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

Kieran O'Neill kone||| @end|ng |rom bcg@c@c@
Fri Apr 24 22:04:05 CEST 2020

Thanks for the reply.

I don't believe --no-vignettes is set anywhere, unless there's some obscure config file for builds specifically that I don't know about, and that gets set in a clean Ubuntu 18.04 install?

Build definitely produces output suggesting it was building the vignette:

==> R CMD build ContiBAIT

* checking for file 'ContiBAIT/DESCRIPTION' ... OK
* preparing 'contiBAIT':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a 'data/datalist' file should be added
* building 'contiBAIT_1.15.0.tar.gz'

Source package written to ~/Work/github?

Also, once I've built the package, it successfully runs all the examples in the vignette without error.

From: Fan, Jean <jeanfan using fas.harvard.edu>
Sent: April 24, 2020 12:51 PM
To: Kieran O'Neill
Cc: bioc-devel using r-project.org
Subject: Re: [Bioc-devel] Help with setting up a build environment to match

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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