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Update on docker Python:3 and adding R:4.x

7 messages · Dave Lange, Dirk Eddelbuettel, Johannes Ranke

Original
Dave Lange
# 
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
Dirk Eddelbuettel
#
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
Dave Lange
# 
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/"
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:

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Dirk Eddelbuettel
    

    

      
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On 24 June 2020 at 19:52, Dave Lange wrote:

        
| ## Now install R
| ## RUN apt install -t buster-cran40 r-base

It's just a guess but something I noticed working with one of my Dockerfiles
is that the above does not work too well -- I think due to the independence
of the 'layers' from each RUN command which I mentioned earlier. So when you
I run apt install, I now always update first so maybe try

   RUN apt update && apt install -y r-base

instead.  (I also removed the -t buster-cran40 as the 'highest version should
win'. That may or may not work. Adjust as needed.)

Dirk

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Johannes Ranke
    

    

      
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Am Donnerstag, 25. Juni 2020, 04:52:37 CEST schrieb Dave Lange:

            

      
      
      
    

        
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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

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Johannes Ranke
    

    

      
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Am Donnerstag, 25. Juni 2020, 05:54:03 CEST schrieb Dirk Eddelbuettel:

            

      
      
      
    

        
Removing -t buster-cran40 only installs R 4.0.x if there are no packages left 
on the system that depend on the lower r-api-35. Therefore this should be OK 
for a docker image which does not come with R.

Johannes

  
  


  


      

    

    
2 days later

    

      
      

        


  

        

      Dave Lange
    

    

      
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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 at jrwb.de>
wrote: