Re: Usinr Sweave / noweb in BEamer presentation

[Rainer M Krug]

On Mon, Mar 2, 2009 at 10:30 PM, Paul Johnson pauljoh...@gmail.com wrote:
 Hello, I don't have any answers, but I have some questions for you.. I
 have an interest because I have been using LyX with Sweave a long
 time, but have not yet needed a beamer Sweave.

I wanted to use it for lectures, where it would be very nice to have
the code and the result.


  I've only spent 40 minutes looking at your case. I don't know what a
 fragile frame is for, but I'll go read more about it.

 The problem is obviously that you have an error in the latex macros in
 your layout file.  Trying to find where those problems might be is,
 well, difficult (since I don't see why you care about changing the
 frame, mainly).

Right - so I decided to use a different approach (see attached file
BeamerSweaveExample3.lyx) which is working.

My question is just: why is Slide 2 working, but Slide 1 or Slide
3 not, when I say echo=TRUE?

I don't have a problem usoing ERT boxes, but I know others, who would
prefer the approch used for Slide 1 or Slide 3 using the Frame
environment.


 On Mon, Mar 2, 2009 at 1:53 AM, Rainer M Krug r.m.k...@gmail.com wrote:
 Hi

 I want to use sweave in a beamer presentation. I found the following article
 http://ggorjan.blogspot.com/2008/09/using-beamer-with-lyx-sweave.html

 and I implemented the laypout file as suggested, but changed it, based
 on the BeamerUserGuide.pdf 3.13 Verbatim Text, tho include a fragile
 frame and a verbatim environment (see layout file attached).

 But there must be something wrong: when I try to compile the attached
 lyx file, it gives an error message ()\\i the LaTeX log:


 I've downloaded your test case on my Ubuntu Linux 8.1 system and I can
 confirm that your fragile frame environment causes the compile to
 fail.  Here's one way to try and figure what is going on. Instead of
 using the LyX Layout approach, just write ERT in your lyx document. If
 that DOES work, then  you have good information because it means the
 fragile frame will work.  Then concentrate on the LyX layout.

As I said, I am not using it any more.


 I suppose it would help if we had a tex file with the fragile frame in
 use, so we could compare the working tex against the tex that LyX
 creates.

 With the existing Layout file you provide, you can see a bit more
 about where this is going wrong if you export the LyX document to TeX
 format.  Then we could compare that TeX file with a working tex file.
 The file LyX creates will default to batchmode, but you can edit that
 tex file and erase line 1, the  batchmode line.  After that, you can
 run  latex or pdflatex on the tex file to see what happens.

 From looking at that tex file, it appears to me there is a mismatch in
 the frame begin and end markers.   Here's a snip


 \lyxframeend{}\lyxfragileframe{Slide 1}

 \includegraphics{beamertest-001}


 \lyxframeend{}\lyxframe{Slide 2}


 Note that your Layout causes a \lyxframeend to be inserted, then a
 \lyxfragileframe, but there is no \lyxfragileframeend, only
 \lyxframeend. Do you think that is related to the trouble?

No - I took the plain frame \lyxframeplain, and changed plain to fragile.


 Here are some latex errors I see when I run that through.  I believe
 the first one is superficial, but the second is more serious.

 (/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty)

 Package hyperref Warning: Option `pdfpagelabels' is turned off
 (hyperref)                because \thepage is undefined.

 Hyperref stopped early
 )
 *hyperref using default driver hdvips*


 (/usr/share/texmf/tex/latex/beamer/themes/color/beamercolorthemewhale.sty))
 (/usr/share/texmf-texlive/tex/generic/babel/babel.sty
 (/usr/share/texmf-texlive/tex/generic/babel/english.ldf
 (/usr/share/texmf-texlive/tex/generic/babel/babel.def)))
 (/usr/share/texmf/tex/latex/R/Sweave.sty
 (/usr/share/texmf-texlive/tex/latex/base/ifthen.sty)
 (/usr/share/texmf-texlive/tex/latex/fancyvrb/fancyvrb.sty
 Style option: `fancyvrb' v2.6, with DG/SPQR fixes 1998/07/17 (tvz)
 No file fancyvrb.cfg.
 ) (/usr/share/texmf/tex/latex/R/upquote.sty
 (/usr/share/texmf-texlive/tex/latex/base/textcomp.sty
 (/usr/share/texmf-texlive/tex/latex/base/ts1enc.def (./beamertest.aux)
 (/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd)
 (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty
 (/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) (./beamertest.out)
 (./beamertest.out)
 No file beamertest.nav.
 )
 Runaway argument?
 ! File ended while scanning use of \next.
 inserted text
                \par
 * beamertest.tex



 I hope you get this working and let us know how you did it.

