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

Dan Tenenbaum dtenenba at fhcrc.org
Tue Oct 7 19:03:07 CEST 2014


This is fixed now.

http://bioconductor.org/spb_reports/STATegRa_0.99.4_buildreport_20141007100210.html

Dan


----- Original Message -----
> From: "Gordon Ball" <gordon.ball at ki.se>
> To: "Andrzej Oleś" <andrzej.oles at gmail.com>, "Dan Tenenbaum" <dtenenba at fhcrc.org>
> Cc: jmacdon at u.washington.edu, bioc-devel at r-project.org, "david Gomez-Cabrero" <david.gomezcabrero at ki.se>
> Sent: Tuesday, October 7, 2014 3:53:40 AM
> Subject: Re: [Bioc-devel] RMarkdown for vignettes (builder issues)
> 
> 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]]
> >>>
> >>> _______________________________________________
> >>> Bioc-devel at r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>
> >>
> >> _______________________________________________
> >> Bioc-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > 
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > 
> 
>



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