[Bioc-devel] BiocStyle for styling Sweave (and other?) vignettes

[Robert Castelo]

hi Martin,

thanks for spotting the problem, the fix works great, i've commited the 
change to the devel branch. regarding my comments, of course the R files 
are the quickest route to reproduce the vignette but i was thinking more 
about the less experienced R user who may find it difficult to 
simultaneously look to the .Rnw and .R files.

cheers,
robert.

On 07/16/2013 04:59 PM, Martin Morgan wrote:
> On 07/16/2013 06:43 AM, Robert Castelo wrote:
>> hi Martin,
>>
>> i have tried it out by simply adding the code snippet you specify
>> below to the
>> preamble of one of the vignettes of 'qpgraph', concretely the one
>> entitled
>> 'qpTxRegNet.Rnw' and once the .tex is generated, the processing with
>> LaTeX gives
>> the following error:
>
> Thanks Robert -- Bioconductor.sty is not playing well with some of your
> other packages; the changes below work, and some of them make sense
> anyway in terms of what Bioconductor.sty provides -- the times,
> mathptmx, hyperref, and fullpage packages are redundant.
>
> Also as currently written the Bioconductor.sty file needs to come before
> \title (and it assumes that there _is_ a \title)
>
> We'll work on an update to make this better.
>
> More below...
>
> Index: qpTxRegNet.Rnw
> ===================================================================
> --- qpTxRegNet.Rnw (revision 78459)
> +++ qpTxRegNet.Rnw (working copy)
> @@ -1,14 +1,13 @@
> %\VignetteIndexEntry{Reverse-engineer transcriptional regulatory
> networks using qpgraph}
> %\VignetteKeywords{qp-graph, microarray, network}
> %\VignettePackage{qpTxRegNet}
> -\documentclass[11pt]{article}
> +\documentclass{article}
>
> -\usepackage{times}
> -\usepackage{mathptmx}
> -\usepackage{graphicx}
> -\usepackage{hyperref}
> +
> +<<style, eval=TRUE, echo=FALSE, results=tex>>=
> +BiocStyle::latex()
> +@
> \usepackage{natbib}
> -\usepackage{fullpage}
>
> \title{Reverse engineering transcriptional regulatory networks \\ from
> gene expression microarray data using {\tt qpgraph}}
>
>>
>> =================
>>
>> (/opt/R/R-3.0.0/lib64/R/develLibrary/BiocStyle/sty/Bioconductor.sty
>>
>> LaTeX Warning: You have requested package
>> `/opt/R/R-3.0.0/lib64/R/develLibrary/
>> BiocStyle/sty/Bioconductor',
>> but the package provides `Bioconductor'.
>>
>> (/soft/texlive/2011/texmf-dist/tex/latex/graphics/color.sty
>> (/soft/texlive/2011/texmf-dist/tex/latex/latexconfig/color.cfg)
>> (/soft/texlive/2011/texmf-dist/tex/latex/graphics/dvipsnam.def))
>>
>> ! LaTeX Error: Missing \begin{document}.
>>
>> See the LaTeX manual or LaTeX Companion for explanation.
>> Type H <return> for immediate help.
>> ...
>>
>> l.30 \pdfpageattr
>> {/Group << /S /Transparency /I true /CS /DeviceRGB>>} %fixe...
>>
>> ? X
>> No pages of output.
>> Transcript written on qpTxRegNet.log.
>>
>> ================
>>
>> the offending line in the .tex file seems to be this one:
>>
>> \usepackage{/opt/R/R-3.0.0/lib64/R/develLibrary/BiocStyle/sty/Bioconductor}
>>
>>
>> because if i comment it then it works, but of course this is *the
>> line* that
>> would give the BioC look and feel to the vignette.
>>
>> i can reproduce this error in my linux box with R 3.0.0 and pdflatex
>> version:
>>
>> $ pdflatex --version
>> pdfTeX 3.1415926-2.3-1.40.12 (TeX Live 2011)
>> kpathsea version 6.0.1
>> Copyright 2011 Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
>> There is NO warranty. Redistribution of this software is
>> covered by the terms of both the pdfTeX copyright and
>> the Lesser GNU General Public License.
>> For more information about these matters, see the file
>> named COPYING and the pdfTeX source.
>> Primary author of pdfTeX: Peter Breitenlohner (eTeX)/Han The Thanh
>> (pdfTeX).
>> Compiled with libpng 1.5.2; using libpng 1.5.2
>> Compiled with zlib 1.2.5; using zlib 1.2.5
>> Compiled with xpdf version 3.02pl5
>>
>> and in my mac osx laptop with R 3.0.1 and pdflatex version:
>>
>> pdfTeX 3.1415926-2.4-1.40.13 (TeX Live 2012)
>> kpathsea version 6.1.0
>> Copyright 2012 Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
>> There is NO warranty. Redistribution of this software is
>> covered by the terms of both the pdfTeX copyright and
>> the Lesser GNU General Public License.
>> For more information about these matters, see the file
>> named COPYING and the pdfTeX source.
>> Primary author of pdfTeX: Peter Breitenlohner (eTeX)/Han The Thanh
>> (pdfTeX).
>> Compiled with libpng 1.5.10; using libpng 1.5.10
>> Compiled with zlib 1.2.7; using zlib 1.2.7
>> Compiled with xpdf version 3.03
>>
>>
>> one of the things i was curious about is how the style handles R code
>> and its
>> output, since i cannot see it at the moment, and neither in the BiocStyle
>> vignette, i just give my $0.02 about two aspects that i think should
>> be discussed:
>>
>> 1. should the plus signs "+" from wrapped code line be removed? they
>> make copy &
>> pasting a wrapped line of R code more difficult.
>>
>> 2. should we consider highlighting R code from output. i'm not
>> referring to
>> highlighting individual keywords, but simply putting in different
>> color or shade
>> input R code from its output. see for instance, the qpgraphSimulate.pdf
>> vignette, i think it's helpful to avoid copying & pasting output lines
>> by mistake.
>
> It seems reasonable to me to move in this direction, improving copy /
> paste and highlighting results. One thing is that the R script
> underlying the vignette is available at
>
> sub(".Rnw", ".R", vignette("qpTxRegNet")$file)
>
> which I admit is not as convenient as cut-and-paste.
>
> Thanks for the feedback.
>
> Martin
>
>>
>>
>> cheers,
>>
>> robert.
>>
>> On 07/14/2013 05:23 PM, Martin Morgan wrote:
>>> Developers --
>>>
>>> Sweave-style vignettes often include copy-pasted versions of basic LaTeX
>>> macros and other commands. We've created the BiocStyle package to make
>>> it easy to add these macros, and a consistent style, to Bioconductor
>>> vignettes -- just add Suggests: BiocStyle to your package DESCRIPTION,
>>> and the following lines inside the preamble (between
>>> \documentclass{article} and \begin{document}) of your vignette
>>>
>>> <<style, eval=TRUE, echo=FALSE, results=tex>>=
>>> BiocStyle::latex()
>>> @
>>>
>>> Details, including illustration of macros and styles, are in the package
>>> vignette
>>>
>>>
>>> http://bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/LatexStyle.pdf
>>>
>>>
>>>
>>>
>>> and on the ?latex help page. Suggestions welcome. Perhaps this can be
>>> extended for non-Sweave vignettes.
>>>
>>> Martin
>>
>
>

-- 
Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550