Hi,
I am trying to install several DataSHIELD packages from github e.g. dsOmics and dsML using the following command from opalr package:
o <- opal.login(user = "administrator", password = "pwd", url = "https://localhost:443", opts=list(ssl_verifyhost=0, ssl_verifypeer=0))
dsadmin.install_github_package(o, 'dsOmics', username='isglobal-brge')
However, I get the following error:
Error: [Server error: (504) Gateway Timeout]
I tried to install other packages available on CRAN and it worked. Do you have any suggestion on how to fix this error?
Thank you.
Best,
Simone
Hi,
The default opal https port on localhost is 8443.
If your system is configured for 443 (coral distribution?), then it may be because installing dsOmics and dependencies takes ~2h…
Note that it also depends on the version of opal: since opal 4.6, installing an R package is a background task, then the request should return a response almost immediately. What version are you using?
And are you a dsOmics developer? otherwise it is recommended to use a prepared docker image of the R server: that will save installation efforts, and you’ll get reproducibility.
Regards
Yannick
Thank you.
I am using Opal version 4.7.1
I was able to install the package using the following docker image: docker-rock-omics/Dockerfile at master · obiba/docker-rock-omics · GitHub
However, if I want to install new packages I would have to modify the Opal docker image and the rock image every time and launch the container again.
Is there a working way to install packages without having to modify the docker image?
Thank you.
Regards,
Simone
If it is for development purpose, you can install R packages trough opal
If it is for production, it is strongly recommended to make docker images that fits your needs (to ensure reproducibility).
Note that:
Regards
Yannick