[Bioc-devel] Some build system news
keith at wehi.EDU.AU
Fri Dec 15 05:52:14 CET 2006
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
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:
 "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
Hope that helps,
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:
> 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
> 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:
> Bioc-devel at stat.math.ethz.ch mailing list
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