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

[Kieran O'Neill]

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
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!




[[alternative HTML version deleted]]

_______________________________________________
Bioc-devel using r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel


	[[alternative HTML version deleted]]