Ubuntu Bionic Beaver (18.04)

I am posting this answer so that it might help someone stumbling over the same problem. The problem was solved with a roundabout trick - it was experimental but it did work out.

So, I was trying to install R 3.5.0 from CRAN directly and it refused to get installed as mentioned in the question. The idea was to install whatever existing version in Ubuntu Bionic (18.04) and upgrade to 3.5.0 (instead of installing R from scratch).

The detailed steps are :

For now remove the source deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/ from Software sources.

Basic cleanup :-

sudo apt-get autoremove
sudo apt-get update
sudo apt-get upgrade

Install whatever existing version in Ubuntu Bionic with
```
sudo apt-get install r-base
```
Re-add the source deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/
sudo apt-get update

-- still shows the warning expected bionic-cran35/ but got bionic

Ignore and proceed with sudo apt-get upgrade
Upgrade all the existing packages in Linux
```
sudo apt-get dist-upgrade
```

And the last command (6th) actually does the job --- R 3.5.0.

PS - The warning still displays in the screen when I update the sources but right now appears to be innocuous. Hopefully the next R update will fix that.

UPDATE : Infact, the bug has been fixed. So we can directly install R as per CRAN website from now on.

Best Answer

Related Solutions

Ubuntu – R 3.5.0 for Ubuntu

Proceed at your own risk.

References

Ubuntu – Unable to install R 3.5.0 in Ubuntu Bionic Beaver (18.04)

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