R SIG Debian - Jun 2020 - Update on docker Python:3 and adding R:4.x

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

My starting point is the debian buster based Python:3 image adding a couple
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.

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
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.

Thanks for the volunteer support I have received here.
Dave Lange
Kenmore, WA

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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 at debian.org

My dockerfile:

FROM python:3

WORKDIR /usr/src/app

COPY requirements.txt ./
COPY languageserver-master ./
COPY radian-master ./
RUN pip3 install --no-cache-dir -r requirements.txt

EXPOSE 8080

RUN apt-key adv --keyserver keys.gnupg.net --recv-key
'E19F5F87128899B192B1A2C2AD5F960A256A04AF'
RUN echo "deb http://cloud.r-project.org/bin/linux/debian
buster-cran40/"
>> /etc/apt/sources.list
RUN apt update \
&& apt-get install -y --no-install-recommends \
ca-certificates \
wget \
&& rm -rf /var/lib/apt/lists/*

## 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 at 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 at debian.org
>
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