[Bioc-devel] Some build system news

[Keith Satterley]

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

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,
***************

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

========================
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.
> 
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