R 4.0.2 en amazon linux

R
linux
aws
2020
Author

José Luis Cañadas Reche

Published

August 20, 2020

Entrada corta sobre como instalar R 4.0.2 en amazon linux, ya que por defecto trae una versión de R de hace 3 años.

La idea es instalar R vía rpm, sacada de aquí, pero el problema es que en amazon linux faltan algunas librerías que están en centos 7 y hay que buscar los rpm.

La solución que me ha funcionado, estando como root en amazon linux

cd /tmp
curl -O http://mirror.ancl.hawaii.edu/linux/centos/7/os/x86_64/Packages/pcre2-utf32-10.23-2.el7.x86_64.rpm
curl -O http://mirror.ancl.hawaii.edu/linux/centos/7/os/x86_64/Packages/pcre2-utf16-10.23-2.el7.x86_64.rpm
curl -O https://rpmfind.net/linux/centos/7.8.2003/os/x86_64/Packages/pcre2-10.23-2.el7.x86_64.rpm
curl -O http://mirror.ancl.hawaii.edu/linux/centos/7/os/x86_64/Packages/pcre2-devel-10.23-2.el7.x86_64.rpm
curl -O https://rpmfind.net/linux/centos/6.10/os/x86_64/Packages/tk-8.5.7-5.el6.x86_64.rpm


## instalar

yum install -y tcl
yum install -y tk-8.5.7-5.el6.x86_64.rpm
yum install -y pcre2-utf32-10.23-2.el7.x86_64.rpm 
yum install -y pcre2-utf16-10.23-2.el7.x86_64.rpm
yum install -y pcre2-10.23-2.el7.x86_64.rpm
yum install -y pcre2-devel-10.23-2.el7.x86_64.rpm

## install R

yum install https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm 
yum-config-manager --enable "rhel-*-optional-rpms"

export R_VERSION=4.0.2

curl -O https://cdn.rstudio.com/r/centos-7/pkgs/R-${R_VERSION}-1-1.x86_64.rpm
yum install -y R-${R_VERSION}-1-1.x86_64.rpm

# y ya estarian en /opt/R/4.0.2/

Y si lo queremos en el dockerfile

FROM amazonlinux:2018.03-with-sources
MAINTAINER canadasreche@gmail.com 

# Update yum
RUN yum -y update 

# set locales
RUN echo "LANG=en_US.utf8" >> /etc/locale.conf
#RUN localedef -c -f UTF-8 -i en_US en_US.UTF-8
RUN export LC_ALL=en_US.UTF-8
RUN yum -y install gcc64 wget gcc gcc-c++ make

# Install system libraries
RUN export MAKE='make -j 8'
RUN yum install -y xorg-x11-xauth.x86_64 xorg-x11-server-utils.x86_64 xterm libXt libX11-devel \
libXt-devel libcurl-devel git compat-gmp4 compat-libffi5 libxml2-devel libjpeg-devel openssl-devel \
boost boost-devel autoconf flex bison libssh2-devel java-1.8.0-openjdk java-1.8.0-openjdk-devel \
fontconfig-devel cairo-devel mesa-libGLU-devel libGL-devel libpng-devel

# Problems with some compilation with R libraries
#RUN yum remove gcc72-c++.x86_64 libgcc72.x86_64 -y \
RUN yum groupinstall 'Development Tools' -y

# Install and update R
RUN yum install -y R-core R-base R-core-devel R-devel
RUN yum update -y R-core R-base R-core-devel R-devel
RUN yum install -y https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
RUN yum-config-manager --enable epel
RUN yum-config-manager --enable "rhel-*-optional-rpms"
RUN yum -y install v8-devel
# ENV JAVA_HOME /usr/java/latest

# Fix problem with c compiler
RUN mkdir ~/.R
RUN echo "CC=gcc64" >> ~/.R/Makevars

# Fix problem with some libraries
RUN ln -s /usr/lib/gcc/x86_64-amazon-linux/4.8.5/libgfortran.so /usr/lib/libgfortran.so
RUN ln -s /usr/lib/gcc/x86_64-amazon-linux/4.8.5/libquadmath.so /usr/lib/libquadmath.so

# Install R 4.0.2

RUN curl -O http://mirror.ancl.hawaii.edu/linux/centos/7/os/x86_64/Packages/pcre2-utf32-10.23-2.el7.x86_64.rpm \
  && curl -O http://mirror.ancl.hawaii.edu/linux/centos/7/os/x86_64/Packages/pcre2-utf16-10.23-2.el7.x86_64.rpm \
  && curl -O https://rpmfind.net/linux/centos/7.8.2003/os/x86_64/Packages/pcre2-10.23-2.el7.x86_64.rpm \
  && curl -O http://mirror.ancl.hawaii.edu/linux/centos/7/os/x86_64/Packages/pcre2-devel-10.23-2.el7.x86_64.rpm \
  && curl -O https://rpmfind.net/linux/centos/6.10/os/x86_64/Packages/tk-8.5.7-5.el6.x86_64.rpm

RUN yum install -y tcl \
  &&  yum install -y tk-8.5.7-5.el6.x86_64.rpm \
  &&  yum install -y pcre2-utf32-10.23-2.el7.x86_64.rpm \
  &&  yum install -y pcre2-utf16-10.23-2.el7.x86_64.rpm \
  &&  yum install -y pcre2-10.23-2.el7.x86_64.rpm \
  &&  yum install -y pcre2-devel-10.23-2.el7.x86_64.rpm


## install R

RUN cd /tmp
RUN curl -O https://cdn.rstudio.com/r/centos-7/pkgs/R-4.0.2-1-1.x86_64.rpm
RUN yum install -y R-4.0.2-1-1.x86_64.rpm

CMD ["bash"]

Y listo ya tendríamos R 4.0.2 en /opt/R/

Para vincularlo con Rstudio server que estaría instalado en esta máquina (que formaría parte de un EMR) solo sería modificar el archivo /etc/rstudio/rserver.conf y añadir la línea

rsession-which-r=/opt/R/4.0.2/bin/R

Y así tendríamos las dos versiones de R, la que viene por defecto en amazon linux y la 4.0.2