On Ubuntu 18.04 LTS, while working R in JupyterNotebook (without Anaconda), the IRKernel is reading the R version 3.4. For using some packages like cowplot it is necessary to have at least version 3.5.
Basically, two steps should be taken:
Update R. These and that answers were a guideline.
Update IRKernel. The offical IRKernel instructions for Linux were useful.
Next, is described the complete procedure
1. Add Key to server
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
2. Add Entry to sources.list
echo 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/' | sudo tee -a /etc/apt/sources.list
Depending on the linux you're using you should change, for example, bionic by xenial or cosmic, check out https://cran.r-project.org/bin/linux/ubuntu/README.html
3. Update Programs
According to the instructions in the above link, we should do the following:
sudo apt-get update
sudo apt-get install r-base
sudo apt-get install r-base-dev
4. Update /.local/share/jupyter/kernels/ir
type R in the console and follow the next steps according to this link
# In the console
R
# Inside R
install.packages(c('repr', 'IRdisplay', 'IRkernel'), type = 'source')
getRversion() # to verify the new R version
IRKernel::installspec()
This should show the following message:
[InstallKernelSpec] Removing existing kernelspec in /home/user_name/.local/share/jupyter/kernels/ir
[InstallKernelSpec] Installed kernelspec ir in /home/user_name/.local/share/jupyter/kernels/ir
As a final remark, you should remove the older version of R, which you can find in ~/R/x86_64-pc-linux-gnu-library, where you will now have two directories with two different versions or R (remove the older one).
Related
I installed Rstudio using anaconda. I think the R was also installed alongside with it (but I read somewhere that Rstudio doesn't come with R: Tell me if I am wrong).
From terminal: which R shows :/home/simo/anaconda3/bin/R.
I tried that:
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
sudo echo "deb http://cran.wustl.edu/bin/linux/ubuntu bionic-cran35/" | sudo tee -a /etc/apt/sources.list
sudo apt update
sudo apt upgrade
but doesn't upgrade the version of R (still R version 3.5.1 (2018-07-02) -- "Feather Spray")
At the first place I want to install: dashHtmlComponents, a dash library.
> install.packages("dashHtmlComponents")
Warning message:
package ‘dashHtmlComponents’ is not available (for R version 3.5.1)
>
But from the dash documentation I read that at least version 3.0.2 of R is required.
What is wrong?
It depends what OS you are on how you would go about doing that. The particular methods for Windows and MacOS are laid out on this page.
As far as if you have R (which it appears you do, but nonetheless), you can run install r-essentials --yes in the terminal (Mac) or Anaconda Prompt (PC). In Linux you can follow the steps here.
Once you do either of these, you should be able to use install.packages('dashHtmlComponents'). I am using R version 3.6.2 and it installs just fine.
I'm using Ubuntu 16.04 on Azure Linux Virtual Machine
lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 16.04.5 LTS
Release: 16.04
Codename: xenial
The current R version for Rstudio/Rserver is 3.4.4 and I would like to update it to the latest version (i.e. version 3.5.2)
R --version
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
From some reasons, the most common method doesn't work:
apt-get update
apt-get upgrade
So I did some research and find this post on biostars.org
One of the posts says the following codes might work
sudo su
echo "deb https://cloud.r-project.org/bin/linux/ubuntu xenial-cran35/" >> /etc/apt/sources.list
apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
apt-get update
apt-get install r-base
apt-get install r-base-dev
However, after apt-get install r-base I'm getting the following error message:
root#VMforR:/usr/local/bin# apt-get install r-base
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
r-base : Depends: r-recommended (= 3.5.2-1xenial) but it is not going to be installed
E: Unable to correct problems, you have held broken packages.
I don't understand what "held broken packages" means, and more importantly, how to update the R base?
What worked for me was to add the PPA of Michael Rutter:
sudo add-apt-repository ppa:marutter/rrutter3.5
sudo apt-get update
Update R:
sudo apt install r-api-3.5
I'm with the 16.04 LTS ubuntu.
Have tried some other methods, the following seems to work:
sudo apt-get install r-base-core=3.5.2-1xenial
Ref:
1. Install particular version(2.15.2) of r-base on ubuntu
2. https://cran.rstudio.com/bin/linux/ubuntu/xenial-cran35/
But I'm not sure if this also work for others or not, as I can't reproduce it.
After
apt-get update
do
apt-get dist-upgrade
first to "move your installation forward". That includes upgrading already installed packages. It should just upgrade your R installation (unless you also switch / need to switch repositories).
The r-sig-debian list is good and patient with basic 'how do it od X for R on Debian/Ubuntu'. Consider subscribing to lurk and/or ask questions.
Mine said some of my packages were missing. So, I ran sudo dpkg --configure -a and then re-run the R --update and it worked to correct the missing package error.
I'm running Ubuntu in Windows Subsystem for Linux, and apt-get update isn't finding the newest versions of r-base. On Ubuntu 16.04, the newest R version it gets is 3.2.3. How do I upgrade to newer versions of R?
It turns out that the version of r-base in the default Ubuntu repository is behind the newest version of r-base from CRAN.
