[Bioc-devel] Some build system news

Keith Satterley keith at wehi.EDU.AU
Fri Dec 15 05:52:14 CET 2006

Hi Herve,

I struck the problem mentioned back in August this year. It is related to Sweave.sty

A copy the email I sent on 24/8/06 follows:
I've been checking the build reports at


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:


I was having the same problem on my machine
R version 2.4.0 Under development (unstable) (2006-08-14 r38872)


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 

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,

There was further discussion of this: The subject name on the messages were:
"texmf error on 7 packages on devel winXP build nodes"
which then became:
"Sweave windows style path (was Re: texmf error on 7 packages on devel winXP 
build nodes)"

Hope that helps,


Keith Satterley
Bioinformatics Division
The Walter and Eliza Hall Institute of Medical Research

Herve Pages wrote:
> Hi all,
> As you might have already seen, we've replaced our main build machine 'gopher5'
> by 'lamb1', a brand new server:
>   http://bioconductor.org/checkResults/2.0/
> It's a 64 bit system running Linux SUSE 10.1 for x86_64.
> "Main" build machine means that a devel package is made publicly available
> (by being pushed to http://bioconductor.org/packages/2.0/bioc/) only if it
> passes the CHECK on 'lamb1' with no error (it can have warnings though).
> Also, maybe you've been wondering what's going on with some package description
> pages:
>   http://bioconductor.org/packages/2.0/bioc/
> As you can see, the individual pages for the packages listed below the GGtools
> package are missing. This problem is related to the migration of all our
> scripts from gopher5 to lamb1 and should get back to a normal state tomorrow
> around noon.
> Also the build results for our new Windows server (liverpool) are
> not looking good for an obscure pdflatex.exe error that occurs
> when building most of the vignettes. We'll investigate this and
> try to fix ASAP. In the meantime, if someone has already seen this problem
> before and can provide some usefull feedback, s/he is more than welcome.
> A typical example can be seen here:
>   http://bioconductor.org/checkResults/2.0/liverpool-ABarray-buildsrc.html
> Thanks!
> Best,
> H.
> _______________________________________________
> Bioc-devel at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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