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 <h...@biostat.ucsf.edu>wrote: > On Mon, Nov 4, 2013 at 12:46 PM, Dan Tenenbaum <dtene...@fhcrc.org> wrote: > > > > > > ----- Original Message ----- > >> From: "Tim Triche, Jr." <tim.tri...@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]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
