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
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