I got it working, but am not entirely happy.

Thanks for your comments,

Rainer





 ###
 ...
 No file BeamerSweaveExample.nav.
 \openout3 = `BeamerSweaveExample.vrb'.

 )
 Runaway argument?
 ! File ended while scanning use of \next.
 ...
 ###

 When I change from Frame (fragile) to Frame, it compiles, but when
 setting one echo=TRUE, it does not as it is not in 

Re: Usinr Sweave / noweb in BEamer presentation

[M. Edward (Ed) Borasky]

Rainer M Krug wrote:
 On Mon, Mar 2, 2009 at 10:30 PM, Paul Johnson pauljoh...@gmail.com wrote:
 Hello, I don't have any answers, but I have some questions for you.. I
 have an interest because I have been using LyX with Sweave a long
 time, but have not yet needed a beamer Sweave.
 
 I wanted to use it for lectures, where it would be very nice to have
 the code and the result.
 
  I've only spent 40 minutes looking at your case. I don't know what a
 fragile frame is for, but I'll go read more about it.

 The problem is obviously that you have an error in the latex macros in
 your layout file.  Trying to find where those problems might be is,
 well, difficult (since I don't see why you care about changing the
 frame, mainly).
 
 Right - so I decided to use a different approach (see attached file
 BeamerSweaveExample3.lyx) which is working.
 
 My question is just: why is Slide 2 working, but Slide 1 or Slide
 3 not, when I say echo=TRUE?
 
 I don't have a problem usoing ERT boxes, but I know others, who would
 prefer the approch used for Slide 1 or Slide 3 using the Frame
 environment.
 
 On Mon, Mar 2, 2009 at 1:53 AM, Rainer M Krug r.m.k...@gmail.com wrote:
 Hi

 I want to use sweave in a beamer presentation. I found the following article
 http://ggorjan.blogspot.com/2008/09/using-beamer-with-lyx-sweave.html

 and I implemented the laypout file as suggested, but changed it, based
 on the BeamerUserGuide.pdf 3.13 Verbatim Text, tho include a fragile
 frame and a verbatim environment (see layout file attached).

 But there must be something wrong: when I try to compile the attached
 lyx file, it gives an error message ()\\i the LaTeX log:

 I've downloaded your test case on my Ubuntu Linux 8.1 system and I can
 confirm that your fragile frame environment causes the compile to
 fail.  Here's one way to try and figure what is going on. Instead of
 using the LyX Layout approach, just write ERT in your lyx document. If
 that DOES work, then  you have good information because it means the
 fragile frame will work.  Then concentrate on the LyX layout.
 
 As I said, I am not using it any more.
 
 I suppose it would help if we had a tex file with the fragile frame in
 use, so we could compare the working tex against the tex that LyX
 creates.

 With the existing Layout file you provide, you can see a bit more
 about where this is going wrong if you export the LyX document to TeX
 format.  Then we could compare that TeX file with a working tex file.
 The file LyX creates will default to batchmode, but you can edit that
 tex file and erase line 1, the  batchmode line.  After that, you can
 run  latex or pdflatex on the tex file to see what happens.

 From looking at that tex file, it appears to me there is a mismatch in
 the frame begin and end markers.   Here's a snip


 \lyxframeend{}\lyxfragileframe{Slide 1}

 \includegraphics{beamertest-001}


 \lyxframeend{}\lyxframe{Slide 2}


 Note that your Layout causes a \lyxframeend to be inserted, then a
 \lyxfragileframe, but there is no \lyxfragileframeend, only
 \lyxframeend. Do you think that is related to the trouble?
 
 No - I took the plain frame \lyxframeplain, and changed plain to fragile.
 
 Here are some latex errors I see when I run that through.  I believe
 the first one is superficial, but the second is more serious.

 (/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty)

 Package hyperref Warning: Option `pdfpagelabels' is turned off
 (hyperref)because \thepage is undefined.

