[R] docker containers and R

Jeff Newmiller jdnewm|| @end|ng |rom dcn@d@v|@@c@@u@
Wed Oct 27 22:39:30 CEST 2021

Docker containers are built from some starting point defined using docker conventions. They have nothing to do with how you may have installed or configured R on your computer, other than perhaps what you learned but forgot about all that stuff. So the answer depends on what docker image you are starting from, and what the requirements are for your packages, but this list is about R, not docker, or docker images, or about specific contributed packages (see the Posting Guide).

Some packages have extensive dependencies, and you may need to explicitly install all of them in your build file to get it to work at all, much less in a minimal container size.

On October 27, 2021 11:52:37 AM PDT, Bogdan Tanasa <tanasa using gmail.com> wrote:
>Dear all, would you please advise :
>shall I have a container that runs R (below), and install specifically a
>package called UMI4Cats, obviously, a lot of other libraries are
>installed.How can I save the docker container that contains the additional
>libraries that I have installed and are required by UMI4Cats ?
>-> % docker run -it --entrypoint=Rscript
>bioconductor/bioconductor_docker:RELEASE_3_13 -e 'capabilities()'
>       jpeg         png        tiff       tcltk         X11        aqua
>       TRUE        TRUE        TRUE        TRUE       FALSE       FALSE
>   http/ftp     sockets      libxml        fifo      cledit       iconv
>       TRUE        TRUE        TRUE        TRUE       FALSE        TRUE
>        NLS       Rprof     profmem       cairo         ICU long.double
>      FALSE        TRUE        TRUE        TRUE        TRUE        TRUE
>    libcurl
>       TRUE
>	[[alternative HTML version deleted]]
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>and provide commented, minimal, self-contained, reproducible code.

Sent from my phone. Please excuse my brevity.

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