[Bioc-devel] BiocStyle::doc_date() not found when testing on Travis via metacran/r-builder

[Andrzej Oleś]

Hi Leonardo,

thank you for reporting your issue with BiocStyle. I haven't experienced it
before.

The error you're getting indicates that BiocStyle might not be loaded
before processing the code from the YAML header. This is normally handled
by the BiocStyle::html_document() function which loads BiocStyle to expose
the functions. You could try using

date: "`r BiocStyle::doc_date()`"

to see whether this helps..

Cheers,
Andrzej

On Tue, Nov 3, 2015 at 5:25 AM, Leonardo Collado Torres <lcollado at jhu.edu>
wrote:

> I should add that in my local machine I have pandoc 1.13.1 installed.
> Also, I just noted that metacran/r-builder uses pandoc 1.12.4.2 at
> https://github.com/metacran/r-builder/blob/master/pkg-build.sh#L17
>
> So this could be a pandoc issue.
>
> On Mon, Nov 2, 2015 at 11:07 PM, Leonardo Collado Torres
> <lcollado at jhu.edu> wrote:
> > Hi,
> > I was going to ask this as an issue at the Bioconductor/BiocStyle
> > repo, but the issue tracker is disabled.
> > I ran into a bug which I'm not sure where it comes from. It happens
> > during R CMD build using BiocStyle to generate an html vignette.
> > For example, here is one such error:
> > Quitting from lines 2-17 (derfinderHelper.Rmd)
> > Error: processing vignette 'derfinderHelper.Rmd' failed with diagnostics:
> > could not find function "doc_date"
> > Execution halted
> > doc_date comes from the yaml for the html vignette in which I use:
> > date: "r doc_date()"
> > The full log for this error message is at:
> >
> https://travis-ci.org/leekgroup/derfinderHelper/builds/88823566#L3158-L3167
> > I used BiocStyle version 1.8.0 (see
> > https://travis-ci.org/leekgroup/derfinderHelper/builds/88823566#L3393)
> > and metacran/r-builder with the following Travis configuration file
> >
> https://github.com/leekgroup/derfinderHelper/blob/86c2f3b38425ee4b089a5aab1716b058926968f7/.travis.yml
> > I got the same error with other packages but wasn't able to reproduce
> > it locally. I tried with pandoc 1.13.1 instead of 1.12.3 and it didn't
> > work either on Travis (using metacran/r-builder). However, switching
> > to R Travis v2 (the one with docs on the Travis website) works.
> > Here is a full log of a case that works
> >
> https://travis-ci.org/leekgroup/derfinderHelper/builds/88925326#L1757-L1765
> > using the same BiocStyle version and the following Travis config file
> >
> https://github.com/leekgroup/derfinderHelper/blob/634aed4148c7bcb69438d0959bd1175ad03bce52/.travis.yml
> > It's also the same R version (3.2.2).
> > I think that something about the R version in metacran/r-builder could
> > be the problem. Before I report this to metacran/r-builder, I was
> > wondering if the BiocStyle maintainers had come up with this type of
> > error before or have any clues on how to resolve it.
> > Thanks,
> > Leo
> > PS I'd like this to work with metacran/r-builder given the R-devel
> > issue with R Travis v2. Although it seems like docker support is on
> > the way https://github.com/kasperdanielhansen/bsseq/issues/5
>
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