 Hyperref stopped early
 )
 *hyperref using default driver hdvips*


 (/usr/share/texmf/tex/latex/beamer/themes/color/beamercolorthemewhale.sty))
 (/usr/share/texmf-texlive/tex/generic/babel/babel.sty
 (/usr/share/texmf-texlive/tex/generic/babel/english.ldf
 (/usr/share/texmf-texlive/tex/generic/babel/babel.def)))
 (/usr/share/texmf/tex/latex/R/Sweave.sty
 (/usr/share/texmf-texlive/tex/latex/base/ifthen.sty)
 (/usr/share/texmf-texlive/tex/latex/fancyvrb/fancyvrb.sty
 Style option: `fancyvrb' v2.6, with DG/SPQR fixes 1998/07/17 (tvz)
 No file fancyvrb.cfg.
 ) (/usr/share/texmf/tex/latex/R/upquote.sty
 (/usr/share/texmf-texlive/tex/latex/base/textcomp.sty
 (/usr/share/texmf-texlive/tex/latex/base/ts1enc.def (./beamertest.aux)
 (/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd)
 (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty
 (/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) 
 (./beamertest.out)
 (./beamertest.out)
 No file beamertest.nav.
 )
 Runaway argument?
 ! File ended while scanning use of \next.
 inserted text
\par
 * beamertest.tex



 I hope you get this working and let us know how you did it.
 
 I got it working, but am not entirely happy.
 
 Thanks for your comments,
 
 Rainer
 



 ###
 ...
 No file BeamerSweaveExample.nav.
 \openout3 = `BeamerSweaveExample.vrb'.

 )
 Runaway argument?
 ! File ended while scanning use of \next.
 ...
 ###

 When I change from Frame (fragile) to Frame, it compiles, but when
 setting one 

Re: Usinr Sweave / noweb in BEamer presentation

[Paul Johnson]

On Tue, Mar 3, 2009 at 3:23 AM, Rainer M Krug r.m.k...@gmail.com wrote:
 On Mon, Mar 2, 2009 at 10:30 PM, Paul Johnson pauljoh...@gmail.com wrote:
 Hello, I don't have any answers, but I have some questions for you.. I
 have an interest because I have been using LyX with Sweave a long
 time, but have not yet needed a beamer Sweave.

 I wanted to use it for lectures, where it would be very nice to have
 the code and the result.



Wow, this is frustrating.  I've hammered on this all night and I've
only succeeded in re-producing the problem as you originally stated
it.

I believe I've gotten down the base of the problem by repeatedly
exporting documents to noweb format and then running them through R.
Recall the transformation from LyX first creates a noweb file *.Rnw
and then it runs R CMD Sweave whatever.Rnw to create the tex file,
which is then processed through latex. It is possible to monitor each
step and see where it goes wrong.

Using ERT in the lyx document can generate a working document. From
the attached example beamerERTSweave.lyx, you should be able to
compile the document even if echo=T.  Processing that into Rnw and
then tex, the working LaTeX is like this:

\begin{frame}[containsverbatim]
\frametitle{Here's a title}

\begin{Schunk}
\begin{Sinput}
 plot(gl(5, 20))
\end{Sinput}
\end{Schunk}
\includegraphics{beamerERTSweave-001}

LaTeX can process that.

All we need to do is create a new Frame environment based on
beamer.layout that will add the right code.   I tried to take the
BeginPlainFrame environment and revise it to create
BeginVerbatimEnvironment.  Like you, I thought this should be a simple
change.

But it fails.  A file you can test is beamertest-1.lyx.

I'm attaching the layout files I was using.

Maybe somebody who writes lots of layout files will take mercy and
tell us how we can modify a frame environment from beamer.layout so
that it creates the proper preamble to create the tex we need.  If we
start with this, which changes are needed?



Style BeginPlainFrame
  Category  Frames
  TocLevel  4
  KeepEmpty 1
  LatexType Command
  LatexName lyxframeend{}\lyxplainframe
  MarginFirst_Dynamic
  NextNoIndent  1
  ParSkip   0
  TopSep2.5
  BottomSep 0.5
  ParSep0
  Align Center
  LabelType Static
  LabelBottomSep0
  LeftMarginM
  LabelSep  xx
  LabelString   Frame (no head/foot/sidebars)

  Font
Series  Bold
SizeLargest
Color   Blue
  EndFont

  LabelFont
Family  Roman
Color   latex
  EndFont

  Preamble
\makeatletter
\long\def\lyxplainframe#...@lyxplainframe#1\@lyxframestop}%
\d...@lyxplainframe{\@ifnextchar{\@@lyxplainframe}{\@@lyxplainframe*}}%
\long\def\@@lyxplainframe#1#...@lyxframestop#3\lyxframeend{%
  \frame#1[plain]{\frametitle{#2}#3}}
\makeatother
  EndPreamble
End


I tried to change lyxplainframe to lyxverbatimframe everywhere and
then simply replace [plain] with [containsverbatim] but it didn't get
the job done.

