[Rd] Windows problem related to using shortPathName for Sweave style file

[Patrick Aboyoun]

In the process of updating R to R 2.7 alpha or R 2.7 beta for the 
BioConductor 2.2 builds on Windows, I have hit a snag because the BioC 
build system has long path names (e.g. D:\biocbld\bbs-2.2-bioc\R) and 
these path names are not resolving properly by MiKTeX 2.7 during 
vignette construction. Take, for example, the attached vignette from 
Biobase, Bioconductor.Rnw. I have built R from source at

E:\paboyoun\bbs-2.2-bioc\R

and the session information for this R is

=== BEGIN R BLOCK ===
 > sessionInfo()
R version 2.7.0 beta (2008-04-09 r45179)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base
=== END R BLOCK ===

Now when I run Sweave on Bioconductor.Rnw using the command

=== BEGIN OS BLOCK ===
E:\paboyoun>bbs-2.2-bioc\R\bin\R CMD Sweave Bioconductor.Rnw
Writing to file Bioconductor.tex
Processing code chunks ...
 1 : term tex

You can now run LaTeX on 'Bioconductor.tex'
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