Do you have a suggestion to resolve the sanity check failures? Change version of EB? Is there a patch or issue I can work on?
thanks John Dey On 8/7/18, 9:50 AM, "[email protected] on behalf of Kenneth Hoste" <[email protected] on behalf of [email protected]> wrote: 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_easybuilders_easybuild-2Dframework_pull_2276&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=3TR-iteG1SyRqQ5yubQg-_2KIAToz9bj5dZrRdW36Hc&m=UEHxw5ZrGms97sCXOnI6jaaWSP50Z74qS6EwuXbORBI&s=fW9DFtAEYScDSdgO9Dx8QR0_6_e6GowlSlbcQ7f-kdE&e=). 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_easybuilders_easybuild-2Deasyconfigs_pull_4889&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=3TR-iteG1SyRqQ5yubQg-_2KIAToz9bj5dZrRdW36Hc&m=UEHxw5ZrGms97sCXOnI6jaaWSP50Z74qS6EwuXbORBI&s=mtyOHICI2aXZ-K90SYDX8UkgR5_Fcz645ieC258ubss&e=). regards, Kenneth