Oh, well.

I'm wondering if this will be useful in the end because it appears to
me that the R output does not want to fit itself very nicely onto the
tight pages of the beamer layout.  But, then again, we might find
enthusiasm to fix margins if we could make documents compile when they
have Schunk in them.

-- 
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas


beamertest-1.lyx
Description: application/lyx


beamerERTSweave.lyx
Description: application/lyx


pjbeamer.layout
Description: Binary data


literate-beamer.layout
Description: Binary data

Re: Usinr Sweave / noweb in BEamer presentation

[Rainer M Krug]

On Mon, Mar 2, 2009 at 10:30 PM, Paul Johnson pauljoh...@gmail.com wrote:
 Hello, I don't have any answers, but I have some questions for you.. I
 have an interest because I have been using LyX with Sweave a long
 time, but have not yet needed a beamer Sweave.

I wanted to use it for lectures, where it would be very nice to have
the code and the result.


  I've only spent 40 minutes looking at your case. I don't know what a
 fragile frame is for, but I'll go read more about it.

 The problem is obviously that you have an error in the latex macros in
 your layout file.  Trying to find where those problems might be is,
 well, difficult (since I don't see why you care about changing the
 frame, mainly).

Right - so I decided to use a different approach (see attached file
BeamerSweaveExample3.lyx) which is working.

My question is just: why is Slide 2 working, but Slide 1 or Slide
3 not, when I say echo=TRUE?

I don't have a problem usoing ERT boxes, but I know others, who would
prefer the approch used for Slide 1 or Slide 3 using the Frame
environment.


 On Mon, Mar 2, 2009 at 1:53 AM, Rainer M Krug r.m.k...@gmail.com wrote:
 Hi

 I want to use sweave in a beamer presentation. I found the following article
 http://ggorjan.blogspot.com/2008/09/using-beamer-with-lyx-sweave.html

 and I implemented the laypout file as suggested, but changed it, based
 on the BeamerUserGuide.pdf 3.13 Verbatim Text, tho include a fragile
 frame and a verbatim environment (see layout file attached).

 But there must be something wrong: when I try to compile the attached
 lyx file, it gives an error message ()\\i the LaTeX log:


 I've downloaded your test case on my Ubuntu Linux 8.1 system and I can
 confirm that your fragile frame environment causes the compile to
 fail.  Here's one way to try and figure what is going on. Instead of
 using the LyX Layout approach, just write ERT in your lyx document. If
 that DOES work, then  you have good information because it means the
 fragile frame will work.  Then concentrate on the LyX layout.

As I said, I am not using it any more.


 I suppose it would help if we had a tex file with the fragile frame in
 use, so we could compare the working tex against the tex that LyX
 creates.

 With the existing Layout file you provide, you can see a bit more
 about where this is going wrong if you export the LyX document to TeX
 format.  Then we could compare that TeX file with a working tex file.
 The file LyX creates will default to batchmode, but you can edit that
 tex file and erase line 1, the  batchmode line.  After that, you can
 run  latex or pdflatex on the tex file to see what happens.

 From looking at that tex file, it appears to me there is a mismatch in
 the frame begin and end markers.   Here's a snip


 \lyxframeend{}\lyxfragileframe{Slide 1}

 \includegraphics{beamertest-001}


 \lyxframeend{}\lyxframe{Slide 2}


 Note that your Layout causes a \lyxframeend to be inserted, then a
 \lyxfragileframe, but there is no \lyxfragileframeend, only
 \lyxframeend. Do you think that is related to the trouble?

No - I took the plain frame \lyxframeplain, and changed plain to fragile.


 Here are some latex errors I see when I run that through.  I believe
 the first one is superficial, but the second is more serious.

 (/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty)

 Package hyperref Warning: Option `pdfpagelabels' is turned off
 (hyperref)                because \thepage is undefined.

