Hi,
I tried to install R/dsBase package via OPAL/admin but got this error:
POST /service/r/cluster/default/packages?name=dsBase&manager=cran : Gateway Time-out (504):
504 Gateway Time-out
nginx/1.18.0
Installation via R script gives similar error:
dsadmin.install_package(o, ‘dsBase’) Error: [Server error: (504) Gateway Timeout]
How do I fix this?
Hi,
See the logs of the R server, it is the one that makes time to respond. Installing R packages is always a pain. This is why it is recommended to use a Docker image for the R server, in order to have a ready-to-use and reproducible R environment.
See documentation: How to Set up DataSHIELD Server Profiles — Opal documentation
Regards
Yannick
Thanks, is there a ready to use R server image? I used the default DataShield docker image (cf Opal doc), which does not contain the dsBase package. Kr, Shiny
Yes, use datashield/rock-base as stated here:
Hi,
I am running now the datashield/rock-base image in parallel to the obiba/rock:latest image. How do i tell OPAL to use the datashield/rock-base process. How do I discover the process in the OPAL / Application interface?
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
b9f80b2c4300 datashield/rock-base “/docker-entrypoint.…” 4 minutes ago Up 4 minutes 8085/tcp magical_kalam
f97152cfc0f0 obiba/opal:latest “/bin/bash /docker-e…” 26 hours ago Up 26 hours 0.0.0.0:8880->8080/tcp, :::8880->8080/tcp, 0.0.0.0:8843->8443/tcp, :::8843->8443/tcp docker_opal_1
8a86431ac6d8 obiba/rock:latest “/docker-entrypoint.…” 26 hours ago Up 26 hours 8085/tcp docker_rock_1
56c5b78ba0c0 mongo:4.2 “docker-entrypoint.s…” 26 hours ago Up 26 hours 27017/tcp docker_mongo_1
4ce40b730886 mysql:5 “docker-entrypoint.s…” 26 hours ago Up 26 hours 3306/tcp, 33060/tcp docker_mysqldata_1
Kr, Shiny
Hi,
It is explained here:
Regards
Yannick
Dear Yannick, thanks, seen that! However, what URL do I have to use for the new Rock server? Currently, http://rock:8085 is registered. Which new URL do I have to fill in in the OPAL/Administration/Apps/Discovery section, so the new Rock server (datashield/rock-base, see output above) is discovered?
Kr, Shiny
It depends on your docker compose settings. In the docker’s local network, the service called rock is accessed via http://rock:8085 then similarly if there is a new R server container running in the same space and you have called it datashield (for instance), then you’ll add http://datashield:8085
Also you have declared 2 different R server profiles, with one that is not for Datashield usage: there is no reason for doing that and it is a potential source of confusion. Just declare that the “rock” service is based on the “datashield/rock-base:latest” image.
Yannick