I am trying to install R in an Ubuntu docker image. I am able to successfully do so using this line:
RUN apt-get update && apt-get install -y r-base
but it is installing r 3.2.3. I need a newer version (3.5.2). Does anyone know how to specify which version to download?
Sure thing:
FROM ubuntu:18.10
ENV DEBIAN_FRONTEND noninteractive
RUN apt-get update && apt-get -y install --no-install-recommends --no-install-suggests \
ca-certificates software-properties-common gnupg2 gnupg1 \
&& apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 \
&& add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/' \
&& apt-get install r-base
Taken from here: https://cran.r-project.org/bin/linux/ubuntu/README.html
And here: https://github.com/noisebrain/Dockerfiles/blob/0668df74b27f514dab19a7afae6715328de72980/Rstudio-server-aib/rstudio-server-aib.dockerfile
root#100d1cda7377:/# R
R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
Related
I am trying to install the R language in the docker file. My Ubuntu version is 18.04 LTS
RUN add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/' && \
apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 \
apt-get update \
apt-get install -y r-base \
rm -rf /var/lib/apt/lists/*
But I am getting the below error. But it is working in my machine and not working docker file.
Reading package lists...
W: GPG error: https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/ InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 51716619E084DAB9
E: The repository 'https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/ InRelease' is not signed.
The command '/bin/bash -c add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/' && apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 apt-get update apt-get install -y r-base rm -rf /var/lib/apt/lists/*' returned a non-zero code: 100
Could anyone help to fix this issue?
Thanks in advance
Add the key before the adding the repo.
Also you need the && after every command to chain them all.
I prefer to use ; after set -uex for long chains so I can easily see which command output is coming from, particularly when it fails.
RUN set -uex; \
apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9; \
add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/'; \
apt-get update; \
apt-get install -y r-base; \
rm -rf /var/lib/apt/lists/*
I'm trying to build a Docker container that runs R with the package RJava. I have tried the following code:
# Install R version 3.6.3
FROM rocker/tidyverse:3.6.3
# Make ~/.R
RUN mkdir -p $HOME/.R
# Install Ubuntu packages && then R packages
RUN install2.r --error \
lubridate magrittr RPostgres DBI broom rlang rJava
However I get the following: installation of package ‘rJava’ had non-zero exit status.
Can anyone help me with this. I'm thinking that maybe it is because Java is not installed. Does anyone know how to install Java on this docker container?
I've tried adding the following to my dockerfile as per another post I found however I get the error saying 'The repository 'http://ppa.launchpad.net/webupd8team/java/ubuntu focal Release' does not have a Release file:
# Install "software-properties-common" (for the "add-apt-repository")
RUN apt-get update && apt-get install -y \
software-properties-common
# Add the "JAVA" ppa
RUN add-apt-repository -y \
ppa:webupd8team/java
# Install OpenJDK-8
RUN apt-get update && \
apt-get install -y openjdk-8-jdk && \
apt-get install -y ant && \
apt-get clean;
# Fix certificate issues
RUN apt-get update && \
apt-get install ca-certificates-java && \
apt-get clean && \
update-ca-certificates -f;
# Setup JAVA_HOME -- useful for docker commandline
ENV JAVA_HOME /usr/lib/jvm/java-8-openjdk-amd64/
RUN export JAVA_HOME
I'm new to docker and any help with this would be much appreciated.
The rocker images are based on debian, not ubuntu. Specifically it is Debian GNU/Linux 10 (buster). With that version, you can install java by installing the package openjdk-11-jdk via apt and you don't need to add any repositories for openjdk-8-jdk.
So a working dockerfile that installs rJava:
FROM rocker/tidyverse:3.6.3
RUN apt-get update && \
apt-get install -y openjdk-11-jdk && \
apt-get install -y liblzma-dev && \
apt-get install -y libbz2-dev
RUN Rscript -e "install.packages('rJava')"
Note: liblzma-dev and libbz2-dev are additional system dependencies for compiling rJava.
If I run this
sudo apt-get install r-base
R 3.4 is installed from the ubuntu repo. So I added the CRAN repositories by doing
sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu eoan-cran35/'
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
sudo apt update
sudo apt install r-base
but then I get
The following packages have unmet dependencies:
r-base: Depends: r-base-core (> = 3.6.3-1eoan) but 3.4.4-1ubuntu1 is going to be installed
Depends: r-recommended (= 3.6.3-1eoan) but 3.4.4-1ubuntu1 is going to be installed
E: Problems cannot be corrected, you have retained broken packages.