The solution is to add R-CRAN to /etc/apt/sources.list, using the instructions here: https://cran.r-project.org/bin/linux/ubuntu/
sudo sh -c 'echo "deb https://cloud.r-project.org/bin/linux/ubuntu xenial-cran35/" >> /etc/apt/sources.list'
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
sudo apt-get update
sudo apt-get install --only-upgrade r-base # This upgrades r-base if it's already installed; otherwise it doesn't install it
As #DirkEddelbuettel said in his comments, this README has helpful information for how you can update your R version in a Windows subsystem for Linux (WSL) setting. For me, I updated from R 3.4 to R 4.0 on Ubuntu 18.04.
I am running bionic (I used lsb_release -a to find out), and I wanted R 4.0 so I picked the appropriate deb line (for me: deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/) to add to my /etc/apt/sources.list file (had to use sudo vim /etc/apt/sources.list to add this line to the end). Then I ran sudo apt-get update and sudo apt-get install r-base. Now I have 4.0.2, the newest version. Just pick the particular Ubuntu/R combo that you want based on the options from the README. I hope this can help someone.
I am new to Linux. I am using Linux mint 18.1. I have installed R using system software manager. My current R version is 3.2. But I want to upgrade it to version 3.4.
How can I do it?
Note: I now keep on GitHub (here) an up-to-date guide to upgrading R on Linux Mint or Ubuntu Linux, which also includes a bit of extra information about system dependencies for tidyverse, the popular set of data-wrangling packages, as well as devtools, the popular R package development... package.
The link provided by FedRo is a good resource, however a slight change would need to be made since you're using Linux Mint 18.1 which uses Xenial repositories rather than Trusty repositories (see here). I also typically use the approach here to deal with packages I've already installed when I upgrade R rather than the approach offered by FedRo. So, for completeness, these are all the steps you'd need to take:
Step 1
Go to CRAN's list of mirrors and find the URL of the mirror that is closest to you. The terminal commands below assume you choose http://cran.wustl.edu/
Step 2
Open a terminal and enter the following commands1 (replacing http://cran.wustl.edu/ with whichever CRAN mirror URL you chose in step 1):
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
sudo echo "deb http://cran.wustl.edu/bin/linux/ubuntu xenial/" | sudo tee -a /etc/apt/sources.list
sudo apt update
sudo apt upgrade r-base r-base-dev
sudo apt update
sudo apt upgrade
Note also that I have put to upgrade r-base and r-base-dev, but I don't know if you have r-base-dev installed. If not, I highly recommend you install it via sudo apt install r-base-dev.
Step 3
Start a new R session and run the following:
update.packages(checkBuilt=TRUE, ask=FALSE)
Then you should be good to go.
Update: Linux Mint 19 and R 3.6.x
Since both Linux Mint and R have seen upgrades since I answered this question, I'm updating for those who come to this answer needing the info for Linux Mint 19 and R 3.6.x.
The only difference is that instead of the command
sudo echo "deb http://cran.wustl.edu/bin/linux/ubuntu xenial/" | sudo tee -a /etc/apt/sources.list
you need to use
sudo echo "deb http://cran.wustl.edu/bin/linux/ubuntu bionic-cran35/" | sudo tee -a /etc/apt/sources.list
(replacing http://cran.wustl.edu/ with whichever CRAN mirror URL you chose in step 1)
1 I put here the full key, though many other guides you may see will use only the "short key."
I have updated this guide to use the full key out of security concerns (see here, for example).
Now it is very simple. Just make:
install.packages("ropenblas")
ropenblas::rcompiler()
I'm working with R now for some month and I'm still a newbie.
I acutall working for a project to build up R RHadoop and Hadoop.
The sandbox + R + RStudio is already running and working.
I wanted to install R + RStudio also on the bigger cluster with several nodes for testing in cluster mode. But when I installed R, is saw, that a new version comes out, 3.2.2. On my sandbox, I'm still working with 3.2.1.
Version 3.2.2 seems to have some problem with my code, so I want to use 3.2.1, but I'm not able to install older version of R.
How can I install R-3.2.1-2.el6.x86_64 on the cluster as well?
I'm working on centos 6.
Regards,
suerte
I don't know if you found a solution at your problem, but here is how I install old R versions :
0) You should be sure to know which linux version you use
lsb_release -a
You should get something like (this is my result in example):
Distributor ID: Ubuntu
Description: Ubuntu 14.04
Release: 14.04
Codename: trusty
So now I know that my linux is a trusty.
1) After that you need to add a cran repository on your /etc/apt/sources.list
You can find cran address here : https://cran.r-project.org/mirrors.html
That give you access to older package. Choose one for your Linux !!
example :
deb https://cloud.r-project.org/bin/linux/ubuntu trusty/
2) You need to add the registry key to don't have certificate problem. I use this command but fell free to find another one on their website :
gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E084DAB9
gpg -a --export E084DAB9 | apt-key add -
3) Here is the tricky part :
1 --> do an apt-get update to have the new repository
2 --> choose your version in the cran and specify it. That should look like something like that :
apt-get -y install r-base-core=3.1.0-1trusty0 #For R
apt-get -y --force-yes install r-doc-html=3.1.0-1trusty0 #For doc
apt-get -y install r-base-dev=3.1.0-1trusty0 # for dev
etc ...
Just be careful, I had some problems when I tried to install r-base=.... and r-recommended= .... All the time, that had install the latest version.
For the cluster I don't know yet but I think a script should work.
Hope that helped.
Regards