Issue with installing DataSHIELD packages on the server-side

[Sofia Siampani]

Dear all,

I am writing on behalf of my colleague in the NFDI4Health project at the Leibniz Institute for Prevention Research and Epidemiology (BIPS) in Germany.

They have installed Opal/DataSHIELD using Docker. Everything was running smoothly for a few months. However, recently, they have been unable to connect via DataSHIELD, and they have realized that the DataSHIELD packages are no longer installed on the server-side.

We attempted to resolve this issue by installing the packages both through the Opal administrative interface and using the opalr package, but unfortunately, it was unsuccessful.

For your reference, I have attached a portion of the opal.log file.

Any insights or assistance you can provide would be greatly appreciated.

Thank you in advance for your help.

Sofia

[Yannick Marcon]

Hi,

The opal log says there are errors in the R server while installing R packages, Then have a look at the R server logs: you can download them from the Opal admin page Administration > R and download log.

Regards

Yannick

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[Sofia Siampani]

Please find attached the R log file.

If I understand correctly, they need to install Cmake, right?

[Yannick Marcon]

Yes exactly, cmake is to be installed. Be prepared for other errors of that kind... that is why we provide a docker image of the R server, to save painful efforts when R base or packages are upgraded by the system.

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[Sofia Siampani]

Ok, thank you! They are using the datashield/rock-base:latest image. Is this error expected with that image?

[Yannick Marcon]

The "latest" you have could not be the latest available, you could need to explicitly docker pull it. Looking at the Docker file history, cmake was added on May 16, 2022.

Regards

Yannick

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