Failed installation of a datashield package in Opal (Docker deployment)

[Sofia Siampani]

Hello,

One of our partnering institutes have an Opal/DataSHIELD set up deployed through Docker. We want to install a datashield package (https://github.com/FlorianSchw/dsIntestinalMicrobiomics) but we get this error in the log file: 

Failed to install 'unknown package' from GitHub: Failed to connect to api.github.com port 443: Connection refused

The docker-compose file has the following format:

version: '3'
services:
  opal:
    image: obiba/opal:latest
    ports:
      - "8843:8443"
      - "8880:8080"
    links:
      - mysqldata
      - mysqlids
      - rock
    environment:
      - JAVA_OPTS=-Xms1G -Xmx8G -XX:+UseG1GC
      - OPAL_ADMINISTRATOR_PASSWORD=password
      - MYSQLDATA_HOST=mysqldata
      - MYSQLDATA_USER=opal
      - MYSQLDATA_PASSWORD=password
      - MYSQLIDS_HOST=mysqlids
      - MYSQLIDS_USER=opal
      - MYSQLIDS_PASSWORD=password
      - ROCK_HOSTS=rock:8085
      - ROCK_ADMINISTRATOR_USER=administrator
      - ROCK_ADMINISTRATOR_PASSWORD=password
    volumes:
      - ./opal:/srv
  mysqldata:
    image: mysql:5
    environment:
      - MYSQL_DATABASE=opal
      - MYSQL_ROOT_PASSWORD=password
      - MYSQL_USER=opal
      - MYSQL_PASSWORD=password
    volumes:
      - ./mysqldata:/var/lib/mysql
  mysqlids:
    image: mysql:5
    environment:
      - MYSQL_DATABASE=opal_ids
      - MYSQL_ROOT_PASSWORD=password
      - MYSQL_USER=opal
      - MYSQL_PASSWORD=password
    volumes:
      - ./mysqlids:/var/lib/mysql
  rock:
    image: datashield/rock-base:latest
    environment:
      - ROCK_ADMINISTRATOR_NAME=administrator
      - ROCK_ADMINISTRATOR_PASSWORD=password

Thank you for your suggestions!

[Yannick Marcon]

Hi,

I just installed this package on opal-demo.obiba.org server and it works with the following parameters

The error that is reported is probably due to the fact that some institutions apply network restrictions for outbound connections. They should ask to their IT department to add proxy rule to access github.com. 

An alternative solution is to download the R package, and install it using the dsadmin.install_local_package function. 

Regards

Yannick

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