From: "Gordon Ball" <gordon.ball at ki.se>
To: "Andrzej Ole?" <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 Ole? 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:
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]: