ERROR with docker version: 20.10.1 on Ubuntu 20.04 LTS

[ewysocka]

Hi, Some time ago, I successfully installed and used MONET on Ubuntu 20.04. A couple of weeks ago, I got an error indicating that MONET cannot find docker installation. When the error appeared, I tried to reinstall MONET. Interestingly during the installation, verification if docker is installed is marked as YES but the installation testing step fails. Here are the commands and their outputs + my docker info:

$ git clone https://github.com/BergmannLab/MONET.git && cd MONET && ./install.sh

Cloning into 'MONET'...
remote: Enumerating objects: 276, done.
remote: Counting objects: 100% (276/276), done.
remote: Compressing objects: 100% (201/201), done.
remote: Total 1107 (delta 135), reused 172 (delta 71), pack-reused 831
Receiving objects: 100% (1107/1107), 70.36 MiB | 7.58 MiB/s, done.
Resolving deltas: 100% (408/408), done.

MONET: MOdularising NEtwork Toolbox
       for mining of molecular and genetic networks

MONET is already installed. Would you like to overwrite? [y|n] y
- Are docker or singularity installed?...
  ...YES
- Copying files...
  ...DONE

Would you like to test the installation? (takes a few mins) [y|n] y
- Testing, thank you for waiting... 
  ERROR: see /tmp/monet_quick_test/console_output.txt

ABORTING: monet WAS NOT INSTALLED.

$ cat /tmp/monet_quick_test/console_output.txt 

ERROR: you specified --container=docker, but docker is not installed
Please visit https://www.docker.com

Installed docker info:

$ docker info

Client:
 Context:    default
 Debug Mode: false
 Plugins:
  app: Docker App (Docker Inc., v0.9.1-beta3)
  buildx: Build with BuildKit (Docker Inc., v0.5.0-docker)

Server:
 Containers: 38
  Running: 3
  Paused: 0
  Stopped: 35
 Images: 108
 Server Version: 20.10.1
 Storage Driver: overlay2
  Backing Filesystem: extfs
  Supports d_type: true
  Native Overlay Diff: true
 Logging Driver: json-file
 Cgroup Driver: cgroupfs
 Cgroup Version: 1
 Plugins:
  Volume: local
  Network: bridge host ipvlan macvlan null overlay
  Log: awslogs fluentd gcplogs gelf journald json-file local logentries splunk syslog
 Swarm: inactive
 Runtimes: runc io.containerd.runc.v2 io.containerd.runtime.v1.linux
 Default Runtime: runc
 Init Binary: docker-init
 containerd version: 269548fa27e0089a8b8278fc4fc781d7f65a939b
 runc version: ff819c7e9184c13b7c2607fe6c30ae19403a7aff
 init version: de40ad0
 Security Options:
  apparmor
  seccomp
   Profile: default
 Kernel Version: 5.8.0-7630-generic
 Operating System: Pop!_OS 20.04 LTS
 OSType: linux
 Architecture: x86_64
 CPUs: 16
 Total Memory: 31GiB
 Name: pop-os
 ID: GUWC:45ES:IYXP:A75L:UEUQ:CTGH:GAO6:O2B2:7T6P:5DWF:43F5:4HKG
 Docker Root Dir: /var/lib/docker
 Debug Mode: false
 Registry: https://index.docker.io/v1/
 Labels:
 Experimental: false
 Insecure Registries:
  127.0.0.0/8
 Live Restore Enabled: false

WARNING: No blkio weight support
WARNING: No blkio weight_device support

[mattiat]

Dear ewysocka, thank you for the report, sorry for the slow answer (I was busy turning in my thesis).

I installed a fresh ubuntu 20.04 to reproduce your error. You are using docker 20.10.1, which is very recent (15th Dec 2020), and is not yet available in ubuntu via the standard Canonical repo (the latest supported there is docker 19.03.11, see my attached screenshot). How did you install docker? Why didn't you use sudo apt install?

Thank you! Mattia

[ewysocka]

Dear Mattia,

Sorry, I didn't noticed your response. Congratulation for submitting your thesis! Good luck for the viva.

About the docker version, I installed it from the Docker repo, as recommended on the docker website for ubuntu installation recommendations. I didn't use the version shipped with the ubuntu distro, that's right.

To fix this problem with Monet, I removed the Docker repo and manually installed the older version (Server Version: 19.03.10) using the DEB package via dpkg. It solved the problem.

I guess we can close the issue.

Thanks! emilia