Hi,
 
I am trying to create a Bioconductor package. Everything installs and checks
fine. Now I'm on my last step, which is to create a vignette. I'm trying to
test the Sweave process, to make sure I can build a vignette. I am stuck at
the texi2dvi stage, which fails when I try to process the example
Sweave-test-1.tex file.
 
I am using Windows binary R distributions, and have the same problem on both
the latest developer version (2.2.0 Beta) and the latest patched version
(2.1.1) . For the Tex processing, I first tried downloading and installing
fpTex, but found that it doesn't have texi2dvi. Some Googling informed me
that recent MiKTeX versions now have that function, so I just downloaded
that (the small installation). Indeed there is a texi2dvi. The first time I
ran it, it downloaded a class file it needed, so now it at least executes.
However, when I try to run it on the test Sweave tex file, I get an error.
Here's the sequence in R:
 
> library(tools)
> example(Sweave)    
[...output suppressed]
> texi2dvi("Sweave-test-1.tex", pdf=TRUE, quiet=FALSE)
Error in texi2dvi("Sweave-test-1.tex", pdf=TRUE, quiet = FALSE) : 
        running texi2dvi on 'Sweave-test-1.tex' failed

[A command window pops up, and the following is from that window: ]
 
This is pdfeTeX, Version 3.141592-1.20a-rc7.2-2.2 (MiKTeX 2.4)
output format initialized to PDF
entering extended mode
(Sweave-test-1.tex
LaTeX2e <2003/12/01>
Babel <v3.8a> and hyphenation patterns for english, french, german, ngerman,
du
mylang, nohyphenation, loaded.
(C:\MiKTex\texmf\tex\latex\base\article.cls
Document Class: article 2004/02/16 v1.4f Standard LaTeX document class
(C:\MiKTex\texmf\tex\latex\base\size10.clo))
(C:\MiKTex\texmf\tex\latex\ltxmisc\a4wide.sty
(C:\MiKTex\texmf\tex\latex\ntgclass\a4.sty))
! Missing \endcsname inserted.
<to be read again>
                   \protect
l.11 \begin
           {document}
?
 
[ Here, I hit a <CR>, and get the following:]

! LaTeX Error: Missing \begin{document}.
 
See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immedi ate help.
 ...
 
l.11 \begin
           {document}
?
 
-----------------
I have also tried running texi2dvi directly on the command line, and get the
same result. I've looked at the manual on the MiKTeX site, but find nothing
that tells me what may be wrong. The Sweave test file looks fine to me. I
have also tried running texify --pdf on the same file on the command line,
but get the same results exactly.
 
I also went to the R-tools site, and went through their page on MiKTeX
issues. Using their second suggestion (since I'm using the recent MiKTeX
version, which defaults to e-TeX mode), I tried changing the mode for
texinfo from e-TeX Extended to e-TeX Compatibility mode: no change in
results. (I'm assuming that texi2dvi is part of texinfo package - please
correct me if I'm wrong.) [I also tried changing texinfo from e-TeX to TeX
mode, and rebuilt/reloade/refreshed, but this did not seem to take: texi2dvi
still reports that it's in e-TeX mode.]
 
Finally, I did try posting this to the bioc-devel list, and got some good
suggestions (which I've tried, results above). They then suggested I move
the question over here.
 
Regards, and thanks,
- Peter Warren
 
 

 

	[[alternative HTML version deleted]]

