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

[Leonardo Collado Torres]

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