Docker 中的 R、Python、rpy2 和 drc 包

Question

I'm trying to build a docker image to execute a python proces which calls (with rpy2) the package drc from R.

I'm using a amazonlinux docker image and to use drc I have de following lines to install it via conda:

RUN conda install -c r rpy2=2.9.4 --yes
RUN conda install -c conda-forge r-drc=3.0_1 --yes

With the image build I enter into a running container with:

docker run -it --entrypoint bash mydockerName

And when I enter to R via R it throws me the next error:

Error: package or namespace load failed for 'utils':
 .onLoad failed in loadNamespace() for 'utils', details:
  call: system(paste(which, shQuote(names[i])), intern = TRUE, ignore.stderr = TRUE)
  error: error in running command
Error: package or namespace load failed for 'stats':
 .onLoad failed in loadNamespace() for 'utils', details:
  call: system(paste(which, shQuote(names[i])), intern = TRUE, ignore.stderr = TRUE)
  error: error in running command
During startup - Warning messages:
1: package 'utils' in options("defaultPackages") was not found
2: package 'stats' in options("defaultPackages") was not found

I've been googling the last days and I'm out of possible solutions...

Many thanks!

Xevi

Answer 1

The rpy2 project has images that could constitute a starting point. conda is not used though. https://github.com/rpy2/rpy2-docker

If conda is needed, look at the images managed by the jupyter project for example.

Answer 2

I fixed a similar problem in a different container type by installing 'which'. This package is often omitted from linux enviroments because there are "better" alternatives. However, R package writers often still depend on 'which'. So figure out how to install this in your container and it may fix the issue.