Thanks much to everyone for the helpful suggestions.  It was indeed a
setwd() issue as suspected.  However, I still have one curious little
niggle that remains:
when I run pdflatex on the generated .tex file, it stops with an error.

! Extra alignment tab has been changed to \cr.
<recently read> \endtemplate

l.27

?

If I hit return, compilation finishes without any obvious issues, but this
will break the build.  Any suggestions as to how this can be fixed?

Thanks again,

--t



*He that would live in peace and at ease, *
*Must not speak all he knows, nor judge all he sees.*

Benjamin Franklin, Poor Richard's
Almanack<http://archive.org/details/poorrichardsalma00franrich>


On Mon, Nov 4, 2013 at 1:17 PM, Henrik Bengtsson <hb@biostat.ucsf.edu>wrote:

> On Mon, Nov 4, 2013 at 12:46 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
> >
> >
> > ----- Original Message -----
> >> From: "Tim Triche, Jr." <tim.triche@gmail.com>
> >> To: bioc-devel@r-project.org
> >> Sent: Monday, November 4, 2013 12:25:19 PM
> >> Subject: [Bioc-devel] disappearing .tex file when running R CMD Sweave
> on a   new vignette
> >>
> >> I get a bizarre error when compiling a newly-added Methylumi
> >> vignette:
> >>
> >> 10 : echo keep.source term verbatim (label = sessioninfo,
> >> methylumi450k.Rnw:136)
> >> Error in driver$finish(drobj) :
> >>   the output file 'methylumi450k.tex' has disappeared
> >> Calls: <Anonymous> -> do.call -> <Anonymous> -> <Anonymous>
> >> Execution halted
> >>
> >> This is bizarre because 1) the file is still there, and 2) all the
> >> heavy
> >> lifting is done.
> >>
> >> sessionInfo(), etc. is included properly and the vignette concludes
> >> with
> >> \end{document}, but nothing I do seems to resolve this driver error.
> >>
> >> Any suggestions would be most appreciated.
> >>
> >
> > Probably has to do with calling setwd() in the vignette? Maybe you need
> an on.exit() that restores the original directory. My guess is that you
> changed directory and then R can't see the tex file because it's in a
> different directory. See
> > http://stackoverflow.com/questions/12162092/r-sweave-output-error
>
> tools::buildVignettes(), which is used by 'R CMD build', tries to
> protect against this by always resetting the working directory after
> weave:ing and tangle:ing a vignette, cf.
> http://svn.r-project.org/R/trunk/src/library/tools/R/Vignettes.R.
> tools::buildVignette() [no plural 's'], which is used by 'R CMD
> Sweave' (which is what Tim uses), should also do this, but looking at
> the code, this may only work properly if argument 'dir' is an absolute
> path, which it may not be the case (not sure).  I've just submitted a
> bug report PR#15530
> [https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15530] with a
> patch on this.
>
> There may also be related issues in the utils::Sweave drivers (looks
> like code running during garbage collection) - I'll let someone else
> look into that.  But, undoing setwd():s in the vignette should solve
> this, iff that's what behind this in the first place.
>
> /Henrik
>
> >
> > Dan
> >
> >
> >> Thanks,
> >>
> >> --t
> >>
> >>
> >> *He that would live in peace and at ease, *
> >> *Must not speak all he knows, nor judge all he sees.*
> >>
> >> Benjamin Franklin, Poor Richard's
> >> Almanack<http://archive.org/details/poorrichardsalma00franrich>
> >>
> >>       [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> Bioc-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >
> > _______________________________________________
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

	[[alternative HTML version deleted]]

