Path of dataSHIELD packages in OS

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1

Hello,

I am using obiba/opal:4.5, which comes with dataSHIELD 6.2.0 I updated the package to 6.3.0. However, after restarting the container, the update disappear. I already have volumes for the paths opal_data:/srv and opal_bin:/opt/opal/bin/. Which volume do I need to add?

Or do I need to add a volume to the Rocker image I am using?

Thanks you

2

I solved it by myself by adding a volume volumes: - rock_libs:/var/lib/rock/R/library to the rocker container

3

Hi,

You should not do it that way, because the R package is not consistent with the R that is in the container.

You have several other options instead:

  • upgrade the rock image version, it is the recommended approach as it is reproducible
  • install the dsBase package using the opal web interface (Administration > DataSHIELD) or the opalr R package (there some dsadmin.install* functions)

Regards Yannick

4

Thanks for your response. I think we are misunderstanding each other: I used the opal web interface to install dsBase 6.3 (instead of 6.2) and a second additional dataSHIELD package. However, after restarting the container, the update and the new package disappeared. That is why I added the volume in the rocker container. What else do you suggest to make the changes persistent?

Regards

Felix