[Bioc-devel] RMarkdown for vignettes (builder issues)

[Gordon Ball]

Sorry to re-open this thread, but it appears that this configuration
works with some builders but not others. There appear to be two
different failure modes:

Works with: oaxaca, perceval (OSX 10.6, 10.9)

Fails with: moscato1 (windows 2008)

    InvalidUrlException
"D:%5Cpackagebuilder%5Cjobs%5CSTATegRa_20141007024617%5CR-libs%5CBiocStyle%5Cresources%5Chtml%5Cbioconductor.css"
"Invalid scheme"

This appears to be an error in specific pandoc versions where it
interprets a windows drive letter as a URL scheme - see
https://github.com/jgm/pandoc/issues/1558

Fails with: zin1 (linux ubuntu 12.04)

    pandoc: Error running filter pandoc-citeproc
    pandoc-citeproc not found in path

The filter for processing references doesn't seem to be available. In
14.04 this is the package `pandoc-citeproc`, but it doesn't appear to be
available for 12.04. I assume this is only an issue if the Rmd document
includes a `bibliography:` field in the header.



Are these issues likely to be addressable for this release? If not, can
we get away with shipping a static vignette to avoid these problems?

(The build log in question is
http://bioconductor.org/spb_reports/STATegRa_0.99.3_buildreport_20141007025338.html
)

Thanks

Gordon Ball


On 04/10/14 00:02, Andrzej Oleś wrote:
> Hi Gordon, James,
> 
> thank you for pointing this out! At the time BiocStyle for markdown
> documents was developed 'rmarkdown' was not yet on CRAN and couldn't
> be used as a vignette builder engine.
> As things changed in the meantime, the approach described by Gordon
> should be just fine. I will update the BiocStyle vignette accordingly.
> 
> Best,
> Andrzej
> 
> On Fri, Oct 3, 2014 at 4:51 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>>
>>
>> ----- Original Message -----
>>> From: "Henrik Bengtsson" <hb at biostat.ucsf.edu>
>>> To: jmacdon at u.washington.edu
>>> Cc: bioc-devel at r-project.org
>>> Sent: Friday, October 3, 2014 6:56:59 AM
>>> Subject: Re: [Bioc-devel] RMarkdown for vignettes
>>>
>>> I think it requires Bioc core to make a statement that pandoc will be
>>> added
>>> to the list of external software that can be assume to exist on the
>>> servers.
>>
>>
>> Pandoc is installed on the build servers. Several packages use it.
>>
>>>
>>> If it is also expected that users should be able to rebuild all
>>> vignettes/documents themselves, then that assumption has to be
>>> extended to
>>> the users as well. BTW, is there such an assumption on
>>> LaTeX-dependent
>>> packages today?
>>>
>>
>> Users only need LaTeX (or pandoc) if they are going to build package vignettes from svn. Source packages (as well as binary packages of course) already contain built vignettes.
>>
>> Dan
>>
>>
>>> Installing pandoc is not that hard and lightweight (much smaller than
>>> LaTeX), but it does add one more installation. On the other hand, it
>>> opens
>>> up for doing lots of other neat things.
>>>
>>> Henrik
>>> On Oct 3, 2014 6:40 AM, "James W. MacDonald" <jmacdon at uw.edu> wrote:
>>>
>>>> Hi Gordon,
>>>>
>>>> Sean Davis has something about this on his blog:
>>>>
>>>>
>>>> http://watson.nci.nih.gov/~sdavis/blog/convert_from_sweave_to_r_markdown_vignettes/
>>>>
>>>> Best,
>>>>
>>>> Jim
>>>>
>>>>
>>>>
>>>> On Fri, Oct 3, 2014 at 9:06 AM, Gordon Ball <gordon.ball at ki.se>
>>>> wrote:
>>>>
>>>>> Hello
>>>>>
>>>>> Is it possible to use (RStudio's) rmarkdown package as a vignette
>>>>> builder for the upcoming release?
>>>>>
>>>>> ie, with the (at least locally working) configuration
>>>>>
>>>>> DESCRIPTION
>>>>>
>>>>>     Suggests: knitr, rmarkdown, BiocStyle
>>>>>     VignetteBuilder: knitr
>>>>>
>>>>> vignette/vignette.Rmd
>>>>>
>>>>>     ---
>>>>>     title: ...
>>>>>     output: BiocStyle::html_document
>>>>>     vignette: >
>>>>>         %% \VignetteEngine{knitr::rmarkdown}
>>>>>         %% \VignetteIndexEntry{...}
>>>>>     ----
>>>>>
>>>>> I couldn't find any explicit reference to markdown vs rmarkdown
>>>>> in the
>>>>> package guidelines. The documentation for [BiocStyle] indicates
>>>>> that it
>>>>> isn't possible to build package vignettes with the newer
>>>>> rmarkdown - is
>>>>> that still correct?
>>>>>
>>>>> I note that the newer [rmarkdown] is now in CRAN, so presumably
>>>>> can be
>>>>> used by the builders - but do they have the non-R dependency
>>>>> (pandoc)
>>>>> available?
>>>>>
>>>>> The rationale for wanting rmarkdown instead markdown is support
>>>>> for a
>>>>> few extended features, particularly being able to cite from a
>>>>> bibtex
>>>>> file (which as far as I know isn't possible with the older
>>>>> markdown).
>>>>>
>>>>> Thanks
>>>>>
>>>>> Gordon Ball
>>>>> Computational Medicine Group
>>>>> Karolinska Institute
>>>>>
>>>>>
>>>>>
>>>>> [BiocStyle]:
>>>>>
>>>>>
>>>> http://www.bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/HtmlStyle.html
>>>>>
>>>>> [rmarkdown]: http://cran.r-project.org/web/packages/rmarkdown/
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> James W. MacDonald, M.S.
>>>> Biostatistician
>>>> University of Washington
>>>> Environmental and Occupational Health Sciences
>>>> 4225 Roosevelt Way NE, # 100
>>>> Seattle WA 98105-6099
>>>>
>>>>         [[alternative HTML version deleted]]
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>
>>>       [[alternative HTML version deleted]]
>>>
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>>>
>>
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