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

[Fan, Jean]

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
6544
6545





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.

Best,
Jean

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.


https://bioconductor.org/checkResults/3.11/bioc-LATEST/contiBAIT/malbec2-buildsrc.htmlv


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


https://travis-ci.org/github/oneillkza/ContiBAIT/builds/674999114


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?


Thanks!




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