[Bioc-devel] texmf error on 7 packages on devel winXP build nodes

[Martin Morgan]

Hi Keith --

Sweave is being a bit clever. When it processes an .Rnw file and sees
a line

\usepackage{Sweave}

it says, oh, this guy knows what he's doing, so tex is probably
configured to find Sweave. On the other hand, when it processes an
.Rnw file and does *not* see \usepackage{Sweave} it says, oh, this guy
must think that *I* know what I'm doing, so when I make the .tex
document I'll put in the path to Sweave.sty that came with R.

The odd consequence of this is that if you add \usepackage{Sweave} to
your vignette and do not have tex configured to find Sweave.sty, then
you end up with an error because tex can't find Sweave. On the other
hand, removing \usepackage{Sweave} fixes the problem because Sweave
knows where it can be found.

To make things work, you can remove \usepackage{Sweave} from your
vignette (but then you won't be able to build the vignette except by
building the R package). Alternatively, you can configuring tex to
find Sweave.sty. How to actually configure tex depends on your
installation. On Windows using MiKTeX there's a graphical interface to
set MiKTeX options. You can add a 'Root' path to point to the file
system location where R has a copy of Sweave.sty (R_HOME\share\texmf)
and then 'Refresh' the file name data base. On linux the strategy is
usually to define an environment variable TEXINPUTS to include the
path.

Thanks for helping to identify why these vignettes are not building on
walpole & matrix.

Hope that helps,

Martin
--
Bioconductor

Keith Satterley <keith at wehi.EDU.AU> writes:

> I've been checking the build reports at
>
> http://bioconductor.org/checkResults/1.9/
>
> and I notice that the following packages, which have exactly three
> errors, on the three Windows XP nodes (walpole,matrix1 & matrix2),
> all have a similar error message as shown below:
> =================
> * creating vignettes ... ERROR
> entering extended mode
>
> C:\texmf\tex\latex\base\article.cls:17: Emergency stoptexi2dvi: pdflatex exited 
> with bad status, quitting.
> texi2dvi: see "ABarray.log" for errors.
> buildVignettes(dir = '.')
> Error in texi2dvi(file = bft, pdf = TRUE, clean = FALSE, quiet = quiet) :
> 	running texi2dvi on 'ABarray.tex' failed
> Execution halted
> =================
> The log file refers to being unable to find Sweave.sty.
>
> The error does not occur on the Windows Server 2003 node(lemming).
>
> The packages that I noticed were:
>
> ABarray
> convert
> afflmGUI
> EBarrays
> goTools
> limma
> limmaGUI
>
> I was having the same problem on my machine
>  >sessionInfo()
> R version 2.4.0 Under development (unstable) (2006-08-14 r38872)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252
>
> attached base packages:
> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets" 
> "base"
>  >
> (Also I have the same problems with R-2.3.1)
> and found that if I placed a copy of Sweave.sty (copied from 
> C:\R\R-x.y.z\share\texmf ) into the doc subdirectory of my package (in mycase 
> affylmGUI and limmaGUI), the error was no longer generated and vignettes were 
> created.
>
> Is this the recommended solution or am I doing something wrong with some other 
> part of my packages? Or is there perhaps some configuration issue with R that 
> should be addressed.
>
> Not sure if this is an R-devel question or Bioc-devel, but since the Bioc XP 
> nodes show the problem, I thought it best to start on this list,
>
> cheers,
>
> Keith
>
> ========================
> Keith Satterley
> Bioinformatics Division
> The Walter and Eliza Hall Institute of Medical Research
>
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