Repo2docker: pinning the R version to an MRAN date

[fomightez]

Could the version of R installed gets tied to the MRAN snapshot with the data specified in runtime.txt as well? Right now with the method for builds without using a Dockerfile, the version of R installed is pinned to one date, see https://github.com/jupyter/repo2docker/blob/master/repo2docker/buildpacks/r.py#L132 .

In contrast, Bioconductor releases are tied to certain versions of R. This can be seen from past and present release notes:

Note from an older release

"The current release of Bioconductor is version 3.4; it works with R version 3.3.1. Users of older R and Bioconductor users must update their installation to take advantage of new features and to access packages that have been added to Bioconductor since the last release."

(Source of similar information still accessible here)

Current release note:

"The current release of Bioconductor is version 3.6; it works with R version 3.4.3. Users of older R and Bioconductor must update their installation to take advantage of new features and to access packages that have been added to Bioconductor since the last release."

And so if somone wants to run the packages associated with a particular past Bioconductor release as they were, they'd need the specific version of R.

I don't know if it would be best to also pin the RStudio version as well or not?

[willingc]

Thanks for raising the questions here. Any other R folks that have thoughts on this?

[yuvipanda]

We should definitely do this! It's a matter of figuring out how to install
different versions of R easily without having to compile them ourselves
(for performance reasons).

On Tue, Mar 13, 2018 at 12:53 PM, Carol Willing [e-mail]
wrote:

Thanks for raising the questions here. Any other R folks that have
thoughts on this?

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[jzf2101]

I think this is already a feature- can we close? @choldgraf ?

[yuvipanda]

This isn't implemented yet, unfortunately. Setting the MRAN date only sets the version of libraries being installed, not R itself.

[jzf2101]

But what about runtime.txt? https://github.com/binder-examples/r/blob/master/runtime.txt

[betatim]

Using runtime.txt does not influence what version of R will be installed, only what version of the R packages.

[HeidiSeibold]

Maybe it helps to take a look at what the Rocker folks are doing?

https://github.com/rocker-org/rocker-versioned

As an example, this gets you R version 3.3.0:

https://github.com/rocker-org/rocker-versioned/blob/master/r-ver/3.3.0/Dockerfile
(Look for R_VERSION=${R_VERSION:-3.3.0})

[nuest]

772 should close this (going back as far as R 3.4).

Also, the rocker/binder image has older versions if a user adds a Dockerfile to the repo.

[nuest]

@betatim Just came across this.. can be closed, right?