README.md

In traitecoevo/dockertest: Docker images from R packages for testing

dockertest

Proof of concept of generating Dockerfiles from R packages and other R projects, and using them to run tests.

Use cases:

• Packages: Build a docker container that contains all your package dependencies, and use this to test installation, tests and R CMD check within, independent of your system. This gives the isolated environment of travis with a much faster cycle time (no installation time, potentially no slower than running the tests in the package directory).
• Projects:
• start: Build images that contain all the dependencies of a project to run in a container-supporting cloud environment
• end: Build images that contain a project in its completely run state.

Below documentation is listed for packages, then for projects. Below that is the general configuration options that apply across all types.

Installing docker

To run the material below you need to have docker installed and running.

Installing dockertest

Dockertest depends on our package callr, which is also not on CRAN, so install that first with devtools

devtools::install_github("traitecoevo/callr")

Now install dockertest

devtools::install_github("traitecoevo/dockertest")

Packages

The package you are supporting must be at the root of a git repository, but you'll want to run dockertest from within a subdirectory (e.g., docker/) because we copy files and clone some repos around. So your directory structure should look like

repo
 +- R/
 +- man/
 +- docker/
 +- DESCRIPTION

Create a file call .Rbuildignore and add a line that says

^docker$

This will keep R CMD check happy. Then from within the docker directory open R and run:

dockertest::build()

to build an image that contains all the package dependencies. By default this image will be called dockertest/<package_name>-test with <package_name> being your package name, converted to lower case. The dockerfile to create the image will be in <package_name>-test/Dockerfile and a script <package_name>-test/launch.sh is created.

In order to aid rapid testing, your sources are not included in this container: instead, the container will clone them when you start it - that way you don't need to rebuild the container every time you update your project, and only when the dependencies are updated.

Running the launch script with no arguments will clone your project from your local disk (so you get the most recent checked in sources -- not your working directory). You can also pass it the names of a program to run, so

<package_name>-test/launch.sh R

will launch R, after cloning the sources.

There are also some convenience scripts that are installed in the docker image so can be used as additional arguments to the launch script:

• <package_name>-test/launch.sh check: Runs R CMD check on the fresh clone
• <package_name>-test/launch.sh devtools_test: Runs devtools::test() on the fresh clone
• <package_name>-test/launch.sh devtools_check: Runs devtools::check() on the fresh clone
• <package_name>-test/launch.sh R_test: clone your repo and launch R in the tests/testthat directory, load the package (with devtools::load_all()) and read all helper files. This means you can start interactively evaluating tests in approximately the way that devtools would work.

Running

dockertest::build("production")

will build a dockerfile that includes the package installed (basically, builds the test image then installs the package into that).

Projects

Non-package projects can be accessed in the same way. As before, you'll want to run dockertest from within a subdirectory (e.g., docker/) because we copy files and clone some repos around. So your directory structure should look like

project
 +- ...
 +- docker/
 +- README

Next you need to specify any depenencies you want included in the image -- see the Configuration section.

Then from within the docker directory, run

dockertest::build()

to build an image that contains project dependencies, and clones your project into /root/<project_name> (which will be the working directory when the container starts).

If you are running docker via docker-machine and want to use something other than the default machine, you can specify the machine name in an argument

dockertest::build(machine = "mymachine")

If machine is missing (or NULL) the first running machine listed by docker-machine ls, or a machine set up with docker-machine env is used.

The dockerfile to create the image will be in <package_name>-test/Dockerfile and a script <package_name>-test/launch.sh is created.

To aid development, project sources are not included in this container: instead, the container will clone them when you start it - that way you don't need to rebuild the container every time you update your project, and only when the dependencies are updated.

Running the launch script with no arguments will clone your project from your local disk (so you get the most recent checked in sources -- not your working directory). You can also pass it the names of a program to run, so

<package_name>-test/launch.sh R

Remake

Remake-based projects can be handled in a more automated way, though this is not selected automatically at present. Running

dockertest::build_remake()

will build a container that has all of the dependencies and the sources unpacked in /root/<project_name> as for "Projects" above. (This is called the "clean" continer and will be called dockertest/<project_name>-clean by default.

