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 <jean...@fas.harvard.edu>
Sent: April 24, 2020 12:51 PM
To: Kieran O'Neill
Cc: bioc-devel@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
<kone...@bcgsc.ca<mailto:kone...@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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