R help - Oct 2021 - docker containers and R

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 ?

https://www.bioconductor.org/help/docker/#running


-> % 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]]

On Wed, 27 Oct 2021 at 20:53, Bogdan Tanasa <tanasa at 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 ?
>
You use "docker commit" - see
https://docs.docker.com/engine/reference/commandline/commit/

But consider making a Dockerfile instead.

Regards
Martin

	[[alternative HTML version deleted]]

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 at 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 ?
>
>https://www.bioconductor.org/help/docker/#running
>
>
>-> % 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]]
>
>______________________________________________
>R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.
-- 
Sent from my phone. Please excuse my brevity.