Docker with R and keras
Having a stable environment is super useful for development. Creating one within a Docker container in many cases is a good idea. Here I show how to create a container for development with R (and RStudio instance), with installed keras and tensorflow packages. This can be particularly useful if you wish to build a forecasting lstm (long short-term memory neural networks) model, which I showed how to do here.
HOW TO
Let’s start with an official rocker tidyverse image. In order to install keras, we need to include tensorflow and its dependencies, like python 3. Additionally I will include R devtools package dependencies.
Next we need to set up python environment to be able to actually run tensorflow.
Then we can proceed with tensorflow and keras installations.
As this container is aimed for providing a forecasting solution, I will include some of the useful R packages in it, like:
- forecast – for creating predictions
- timetk – for time series creation
- dplyr – for data manipulations
To do so, and to be able to control package versions, I decided to use R renv package. That requires having a renv.lock file in place, containing a list of said packages and their dependencies. Check here if you do not know how to start with renv.
I created my renv.lock file by installing packages of choice in the “empty” container. Then I recreated the container. Specified packages are installed with an R script install_packages.R.
Lastly, I specify the R libpath, in order to be able to install additional packages in the container, if need be.
And this is how the Dockerfile looks like:
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FROM rocker/tidyverse:4.2.1 # install package dependencies RUN apt-get update -qq \ && apt-get install -y --no-install-recommends \ ssh \ # for devtools make \ libcurl4-openssl-dev \ libssl-dev \ git \ libicu-dev \ pandoc \ libxml2-dev \ libgit2-dev \ libssh2-1-dev \ # tensorflow libpng-dev \ python3 \ && apt-get clean \ && rm -rf /var/lib/apt/lists/ # set environment variables ENV WORKON_HOME /opt/virtualenvs ENV PYTHON_VENV_PATH $WORKON_HOME/r-tensorflow # install python3 tools RUN apt-get update && apt-get install -y --no-install-recommends \ libpython3-dev \ python3-venv && \ rm -rf /var/lib/apt/lists/* # create python virtual environment RUN python3 -m venv ${PYTHON_VENV_PATH} # setup python environment RUN chown -R rstudio:rstudio ${WORKON_HOME} ENV PATH ${PYTHON_VENV_PATH}/bin:${PATH} # install python libraries USER rstudio RUN pip3 install \ tensorflow-cpu==2.9.2 \ tensorflow-probability==0.14.1 \ keras==2.9.0 \ --no-cache-dir USER root COPY . . # install R packages RUN Rscript install_packages.R # set R lib path to be able to install packages RUN echo ".libPaths('/usr/local/lib/R/site-library')\n" >> /home/rstudio/.Rprofile RUN chown -R rstudio /usr/local/lib/R/site-library # setup config for rstudio user RUN mkdir -p $HOME/.R/ \ # compiler flags && echo "CXXFLAGS=-O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -flto -ffat-lto-objects -Wno-unused-local-typedefs -Wno-ignored-attributes -Wno-deprecated-declarations\n" >> $HOME/.R/Makevars \ && echo "options(mc.cores = parallel::detectCores())\n" >> /home/rstudio/.Rprofile |
Contents of renv.lock file:
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"Source": "Repository", "Repository": "RSPM", "Hash": "62f4b5da3e08d8e5bcba6cac15603f70", "Requirements": [] }, "vroom": { "Package": "vroom", "Version": "1.5.7", "Source": "Repository", "Repository": "RSPM", "Hash": "976507b5a105bc3bdf6a5a5f29e0684f", "Requirements": [ "bit64", "cli", "cpp11", "crayon", "glue", "hms", "lifecycle", "progress", "rlang", "tibble", "tidyselect", "tzdb", "vctrs", "withr" ] }, "waldo": { "Package": "waldo", "Version": "0.4.0", "Source": "Repository", "Repository": "RSPM", "Hash": "035fba89d0c86e2113120f93301b98ad", "Requirements": [ "cli", "diffobj", "fansi", "glue", "rematch2", "rlang", "tibble" ] }, "warp": { "Package": "warp", "Version": "0.2.0", "Source": "Repository", "Repository": "RSPM", "Hash": "2982481615756e24e79fee95bdc95daa", "Requirements": [] }, "whisker": { "Package": "whisker", "Version": "0.4", "Source": "Repository", "Repository": "RSPM", "Hash": "ca970b96d894e90397ed20637a0c1bbe", "Requirements": [] }, "withr": { "Package": "withr", "Version": "2.5.0", "Source": "Repository", "Repository": "RSPM", "Hash": "c0e49a9760983e81e55cdd9be92e7182", "Requirements": [] }, "xfun": { "Package": "xfun", "Version": "0.33", "Source": "Repository", "Repository": "RSPM", "Hash": "1a666f915cd65072f4ccf5b2888d5d39", "Requirements": [] }, "xml2": { "Package": "xml2", "Version": "1.3.3", "Source": "Repository", "Repository": "RSPM", "Hash": "40682ed6a969ea5abfd351eb67833adc", "Requirements": [] }, "xopen": { "Package": "xopen", "Version": "1.0.0", "Source": "Repository", "Repository": "RSPM", "Hash": "6c85f015dee9cc7710ddd20f86881f58", "Requirements": [ "processx" ] }, "xtable": { "Package": "xtable", "Version": "1.8-4", "Source": "Repository", "Repository": "RSPM", "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2", "Requirements": [] }, "xts": { "Package": "xts", "Version": "0.12.1", "Source": "Repository", "Repository": "RSPM", "Hash": "ca2fd4ad8ef78cca3aa2b30f992798a8", "Requirements": [ "zoo" ] }, "yaml": { "Package": "yaml", "Version": "2.3.5", "Source": "Repository", "Repository": "RSPM", "Hash": "458bb38374d73bf83b1bb85e353da200", "Requirements": [] }, "zeallot": { "Package": "zeallot", "Version": "0.1.0", "Source": "Repository", "Repository": "RSPM", "Hash": "ee9b643aa8331c45d8d82eb3a137c9bc", "Requirements": [] }, "zip": { "Package": "zip", "Version": "2.2.1", "Source": "Repository", "Repository": "RSPM", "Hash": "a7e91189fa51d9029a30eba3831ce53f", "Requirements": [] }, "zoo": { "Package": "zoo", "Version": "1.8-11", "Source": "Repository", "Repository": "RSPM", "Hash": "874a5b77fe0cfacf2a3450069ae70926", "Requirements": [ "lattice" ] } } } |
And package installation script:
|
1 2 3 4 5 6 7 8 |
library(devtools) devtools::install_version(package = "renv", version = "0.15.5", repos = "https://cloud.r-project.org", upgrade = FALSE) library(renv) renv::consent(provided = TRUE) renv::restore() |