[Bioc-devel] Help with setting up a build environment to match

Fan, Jean je@n|@n @end|ng |rom |@@@h@rv@rd@edu
Fri Apr 24 21:51:44 CEST 2020

Hi Kieran,

It looks like your Travis build is failing because of your vignettes:

Error: processing vignette 'contiBAIT.Rnw' failed with diagnostics:
6542 chunk 13 (label = orderAllLinkageGroupsExampleb)
6543Error in if (spearmanCor < 0) { : missing value where TRUE/FALSE needed

The BioC Test servers point to the same vignette issue.

Your R CMD build runs may have --no-build-vignettes or --no-vignettes by default.


On Apr 24, 2020, at 3:11 PM, Kieran O'Neill <koneill using bcgsc.ca<mailto:koneill using bcgsc.ca>> wrote:

A package I maintain, contiBAIT, is failing to build on the BioC test servers.


It's also failing on my Travis build set up on GitHub


But I can't reproduce this in my local environment. R CMD build runs just fine against the source, with no errors. I'm even running Ubuntu 18.04.

Can anyone suggest a relatively easy way to exactly reproduce the build environment on Travis or the BioC build servers so  I can reproduce this error and debug it?


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