add info for multiple R versions for linux

achubaty · Nov 23, 2016 · 14a7ba3 · 14a7ba3
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diff --git a/using-multiple-R-versions-on-linux.Rmd b/using-multiple-R-versions-on-linux.Rmd
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+---
+title: "Using multiple R versions on Linux"
+author: "Alex M. Chubaty"
+date: "November 23, 2016"
+output: 
+  pdf_document: 
+    highlight: pygments
+    toc: yes
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+
+Unlike on Windows, most R users on linux tend to work with a single version of R -- whichever version is available in their software repositories.
+With a little bit of work, it is possible to use multiple versions of R on Linux; however, you will need an account with `sudo` privileges to set this up.
+
+The most common use case is to install R-devel alongside the current R version in order to facilitate package checking and testing prior to CRAN submission.
+Additionally, you may wish to maintain older versions of R to maintain compatibility and reproducbility of old code/scripts, or to rerun old anasyses.
+
+# Using Docker
+
+This is the preferred solution, as it is self-contained.
+Everytime you start an instance of R in a Docker container, it starts in a "factory fresh" state, which means you will need to install additional packages into each new instance or save (commit) your changes for later reuse.
+The advantages here are that packages installed for each project are kept separate, ensuring proper reproducibility and portability.
+(Although [`packrat`](https://rstudio.github.io/packrat/) is also good for maintaining separate package libraries per project, it doesn't ensure system dependency separation.)
+
+Please note that this guide is intended only to get you started with using R with Docker, not to be a full tutorial for more advanced Docker use.
+See the offical [Docker documentation](https://docs.docker.com/) and the [rocker project](https://github.com/rocker-org/rocker) for more advanced usage, including using containers with Rstudio Server installed or using a virtual X server.
+
+## Older R versions
+
+1. Install Docker following the instructions [here](https://docs.docker.com/engine/installation/).
+
+2. Download the image for the version of R you wish to use:
+
+    ```bash
+    docker pull r-base:3.2.2
+    ```
+
+3. Start a container running the R version of your choice:
+
+    ```bash
+    docker run -it --rm r-base:3.2.2
+    ```
+
+    \* NOTE: the `--rm` flag tells docker to remove the container after use.
+    If you wish to keep the container for reuse later (*e.g.*, so you don't need to reinstall packages, etc.), then omit this.
+
+## R-devel
+
+1. Install Docker following the instructions [here](https://docs.docker.com/engine/installation/).
+2. Download the latest R-devel image:
+
+    ```bash
+    docker pull rocker/drd
+    ```
+3. Start a container running R-devel:
+
+    ```bash
+    docker run -it --rm rocker/drd Rdevel
+    ```
+    
+    \* NOTE: the `--rm` flag tells docker to remove the container after use.
+    If you wish to keep the container for reuse later (*e.g.*, so you don't need to reinstall packages, etc.), then omit this.
+
+\newpage
+
+# Metal installation
+
+As noted above, using Docker is likely a better solution, as this approach doesn't maintain separation between packages installed for different versions (except R-devel).
+
+## Older R versions
+
+1. Install prerequisites for building R from source:
+
+    ```bash
+    sudo apt-get build-dep r-base
+    ```
+
+2. Create directories to keep the R source code:
+
+    ```bash
+    mkdir ~/R/src
+    ```
+
+3. Get the source code for the version of R you wish to install:
+
+    ```bash
+    cd ~/R/src/
+    wget https://cran.r-project.org/src/base/R-3/R-3.2.2.tar.gz
+    tar -xvzf R-3.2.2.tar.gz
+    ```
+
+4. Install:
+
+    ```bash
+    cd ~/R/src/R-3.2.2
+    ./configure --prefix=/usr/local/lib/R-3.2.2 --enable-R-shlib --with-blas --with-lapack
+    make
+    sudo make install
+    ```
+
+5. Create symlink:
+
+    ```bash
+    sudo ln -s /usr/local/lib/R-3.2.2/bin/R /usr/local/bin/R-3.2.2
+    ```
+
+6. Run a specific R version:
+
+    From the commandline, simply do:
+    
+    ```bash
+    R-3.2.2
+    ```
+
+## R-devel
+
+1. Install prerequisites for building R from source:
+
+    ```bash
+    sudo apt-get build-dep r-base
+    sudo apt-get install subversion ccache xorg-dev
+    ```
+
+2. Create directories to keep the R-devel source code and to `make` it:
+
+    ```bash
+    mkdir ~/R/src
+    mkdir ~/R/src/R-devel-build
+    ```
+
+3. Get the latest version of R-devel from the subversion repository:
+
+    ```bash
+    cd ~/R/src
+    svn co https://svn.r-project.org/R/trunk r-devel/R 
+    ```
+
+4. Link the recommended packages for building R:
+
+    ```bash
+    cd ~/R/src/r-devel/R
+    bash ./tools/rsync-recommended
+    bash ./tools/link-recommended
+    ```
+
+5. Create the installation script in `~/R/bin/build-R-devel.sh`:
+
+    ```bash
+    ## ~/R/bin/build-R-devel.sh
+    #!/bin/sh
+    cd ~/R/src/R-devel-build
+    # R_PAPERSIZE=letter                        \
+    # R_BATCHSAVE="--no-save --no-restore"      \
+    # R_BROWSER=xdg-open                        \
+    # PAGER=/usr/bin/pager                      \