I swear I tried every line of code from every forum I found but nothing solved this issue. I tried:
sudo apt update && sudo apt-get autoclean && sudo apt-get clean && sudo apt-get autoremove
sudo apt install --fix-broken
sudo apt-get install -f
sudo apt dist-upgrade -y
sudo apt full-upgrade
I also tried disabling ubuntu repos and use only the CRAN repositories, but it doesnt work.
I tried installing r-base 3.4 and upgrading from that but nothing.
I really don't know what else to do, any ideas?
It depend of the version of Linux Mint you are running, but based on your code, you are trying to install r-base for Ubuntu 19.10 eoan (which is not a LTS).
The last version of Linux Mint 19.3 is based on Ubuntu 18.04 Bionic, so you should edit your /etc/apt/sources.list file and add
deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/
Then:
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
sudo apt-get update
sudo apt-get upgrade
sudo apt-get install r-base-dev
All informations from cran are here: https://cran.r-project.org/
For Linux Mint, check this page (https://www.linuxmint.com/rel_tricia_xfce_whatsnew.php):
> Linux Mint 19.3 features Xfce 4.14, a Linux kernel 5.0 and an Ubuntu 18.04 package base.
I have been trying to but struggling to install R and RStudio on my Chromebook Samsung 3. I have it set-up with Crouton with XFCE/Xiwi and use Trusty. I can install R just fine but either can't install Rstudio at all or can get the icon for Rstudio to show up but nothing happens when I click on it. Can someone give me a process on how to install these effectively on my device?
UPDATE 2020:
I am no longer using Crouton, but rather the built in Linux option (Crostini). In the Linux terminal, I did the following:
sudo apt-get update; sudo apt-get upgrade; sudo apt-get update --fix-missing; sudo apt autoclean; sudo apt-get clean; sudo apt-get autoremove
sudo apt install -y gnupg2
sudo apt-key adv --keyserver keys.gnupg.net --recv-key 'E19F5F87128899B192B1A2C2AD5F960A256A04AF'
sudo vi /etc/apt/sources.list
Add this line. Can use a different mirror if desired. (Note: older versions of Crostini were running Stretch by default instead of Buster)
deb http://cran.rstudio.com/bin/linux/debian buster-cran35/
Then back in the terminal
sudo apt-get install xclip
sudo apt install -y r-base r-base-dev
sudo apt-get install gdebi-core
sudo apt install -y libgstreamer1.0 libgstreamer-plugins-base1.0 libxslt-dev libnss3
sudo apt --fix-broken install
sudo curl -o rstudio.deb https://download1.rstudio.org/desktop/bionic/amd64/rstudio-1.2.5033-amd64.deb
sudo dpkg -i rstudio.deb
sudo apt-get update; sudo apt-get upgrade; sudo apt --fix-broken install; sudo apt-get update --fix-missing; sudo apt autoclean; sudo apt-get clean; sudo apt-get autoremove
ORIGINAL ANSWER:
It admittedly took me a long time, but I was finally able to install R and RStudio on my Chromebook Samsung 3. I have it set-up with Crouton with XFCE/Xiwi and use Trusty. After setting up Crouton, etc. here is what I had to do in the Linux terminal:
sudo apt-get install software-properties-common
sudo apt-get install selinux-policy-default
sudo apt-get install libqpol1
Add these lines:
deb https://<FOO>/bin/linux/ubuntu trusty/
deb https://<FOO>/ trusty-backports main restricted universe
to file
/etc/apt/sources.list
(replace FOO with the CRAN mirror of your choice and replace trusty if applicable)
Terminal:
sudo apt-get update
sudo apt-get install r-base
sudo apt-get install r-base-dev
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
sudo add-apt-repository ppa:marutter/rrutter
sudo apt update
sudo apt upgrade
sudo apt upgrade r-base r-base-dev
sudo apt-get install gdebi-core
wget https://download2.rstudio.org/rstudio-server-1.1.442-amd64.deb
sudo gdebi rstudio-server-1.1.442-amd64.deb
wget https://download1.rstudio.org/rstudio-0.99.896-amd64.deb
sudo apt-get install libxslt1-dev
sudo gdebi rstudio-0.99.896-amd64.deb
cd /usr/bin/
rstudio
source
source
source
source
I am trying to install the latest version of R (3.4.0) due to some incompatibility issues with dowloading of a package called "Slam". I have downloaded the tar.gz file of 3.4.0 but there are some issues with the make file for installation.
I have uninstalled the r-base of 3.2.3. Now when I'm installing R again, I get the same version instead of the upgrade version. I even ran the sudo apt-get update command but in vain.
you need to install from the CRAN repos not the ubuntu ones. add the key, then the repository, update and the apt-get
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
sudo apt-get install r-base