[Bioc-devel] vignette LaTeX errors on the windows version (it builds in my laptop! 8-?)

[Robert Castelo]

dear Patrick,

I didn't know about mathptm being deprecated and succeeded by mathptmx.
I will update the latex source of my vignette to use mathptmx instead of
mathptm.


thanks for your help!!
robert.



On Fri, 2009-01-23 at 08:22 -0800, Patrick Aboyoun wrote:
> Robert,
> The issue was that mathptm TeX package was not installed on gewurz. I 
> installed this package and it builds fine now. I did some research and 
> it turns out that mathptm has been deprecated and is being succeeded by 
> mathptmx.
> 
> http://www.ctan.org/tex-archive/help/Catalogue/entries/mathptm.html
> 
> 
> Cheers,
> Patrick
> 
> 
> Robert Castelo wrote:
> > hi again,
> >
> > about my message below, just in case this rings the bell of anybody, i
> > installed windows xp in my macbook pro and all the stuff for developing
> > packages for R and bioconductor using the pre-release and development
> > versions, respectively, and i could run R CMD check without problems.
> > i'm using MiKTeX.
> >
> > since i cannot reproduce the problem i'm tempted to think that something
> > may be broken on the latex distribution at this server 'gewurz' but
> > again most packages build fine on this server, so something must be
> > going on in the latex source of the vignette from my package.
> >
> > these are the first lines of that source:
> >
> > %\VignetteIndexEntry{Reverse-engineer transcriptional regulatory
> > networks using qpgraph}
> > %\VignetteKeywords{qp-graph, microarray, network}
> > %\VignettePackage{qpTxRegNet}
> > \documentclass[11pt]{article}
> >
> > \usepackage{times}
> > \usepackage{mathptm}
> > \usepackage{graphicx}
> > \usepackage{hyperref}
> > \usepackage{natbib}
> > \usepackage{fullpage}
> >
> > \title{Reverse engineering transcriptional regulatory networks \\ from
> >        gene expression microarray data using {\tt qpgraph}}
> > \author{Robert Castelo and Alberto Roverato}
> >
> > \begin{document}
> > ....
> >
> > again, any help will be appreciated,
> >
> > robert.
> >
> > -------- Forwarded Message --------
> > From: Robert Castelo <robert.castelo at upf.edu>
> > To: bioc-devel at stat.math.ethz.ch
> > Subject: [Bioc-devel] vignette LaTeX errors on the windows version
> > Date: Tue, 20 Jan 2009 13:24:02 +0100
> >
> > dear fellow developers,
> >
> > i'm maintainer of a recently accepted package called 'qpgraph' and i've
> > encounter the following error in the BUILD report of the windows version
> > compiled at the server 'gewurz':
> >
> > Error in texi2dvi(file = bft, pdf = TRUE, clean = FALSE, quiet =
> > quiet) : 
> >   running 'texi2dvi' on 'qpTxRegNet.tex' failed
> >
> > LaTeX errors:
> > D:/biocbld/bbs-2.4-bioc/meat/qpgraph/inst/doc/qpTxRegNet.tex:78: Font \csname\e
> > ndcsname=psyr at 10.95pt not loadable: Metric (TFM) file not found
> > I wasn't able to read the size data for this font,
> > so I will ignore the font specification.
> > [Wizards can fix TFM files using TFtoPL/PLtoTF.]
> > D:/biocbld/bbs-2.4-bioc/meat/qpgraph/inst/doc/qpTxRegNet.tex:78: Font \csname\e
> > ndcsname=psyr at 10.95pt not loadable: Metric (TFM) file not found
> > I wasn't able to read the size data for this font,
> > so I will ignore the font specification.
> > [Wizards can fix TFM files using TFtoPL/PLtoTF.]
> > D:/biocbld/bbs-2.4-bioc/meat/qpgraph/inst/doc/qpTxRegNet.tex:503: Font \csname\
> > endcsname=psyr at 10.95pt not loadable: Metric (TFM) file not found
> > I wasn't able to read the size data for this font,
> > so I will ignore the font specification.
> > [Wizards can fix TFM files using TFtoPL/PLtoTF.]
> > D:/biocbld/bbs-2.4-bioc/meat/qpgraph/inst/doc/qpTxRegNet.tex:503
> > Calls: buildVignettes -> texi2dvi
> > Execution halted
> >
> > the entire BUILD report for 'gewurz' can be retrieved directly through this link:
> >
> > http://bioconductor.org/checkResults/2.4/bioc-LATEST/qpgraph/gewurz-buildsrc.html
> >
> > i develop on a linux box where this problem does not appear and therefore i'd appreciate
> > if any of you can give me some hint on how can i fix this error.
> >
> >
> > thanks!!
> > robert.
> >
> > _______________________________________________
> > Bioc-devel at stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> > _______________________________________________
> > Bioc-devel at stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >   
> 
>