Computation

I tried to create my first report and it takes a very long time. It uses up all my memory.

You should first install all the packages suggested by dataquieR to have its full functionality. You can use the following dataquieR function:

prep_check_for_dataquieR_updates(beta = FALSE, deps = TRUE)



Report Generation and Rendering

Report rendering is very slow or appears to hang while “Mounting indicator pages”. Can this be caused by network/proxy settings?

Yes. In some versions before the next beta release 2.8.10.9000 or the next regular release 2.8.11, report rendering may perform synchronous online checks for documentation links while composing the HTML report. On Linux servers, HPC nodes, or Docker containers without direct outbound HTTPS access, this can make the rendering step very slow or look stuck, especially around “Mounting indicator pages”.

As a workaround, make sure the R process or Docker container has working proxy environment variables, for example http_proxy, https_proxy, HTTP_PROXY, HTTPS_PROXY, and suitable no_proxy/NO_PROXY values for local/internal hosts. Alternatively, allow direct HTTPS access to dataquality.qihs.uni-greifswald.de.

This behavior is expected to be fixed in the next beta release 2.8.10.9000 or in release 2.8.11, so report rendering will no longer depend on synchronous online reference checks by default.


On my Linux system/HPC cluster, I have trouble using Cairo, because the underlying system dependencies (e.g, libharfbuzz-icu.so.0) are missing or not working. What can I do?

You can switch your bitmap type for all compute nodes during the report rendering to something supported and different from Cairo:

r <- dq_report2(...
print(r, advanced_options = list(bitmapType = "Xlib"), dir = "/tmp/report")

See: