Takes a vector of package names. Returns the code to install dependencies for Docker / Ubuntu 18.04
Also can process a lock file to achieve the same effect (2 separate functions)
Last updated package lookup table on 20-01-2021 from https://packagemanager.rstudio.com/client/#/repos/1/overview
There are a variety of methods for installing packages directly from gitlab. You may want to research these and find the most appropriate for you.
You can try running the following code from within R Studio (assuming you know your gitlab username and password and your account has access to the repo):
cred <- git2r::cred_user_pass(rstudioapi::askForPassword("Username"),
rstudioapi::askForPassword("Password"))
devtools::install_git("https://gitlab.com/n-humphries-gen/dependency-generator-r-ubuntu.git",
credentials = cred,
build_opts = c("--no-resave-data"),
build_vignettes = TRUE)
Alternatively, you could clone the entire repo and build manually.
As follows
library(dockubu)
dockubu::generateDockerText(c("gert", "sf", "rkafka"))
# Get list of packages from lockfile
dockubu::packageVectorFromlockfile("G:\\Projects\\renv.lock")
There is a dependency conflict relating to libcurl4-gnutls-dev, this external repo installs a version og libgit2 that doesn't require it.
This dep must be installed from a different source, if it's required, it will add it at the TOP of the dockerfile. It will look something like
add-apt-repository 'deb [trusted=yes] http://ppa.launchpad.net/cran/libgit2/ubuntu <UBUNTU CODENAME> main'
Here you should replace with your ubuntu codename, e.g. focal. The code generated MUST go at the top. It'll look something like.. `RUN apt-get update && \ apt-get install -y software-properties-common
RUN add-apt-repository 'deb [trusted=yes] http://ppa.launchpad.net/cran/libgit2/ubuntu focal main' && \
apt-get update && \
apt-get -y install libgit2-dev`
The above code can be generated in two ways, one with the ppa and one with the hardcoded link (sometimes the ppa doesn't work on versions of rocker and vice versa..)
With ppa = TRUE
> dockubu::generateDockerText("git2r", ppa = TRUE)
RUN apt-get update && \
apt-get install -y software-properties-common
RUN add-apt-repository -y ppa:cran/libgit2 && \
apt-get update && \
apt-get -y install libgit2-dev
...
With ppa = FALSE
> dockubu::generateDockerText("git2r", ppa = FALSE)
RUN apt-get update && \
apt-get install -y software-properties-common
RUN add-apt-repository 'deb [trusted=yes] http://ppa.launchpad.net/cran/libgit2/ubuntu <UBUNTU CODENAME> main' && \
apt-get update && \
apt-get -y install libgit2-dev
...
It is recommended to not include dockubu in the renv lockfile, as it is not necessary for your docker container (more than likely).
If renv is activated, you can remove dockubu from it by using dockubu::removeFromRenv()
By using dockubu::lockFileDeps() you can generate docker text for the project you are currently working on (if renv is activated). You can pass a lockfile located anywhere on your system (if you're not in a renv project) by doing dockubu::lockFileDeps("/path/to/lockfile/").
DEVELOPMENT
- Nik Humphries ([email protected])
- R installation and R packages (dplyr, magrittr, tibble, stringr)
R
Copyright (c) 2020 Arcadis Nederland B.V.
Without prior written consent of Arcadis Nederland B.V., this code may not be published or duplicated.