Hi John, On 07/08/2018 03:25, John Dey wrote:
I have never seen a sanity check failure for R extensions until upgrading to EB 3.6.2. I now have 53 failures. How is EB testing sanity? Many of these packages output citation information, copyright notices, brief tutorials, etc... when loaded with library command.
It sounds like you're being bitten by a bug fix that was added in EasyBuild v3.4.0 (cfr. https://github.com/easybuilders/easybuild-framework/pull/2276).
The sanity check for R packages was supposed to check that loading the actual library worked by passing "library(foo)" as a command to R via stdin, but it was silently being skipped due to a bug in the EasyBuild framework.
Checking that way ensures that all dependencies required for that R package are also available (see for example https://github.com/easybuilders/easybuild-easyconfigs/pull/4889).
regards, Kenneth