+    # PERL=/usr/bin/perl                        \
+    # R_UNZIPCMD=/usr/bin/unzip                 \
+    # R_ZIPCMD=/usr/bin/zip                     \
+    # R_PRINTCMD=/usr/bin/lpr                   \
+    # LIBnn=lib                                 \
+    # AWK=/usr/bin/awk                          \
+    # CC="ccache gcc"                           \
+    # CFLAGS="-ggdb -pipe -std=gnu99 -Wall -pedantic -DTESTING_WRITE_BARRIER" \
+    # CXX="ccache g++"                          \
+    # CXXFLAGS="-ggdb -std=c++0x -pipe -Wall -pedantic" \
+    # FC="ccache gfortran"                      \
+    # FCFLAGS="-ggdb -pipe -Wall -pedantic"     \
+    # F77="ccache gfortran"                     \
+    # FFLAGS="-ggdb -pipe -Wall -pedantic"      \
+    # MAKE="make -j4"                           \
+    # ./configure                               \
+    #     --prefix=/usr/local/lib/R-devel       \
+    #     --enable-R-shlib                      \
+    #     --enable-strict-barrier               \
+    #     --with-blas                           \
+    #     --with-lapack                         \
+    #     --with-readline                       \
+    #     --with-recommended-packages           \
+    #     --program-suffix=dev
+    
+    R_PAPERSIZE=letter                              \
+    R_BATCHSAVE="--no-save --no-restore"            \
+    R_BROWSER=xdg-open                              \
+    PAGER=/usr/bin/pager                            \
+    PERL=/usr/bin/perl                              \
+    R_UNZIPCMD=/usr/bin/unzip                       \
+    R_ZIPCMD=/usr/bin/zip                           \
+    R_PRINTCMD=/usr/bin/lpr                         \
+    LIBnn=lib                                       \
+    AWK=/usr/bin/awk                                \
+    CC="ccache gcc"                                 \
+    CFLAGS="-ggdb -pipe -std=gnu99 -Wall -pedantic" \
+    CXX="ccache g++"                                \
+    CXXFLAGS="-ggdb -pipe -Wall -pedantic"          \
+    FC="ccache gfortran"                            \
+    F77="ccache gfortran"                           \
+    MAKE="make -j4"                                 \
+    ../r-devel/R/configure                          \
+        --prefix=/usr/local/lib/R-devel             \
+        --enable-R-shlib                            \
+        --with-blas                                 \
+        --with-lapack                               \
+        --with-readline                             \
+        --with-recommended-packages                 \
+        --program-suffix=dev
+    
+    make 
+    
+    echo "*** Done -- now run 'make install'"
+    ```
+
+6. Give the script execute permissions:
+
+    ```bash
+    chmod a+x ~/R/bin/build-R-devel.sh
+    ```
+
+7. Make and install R-devel:
+
+    ```bash
+    bash ~/R/bin/build-R-devel.sh
+    
+    cd ~/R/src/R-devel-build
+    sudo make install
+    ```
+
+8. Create custom script to launch R-devel in `~/R/bin/R-devel.sh`:
+
+    ```bash
+    ## ~/R/bin/R-devel.sh
+    #!/bin/bash
+    export R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R-devel/lib/R/library:/usr/local/lib/R/site-library:/usr/lib/R/site-library'}
+    export PATH="/usr/local/lib/R-devel/bin:$PATH"
+    R "$@"
+    ```
+
+    Be sure to give the script execute permissions:
+    
+    ```bash
+    chmod a+x ~/R/bin/R-devel.sh
+    ```
+
+9. Create custom script to launch Rscript-devel in `~/R/bin/Rscript-devel.sh`:
+
+    ```bash
+    ## ~/R/bin/Rscript-devel.sh
+    #!/bin/bash
+    export R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R-devel/lib/R/library:/usr/local/lib/R/site-library:/usr/lib/R/site-library'}
+    export PATH="/usr/local/lib/R-devel/bin:$PATH"
+    Rscript "$@"
+    ```
+
+    Be sure to give the script execute permissions:
+    
+    ```bash
+    chmod a+x ~/R/bin/Rscript-devel.sh
+    ```
+
+10. Create symlinks to launch R-devel and Rscript-devel:
+
+    ```bash
+    sudo ln -s ~/R/bin/R-devel.sh /usr/local/bin/R-devel
+    sudo ln -s ~/R/bin/R-devel.sh /usr/local/bin/Rscript-devel
+    ```
+
+11. Create a script used to update R-devel in `~/R/bin/update-R-devel.sh`:
+
+    This could be turned into a `cron` job.
+    
+    ```bash
+    ## ~/R/bin/update-R-devel.sh
+    #!/bin/bash
+    
+    # update source code
+    cd ~/R/src/r-devel/R
+    svn update
+    bash ./tools/rsync-recommended
+    bash ./tools/link-recommended
+    bash build-R-devel.sh
+    
+    # make and install
+    cd ~/R/src/R-devel-build
+    sudo make install
+    
+    # update R packages
+    Rscript-devel -e 'update.packages(ask = FALSE)'
+    ```
+
+    Be sure to give the script execute permissions:
+    
+    ```bash
+    chmod a+x ~/R/bin/update-R-devel.sh
+    ```
+
+12. Run R-devel:
+
+    From the commandline, simply do:
+    
+    ```bash
+    R-devel
+    ```
+
+\newpage
+
+# References
+
+- http://stackoverflow.com/a/24019938/1380598
+- https://stat.ethz.ch/pipermail/r-sig-debian/2012-August/001937.html
+- http://singmann.org/installing-r-devel-on-linux/
+- https://hub.docker.com/r/rocker/drd/~/dockerfile/
+- https://support.rstudio.com/hc/en-us/articles/218004217-Building-R-from-source
+
diff --git a/using-multiple-R-versions-on-linux.pdf b/using-multiple-R-versions-on-linux.pdf