[R-sig-Debian] Update on docker Python:3 and adding R:4.x

[Dave Lange]

Thanks for all the feedback these comments will all go in my dockerfile for
my next attempt.

Dave

On Wed, Jun 24, 2020 at 11:46 PM Johannes Ranke <johannes.ranke using jrwb.de>
wrote:

> Am Donnerstag, 25. Juni 2020, 04:52:37 CEST schrieb Dave Lange:
> > My dockerfile:
> >
> ...
>
> > RUN apt update \
> > && apt-get install -y --no-install-recommends \
> > ca-certificates \
> > wget \
> > && rm -rf /var/lib/apt/lists/*
>
> Any reason why you remove the contents of /var/lib/apt/lists? On my
> system,
> this directory holds PGP signed information about each repository, so this
> may
> well be the reason why later buster-cran40 is said not to be available in
> the
> sources.
>
> Johannes
>
> >
> > ## Now install R
> > ## RUN apt install -t buster-cran40 r-base
> >
> > ## CMD ["R"]
> > CMD python
> >
> > On Wed, Jun 24, 2020 at 4:38 PM Dirk Eddelbuettel <edd using debian.org>
> wrote:
> > > On 24 June 2020 at 15:15, Dave Lange wrote:
> > > |  I continue to receive an error installing R via dockerfile on a
> buster
> > > |
> > > | image python:3.
> > > | E: The value 'buster-cran40' is invalid for APT::Default-Release as
> such
> > >
> > > a
> > >
> > > | release is not available in the sources
> > >
> > > Do you have the Dockerfile in public repo we can look at?
> > >
> > > | My starting point is the debian buster based Python:3 image adding a
> > >
> > > couple
> > >
> > > This is an R list so please tell us more about Python:3. What it is
> based
> > > on?
> > >
> > > Hypothetically, could you just start from debian:buster, add python3
> and
> > > then
> > > add the buster-cran40 repo by Johannes?
> > >
> > > | of python specific configurations and then using the commands in the
> R
> > > | project documentation for installing R on Buster. I got slightly
> > >
> > > different
> > >
> > > | answers when I used apt versus apt-get. There were warnings about
> > > | unverified sources solved by a reference to the certificate key.
> > >
> > > You generally must install a key to validate a repository. This could
> even
> > > be
> > > your error.
> > >
> > > In any event, this is all "academic". Maybe bring us the famous
> "MCVE": a
> > > minimally complete verifiable example. Otherwise we have simply no idea
> > > what
> > > you may be doing.
> > >
> > > | It turns out building the python container and commenting the R
> commands
> > > | out allowed me to manually step through my dockerfile lines. Its
> > >
> > > repeatable
> > >
> > > | that the R install fails with the error above when in the dockerfile.
> > > | Running the commands manually allows the installation to finish
> > > | successfully.  I sense that docker is multithreaded and hits the "use
> > > | buster-cran40" before it defines buster-cran40. Manually stepping
> > > | through
> > >
> > > I doubt that. Docker is very carefully "layered". Each RUN command
> results
> > > in
> > > one layer on filesystem. You can build them one by one. There is no
> > > concurrency as each subsequent RUN needs / depends upon previous ones.
> > >
> > > | the commands keeps the preferred order. At this point I'm happy with
> a
> > > | repeatable process.
> > > |
> > > | It sounds like I have been re-inventing the wheel, which has been
> > > | educational for me. If someone wants to change my starting point to
> > > | something that already has stable/latest production for debian,
> Python3
> > >
> > > and
> > >
> > > | R4 and will be updated for the future I would appreciate the head
> start.
> > >
> > > Should be easy. Look at the variety of Dockerfiles is maintain inside
> the
> > > Rocker Project -- while most are based on Debian's testing release you
> can
> > > still look at them (though note that some are also Ubuntu based)
> > >
> > > You could start at  https://github.com/rocker-org/rocker  but also
> look at
> > > other repositories in the same org at GH.
> > >
> > > Dirk
> > >
> > > --
> > > http://dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org
> >
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> >
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