CODEWITHSUNDEEP
rdockerdockerfilereticulate
Alex Yahiaoui Martinez
Alex Yahiaoui Martinez

Reputation: 1004

Running the R package reticulate in Docker environment

In a previous work, I used the 'reticulate' package to run the Autogluon autoML library in R. The code works well in my current configuration (Ubuntu 20.4, R 4.10, reticulate v. 125).

However, this code doesn't work in Docker.

Dockerfile

FROM rocker/r-ver:4.1.0

## Install R packages
RUN R -q -e 'install.packages("remotes")'
RUN R -q -e 'remotes::install_github("rstudio/reticulate")'

# Install Autogluon
RUN R -q -e 'reticulate::install_miniconda()'
RUN R -q -e 'reticulate::conda_create(envname = "r-autogluon", packages = c("python=3.8.13", "numpy"))'
# RUN R -q -e 'reticulate::conda_list()'
RUN R -q -e 'reticulate::conda_install(envname = "r-autogluon", packages = "autogluon", pip = TRUE)'
RUN R -e 'reticulate::use_condaenv("r-autogluon", required = TRUE)'
# RUN -q -e 'reticulate::py_config()'

EXPOSE 3838
CMD R -e 'reticulate::import("autogluon.tabular")'

# Run in shell
# sudo docker build --no-cache -t demo .
# sudo docker run --rm -p 3838:3838 demo

I meet this error and I don't know how to solve it!

reticulate::import("autogluon.tabular") Error in py_module_import(module, convert = convert) : ModuleNotFoundError: No module named 'autogluon' Calls: -> py_module_import Execution halted

Tracks

Anybody has a solution ?

Upvotes: 13

Views: 1362

Answers (1)

Waldi
Waldi

Reputation: 41260

RUN R -e executes the command and closes the session : reticulate::import doesn't find autogluon.tabular because reticulate::use_condaenv('r-autogluon') ran in another session, so that the r-autogluon environment isn't set in the current session.

In order to run specific initialization commands at session launch, you need to modify Rprofile, see R startup, or ?Startup.

You could COPY a modified version of Rprofile, or modify directly the file:

FROM rocker/r-ver:4.1.0

## Install R packages
RUN R -q -e 'install.packages("remotes")'
RUN R -q -e 'remotes::install_github("rstudio/reticulate")'

# Install Autogluon
RUN R -q -e 'reticulate::install_miniconda()'
RUN R -q -e 'reticulate::conda_create(envname = "r-autogluon", packages = c("python=3.8.13", "numpy"))'
# RUN R -q -e 'reticulate::conda_list()'
RUN R -q -e 'reticulate::conda_install(envname = "r-autogluon", packages = "autogluon", pip = TRUE)'


## Modify Rprofile
RUN R -e 'write("reticulate::use_condaenv(\"r-autogluon\", required = TRUE)",file=file.path(R.home(),"etc","Rprofile.site"),append=TRUE)'
RUN R -e 'write("reticulate::import(\"autogluon.tabular\")",file=file.path(R.home(),"etc","Rprofile.site"),append=TRUE)'

EXPOSE 3838

Running the container in interactive mode now shows that autogluon.tabular is loaded (R is automatically launched because r-ver docker file ends with CMD ["R"]):

docker run --rm -ti demo

R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

Module(autogluon.tabular)
>

Upvotes: 9

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