In addition, you can pass build_remake an target name as an argument and it will build that as part of the build:

dockertest::build_remake("all")

will build a container based on the clean container by making the "all" target. The resulting container will be called dockertest/<project_name>-<target_name>.

Configuration

Dependencies are added via a yaml file saved at `root/docker/dockertest.yml. See here for a worked example. These must be specified before you build your container.

Base image

Dockerfiles use FROM r-base by default - this is the official R docker image. You can change the base image with the image: key (no effect on remake images, which are always built FROM richfitz/remake)

image: rocker/ropensci

Image names

For packages and projects:

names:
  test: dockerhubname/imagename
  run: dockerhubname/anotherimagename

For remake files:

names:
  clean: dockerhubname/imagename
  all: dockerhubname/imagename_all
  anothertarget: dockerhubname/imagename_anothertarget

Dependency identification

For packages, most dependency information can be gathered from DESCRIPTION and for remake projects most can be gathered from package lists in remake.yml. However some may still be required, and can be specified in yaml format in the file dockertest.yml within the working directory (the keys here follow the format of the new r travis support:

r_packages:
  - an.r.package
r_github_packages:
  - richfitz/RcppR6
r_local_packages:
  - ../path/to/local/package

The r_packages section should generally be required only for non-remake projects, as both packages and remake projects should identify all packages. However, sometimes a package that is listed in Suggests of a package that you depend on is really needed.

The r_github_packages section is useful for non-CRAN packages or where a more recent version is required.

The r_local_packages section lists local packages relative to the project root (not the working directory). They must also be git repositories as we'll clone them. The package name need not match the repository or directory name (the true package name will be gathered from the DESCRIPTION) but the package must not be in a subdirectory. The path here will usually start with ../.

System depenendencies are also automatically detected for some packages. We attempt to work out what system dependencies might be required for your package, and its dependencies, by scanning through all the packages that your package depends on (and their dependencies and so on), then looking at the SystemDependencies field and translating that into a set of Debian packages. This process is unsurprisingly pretty flakey, but if it's useful it will be fairly easy to extend (just edit this file to turn unparseable SystemDependencies fields into something that looks like Depends and this file to turn that into a set of Debian packages. Eventually we can use metacran/sysreqs but that's a way off so far.

dockertest will also scan for system dependencies in a .travis.yml file if that exists, by looking for calls to apt-get install.

R packages for which system dependencies could not be resolved will result in a message. You can manually specify system package requirements for these packages by listing them in the apt_packages field (list Debian package name)

apt_packages:
  - libgsl0-dev

You may also want to list the R packages to ignore as

system_ignore_packages:
  - package1
  - package2

which will suppress the message.

Other options

• deps_only: (true / false) -- Don't arrange to put a copy of the sources into the docker container. A copy is still available in the self directory though, which might get mounted into the container.
• keep_git: (true / false) -- Keep the .git directory in the container
• inplace: (true / false) -- By default, docker will clone your project into the directory self, so that it avoids any uncommited files (which may be large and result in sending a lot of context to the build daemon). To avoid this and build in place set inplace: true

If project source is a moving target, then setting deps_only: true and keep_git: true is probably a good idea.

Modules

Modules can be loaded which include bundles of dependencies. For example

modules:
  - rrqueue

will install packages required for rrqueue. Other modules are:

• remake
• callr

Modules are just dockertest yaml files containing only the fields r_packages, r_github_packages, apt_packages and commands. If a module foo is listed, dockertest looks for foo.yml, first in the working directory and then in dockertest's files for foo.yml. Use them to keep complexity out of the main dockertest file, or to create reusable combinations of packages.

Additional commands

The commands: section can be used to add arbitrary docker commands to the Dockerfile at given points. For example, in the dockertest bootstrap, we use:

commands:
  install_dockertest_scripts:
    command: RUN r -e 'dockertest:::copy_scripts_dir("/usr/local/bin")'
    after: github

which runs a bit of R code after installing the github packages. Valid options for after are (in order if execution) apt_packages: after apt packages are installed but before any R packages are installed r_packages: after CRAN packages are installed r_github_packages: after github packages are installed r_local_packages: after local packages are installed * workdir after the WORKDIR directive, so very late in the build

Multiple entries are allowed for a given after setting; don't rely on the order though.

traitecoevo/dockertest documentation built on May 31, 2019, 7:42 p.m.