Re: [Bioc-devel] disappearing .tex file when running R CMD Sweave on a new vignette
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.
\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 wrote:
> On Mon, Nov 4, 2013 at 12:46 PM, Dan Tenenbaum wrote:
> >
> >
> > - Original Message -
> >> From: "Tim Triche, Jr."
> >> 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: -> do.call -> ->
> >> 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
>
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Re: [Bioc-devel] disappearing .tex file when running R CMD Sweave on a new vignette
On Mon, Nov 4, 2013 at 12:46 PM, Dan Tenenbaum wrote:
>
>
> - Original Message -
>> From: "Tim Triche, Jr."
>> 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: -> do.call -> ->
>> 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
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Re: [Bioc-devel] disappearing .tex file when running R CMD Sweave on a new vignette
That's got to be it. Thanks!
--t
> On Nov 4, 2013, at 12:46 PM, Dan Tenenbaum wrote:
>
>
>
> - Original Message -
>> From: "Tim Triche, Jr."
>> 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$finish(drobj) :
>> the output file 'methylumi450k.tex' has disappeared
>> Calls: -> do.call -> ->
>> Execution halted
>>
>> This is bizarre because 1) the file is still there, and 2) all the
>> heavy
>> lifting is done.
>>
>> sessionInfo(), etc. is included properly and the vignette concludes
>> with
>> \end{document}, but nothing I do seems to resolve this driver error.
>>
>> Any suggestions would be most appreciated.
>
> Probably has to do with calling setwd() in the vignette? Maybe you need an
> on.exit() that restores the original directory. My guess is that you changed
> directory and then R can't see the tex file because it's in a different
> directory. See
> http://stackoverflow.com/questions/12162092/r-sweave-output-error
>
> Dan
>
>
>> Thanks,
>>
>> --t
>>
>>
>> *He that would live in peace and at ease, *
>> *Must not speak all he knows, nor judge all he sees.*
>>
>> Benjamin Franklin, Poor Richard's
>> Almanack<http://archive.org/details/poorrichardsalma00franrich>
>>
>>[[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
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Re: [Bioc-devel] disappearing .tex file when running R CMD Sweave on a new vignette
- Original Message -
> From: "Tim Triche, Jr."
> To: bioc-devel@r-project.org
> Sent: Monday, November 4, 2013 12:25:19 PM
> Subject: [Bioc-devel] disappearing .tex file when running R CMD Sweave on a
> new vignette
>
> I get a bizarre error when compiling a newly-added Methylumi
> vignette:
>
> 10 : echo keep.source term verbatim (label = sessioninfo,
> methylumi450k.Rnw:136)
> Error in driver$finish(drobj) :
> the output file 'methylumi450k.tex' has disappeared
> Calls: -> do.call -> ->
> 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
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
>
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[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: -> do.call -> ->
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.
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
[[alternative HTML version deleted]]
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