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

[Patrick Aboyoun]

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.
>
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