BergmannLab / MONET

MONET : MOdularising NEtwork Toolbox - https://doi.org/10.1093/bioinformatics/btaa236
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ERROR: docker build returned an error #44

Closed ewysocka closed 3 years ago

ewysocka commented 3 years ago

Hi,

I'm getting an error when running Monet. My docker (Server Version: 19.03.10) works fine when a different than 19.10 version of ubuntu is given (e.g. 20.04). Looks like 19.10 is not supported anymore.


$ cat /tmp/docker_build_output

Sending build context to Docker daemon  3.584kB
Step 1/10 : FROM ubuntu:19.10
 ---> 2f6c85efea61
Step 2/10 : LABEL maintainer="Mattia Tomasoni <mattia.tomasoni@unil.ch>"
 ---> Using cache
 ---> fa800fb840ee
Step 3/10 : RUN apt-get update
 ---> Running in d037f5a0a1c4
Ign:1 http://archive.ubuntu.com/ubuntu eoan InRelease
Ign:2 http://security.ubuntu.com/ubuntu eoan-security InRelease
Ign:3 http://archive.ubuntu.com/ubuntu eoan-updates InRelease
Err:4 http://security.ubuntu.com/ubuntu eoan-security Release
  404  Not Found [IP: 91.189.88.142 80]
Ign:5 http://archive.ubuntu.com/ubuntu eoan-backports InRelease
Err:6 http://archive.ubuntu.com/ubuntu eoan Release
  404  Not Found [IP: 91.189.88.152 80]
Err:7 http://archive.ubuntu.com/ubuntu eoan-updates Release
  404  Not Found [IP: 91.189.88.152 80]
Err:8 http://archive.ubuntu.com/ubuntu eoan-backports Release
  404  Not Found [IP: 91.189.88.152 80]
Reading package lists...
E: The repository 'http://security.ubuntu.com/ubuntu eoan-security Release' does not have a Release file.
E: The repository 'http://archive.ubuntu.com/ubuntu eoan Release' does not have a Release file.
E: The repository 'http://archive.ubuntu.com/ubuntu eoan-updates Release' does not have a Release file.
E: The repository 'http://archive.ubuntu.com/ubuntu eoan-backports Release' does not have a Release file.
The command '/bin/sh -c apt-get update' returned a non-zero code: 100```
mattiat commented 3 years ago

Dear Emilia, sorry for the long wait (I defended my thesis last week!). Thank you very much for your input. I now switched to ubuntu 20.04.

Cheers, Mattia

mattiat commented 3 years ago

Hello again Emilia, I was wondering whether things are working out for you? I received positive feedback on this regard from another user.

Best, Mattia

ewysocka commented 3 years ago

Hello Mattia,

I'm sorry for not tracking the evolution of this issue! I've just pulled and reinstalled MONET. This time there is a slight problem with the pip URL when I'm running K1 method. It has changed apparently :

(base) ➜   cat /tmp/docker_build_output 

Sending build context to Docker daemon  3.584kB
Step 1/13 : FROM ubuntu:20.04
 ---> f63181f19b2f
Step 2/13 : LABEL maintainer="Mattia Tomasoni <mattia.tomasoni@unil.ch>"
 ---> Using cache
 ---> f7aa9d1ab0d3
Step 3/13 : RUN apt update
 ---> Using cache
 ---> 0dd4c7505faa
Step 4/13 : RUN apt -y install python2
 ---> Using cache
 ---> deb1de8457ae
Step 5/13 : RUN apt -y install curl
 ---> Using cache
 ---> af8ab386d594
Step 6/13 : RUN curl https://bootstrap.pypa.io/2.7/get-pip.py --output get-pip.py
 ---> Using cache
 ---> f29f3aca0dcc
Step 7/13 : RUN python2 get-pip.py
 ---> Running in 78e2fddc91ab

Hi there!

The URL you are using to fetch this script has changed, and this one will no
longer work. Please use get-pip.py from the following URL instead:

    https://bootstrap.pypa.io/pip/2.7/get-pip.py

Sorry if this change causes any inconvenience for you!

We don't have a good mechanism to make more gradual changes here, and this
renaming is a part of an effort to make it easier to us to update these
scripts, when there's a pip release. It's also essential for improving how we
handle the `get-pip.py` scripts, when pip drops support for a Python minor
version.

There are no more renames/URL changes planned, and we don't expect that a need
would arise to do this again in the near future.

Thanks for understanding!

- Pradyun, on behalf of the volunteers who maintain pip.

It's not the docker problem anymore so we can close the issue.

Congratulations on your thesis defence!

Cheers, Emilia