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N0rbert avatar Ubuntu

Is it possible to prevent R package conflicts while upgrading Ubuntu 16.04 LTS with R from CRAN to Ubuntu 18.04 LTS?

zw flag
N0rbert

I have fully updated Ubuntu 16.04.7 LTS amd64 which was configured for RMarkdown/bookdown, LaTeX publishing using the following commands:

sudo apt-get install apt-transport-https

cat <<EOF | sudo tee /etc/apt/sources.list.d/r-cran.list
deb https://cloud.r-project.org/bin/linux/ubuntu xenial/
EOF
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9

sudo apt-get update

sudo apt-get install -y r-base-dev libssl-dev libjpeg62 libgstreamer0.10-0 libgstreamer-plugins-base0.10-0 calibre
sudo apt-get install -y biber texlive-lang-cyrillic fonts-cmu texlive-xetex texlive-fonts-extra texlive-math-extra font-manager ttf-mscorefonts-installer lmodern
sudo apt-get install -y build-essential libcurl4-openssl-dev libxml2-dev libcairo2-dev git

wget https://github.com/jgm/pandoc/releases/download/2.11.4/pandoc-2.11.4-1-amd64.deb -O /tmp/pandoc.deb
sudo apt-get install -y /tmp/pandoc.deb

wget -c https://download1.rstudio.org/desktop/xenial/amd64/rstudio-1.4.1106-amd64.deb -O /tmp/rstudio.deb
sudo apt-get install -y /tmp/rstudio.deb

mkdir -p ~/R/x86_64-pc-linux-gnu-library/3.4
R -e "install.packages(c('bookdown','tikzDevice','xaringan'), repos='http://cran.rstudio.com/', lib='/home/$USER/R/x86_64-pc-linux-gnu-library/3.4')"

This means that its /etc/apt/sources.list /etc/apt/sources.list.d/*.list contains the following lines:

$ grep ^deb -r /etc/apt/ --include=*.list
/etc/apt/sources.list.d/r-cran.list:deb https://cloud.r-project.org/bin/linux/ubuntu xenial/
/etc/apt/sources.list:deb http://archive.ubuntu.com/ubuntu/ xenial main restricted
/etc/apt/sources.list:deb http://archive.ubuntu.com/ubuntu/ xenial-updates main restricted
/etc/apt/sources.list:deb http://archive.ubuntu.com/ubuntu/ xenial universe
/etc/apt/sources.list:deb http://archive.ubuntu.com/ubuntu/ xenial-updates universe
/etc/apt/sources.list:deb http://archive.ubuntu.com/ubuntu/ xenial multiverse
/etc/apt/sources.list:deb http://archive.ubuntu.com/ubuntu/ xenial-updates multiverse
/etc/apt/sources.list:deb http://archive.ubuntu.com/ubuntu/ xenial-backports main restricted universe multiverse
/etc/apt/sources.list:deb http://security.ubuntu.com/ubuntu xenial-security main restricted
/etc/apt/sources.list:deb http://security.ubuntu.com/ubuntu xenial-security universe
/etc/apt/sources.list:deb http://security.ubuntu.com/ubuntu xenial-security multiverse

and this system has the following set of R packages:

$ dpkg -l | grep "^ii  r-"
ii  r-base                                3.4.4-1xenial0                                  all          GNU R statistical computation and graphics system
ii  r-base-core                           3.4.4-1xenial0                                  amd64        GNU R core of statistical computation and graphics system
ii  r-base-dev                            3.4.4-1xenial0                                  all          GNU R installation of auxiliary GNU R packages
ii  r-base-html                           3.4.4-1xenial0                                  all          GNU R html docs for statistical computing system functions
ii  r-cran-boot                           1.3-20-1xenial0                                 all          GNU R package for bootstrapping functions from Davison and Hinkley
ii  r-cran-class                          7.3-14-2xenial0                                 amd64        GNU R package for classification
ii  r-cran-cluster                        2.0.7-1-1xenial0                                amd64        GNU R package for cluster analysis by Rousseeuw et al
ii  r-cran-codetools                      0.2-15-1cran1xenial0                            all          GNU R package "Code Analysis Tools for R"
ii  r-cran-foreign                        0.8.70-1xenial0                                 amd64        GNU R package to read/write data from other stat. systems
ii  r-cran-kernsmooth                     2.23-15-3xenial0                                amd64        GNU R package for kernel smoothing and density estimation
ii  r-cran-lattice                        0.20-38-1cran1xenial0                           amd64        GNU R package "Trellis Graphics for R"
ii  r-cran-mass                           7.3-50-1xenial0                                 amd64        GNU R package of Venables and Ripley's MASS
ii  r-cran-matrix                         1.2-14-1xenial0                                 amd64        GNU R package of classes for dense and sparse matrices
ii  r-cran-mgcv                           1.8-28-1cran1xenial0                            amd64        GNU R package "Mixed GAM Computation Vehicle with
ii  r-cran-nlme                           3.1.137-1xenial0                                amd64        GNU R package for (non-)linear mixed effects models
ii  r-cran-nnet                           7.3-12-2xenial0                                 amd64        GNU R package for feed-forward neural networks
ii  r-cran-rpart                          4.1-15-1cran1xenial0                            amd64        GNU R package "Recursive Partitioning and Regression
ii  r-cran-spatial                        7.3-11-1xenial0                                 amd64        GNU R package for spatial statistics
ii  r-cran-survival                       2.44-1.1-1cran1xenial0                          amd64        GNU R package "Survival Analysis"
ii  r-doc-html                            3.4.4-1xenial0                                  all          GNU R html manuals for statistical computing system
ii  r-recommended                         3.4.4-1xenial0                                  all          GNU R collection of recommended packages [metapackage]

From previous experience I know that some of R packages are newer than versions from Ubuntu 18.04.6 LTS official repository.

How should I upgrade this Ubuntu 16.04.7 LTS to Ubuntu 18.04.6 LTS correctly in this situation?

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N0rbert avatar Ubuntu
zw flag
N0rbert

To run upgrade process from Ubuntu 16.04.7 LTS with R 3.4 from CRAN flawlessly one should do the following:

  1. Backup a list of installed R packages

    dpkg -l | grep "^ii  r-" | awk '{print $2}' > ~/r-debs.txt

  2. Remove CRAN r-cran.list APT sources file by

    sudo rm /etc/apt/sources.list.d/r-cran.list

  3. Remove R packages

    sudo apt-get autoremove $(cat r-debs.txt) --purge

  4. Install R packages back using versions from official repositories

    sudo apt-get install $(cat r-debs.txt)

  5. Install possible updates

    sudo apt-get update
sudo apt-get dist-upgrade

    then reboot.

  6. Upgrade Ubuntu as usual using sudo do-release-upgrade or update-manager -c .

  7. Upgrade RStudio using command below:

    wget -c https://download1.rstudio.org/desktop/bionic/amd64/rstudio-1.4.1717-amd64.deb -O /tmp/rstudio.deb
sudo apt-get install -y /tmp/rstudio.deb

The resulting Ubuntu 18.04.6 LTS system will have fully-functional R 3.4 from official repository.

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