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
--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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