 Hyperref stopped early
 )
 *hyperref using default driver hdvips*


 (/usr/share/texmf/tex/latex/beamer/themes/color/beamercolorthemewhale.sty))
 (/usr/share/texmf-texlive/tex/generic/babel/babel.sty
 (/usr/share/texmf-texlive/tex/generic/babel/english.ldf
 (/usr/share/texmf-texlive/tex/generic/babel/babel.def)))
 (/usr/share/texmf/tex/latex/R/Sweave.sty
 (/usr/share/texmf-texlive/tex/latex/base/ifthen.sty)
 (/usr/share/texmf-texlive/tex/latex/fancyvrb/fancyvrb.sty
 Style option: `fancyvrb' v2.6, with DG/SPQR fixes 1998/07/17 (tvz)
 No file fancyvrb.cfg.
 ) (/usr/share/texmf/tex/latex/R/upquote.sty
 (/usr/share/texmf-texlive/tex/latex/base/textcomp.sty
 (/usr/share/texmf-texlive/tex/latex/base/ts1enc.def (./beamertest.aux)
 (/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd)
 (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty
 (/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) (./beamertest.out)
 (./beamertest.out)
 No file beamertest.nav.
 )
 Runaway argument?
 ! File ended while scanning use of \next.
 inserted text
                \par
 * beamertest.tex



 I hope you get this working and let us know how you did it.

I got it working, but am not entirely happy.

Thanks for your comments,

Rainer





 ###
 ...
 No file BeamerSweaveExample.nav.
 \openout3 = `BeamerSweaveExample.vrb'.

 )
 Runaway argument?
 ! File ended while scanning use of \next.
 ...
 ###

 When I change from Frame (fragile) to Frame, it compiles, but when
 setting one echo=TRUE, it does not as it is not in 

Re: Usinr Sweave / noweb in BEamer presentation

[M. Edward (Ed) Borasky]

Rainer M Krug wrote:
 On Mon, Mar 2, 2009 at 10:30 PM, Paul Johnson pauljoh...@gmail.com wrote:
 Hello, I don't have any answers, but I have some questions for you.. I
 have an interest because I have been using LyX with Sweave a long
 time, but have not yet needed a beamer Sweave.
 
 I wanted to use it for lectures, where it would be very nice to have
 the code and the result.
 
  I've only spent 40 minutes looking at your case. I don't know what a
 fragile frame is for, but I'll go read more about it.

 The problem is obviously that you have an error in the latex macros in
 your layout file.  Trying to find where those problems might be is,
 well, difficult (since I don't see why you care about changing the
 frame, mainly).
 
 Right - so I decided to use a different approach (see attached file
 BeamerSweaveExample3.lyx) which is working.
 
 My question is just: why is Slide 2 working, but Slide 1 or Slide
 3 not, when I say echo=TRUE?
 
 I don't have a problem usoing ERT boxes, but I know others, who would
 prefer the approch used for Slide 1 or Slide 3 using the Frame
 environment.
 
 On Mon, Mar 2, 2009 at 1:53 AM, Rainer M Krug r.m.k...@gmail.com wrote:
 Hi

 I want to use sweave in a beamer presentation. I found the following article
 http://ggorjan.blogspot.com/2008/09/using-beamer-with-lyx-sweave.html

 and I implemented the laypout file as suggested, but changed it, based
 on the BeamerUserGuide.pdf 3.13 Verbatim Text, tho include a fragile
 frame and a verbatim environment (see layout file attached).

 But there must be something wrong: when I try to compile the attached
 lyx file, it gives an error message ()\\i the LaTeX log:

 I've downloaded your test case on my Ubuntu Linux 8.1 system and I can
 confirm that your fragile frame environment causes the compile to
 fail.  Here's one way to try and figure what is going on. Instead of
 using the LyX Layout approach, just write ERT in your lyx document. If
 that DOES work, then  you have good information because it means the
 fragile frame will work.  Then concentrate on the LyX layout.
 
 As I said, I am not using it any more.
 
 I suppose it would help if we had a tex file with the fragile frame in
 use, so we could compare the working tex against the tex that LyX
 creates.

 With the existing Layout file you provide, you can see a bit more
 about where this is going wrong if you export the LyX document to TeX
 format.  Then we could compare that TeX file with a working tex file.
 The file LyX creates will default to batchmode, but you can edit that
 tex file and erase line 1, the  batchmode line.  After that, you can
 run  latex or pdflatex on the tex file to see what happens.

 From looking at that tex file, it appears to me there is a mismatch in
 the frame begin and end markers.   Here's a snip


 \lyxframeend{}\lyxfragileframe{Slide 1}

 \includegraphics{beamertest-001}


 \lyxframeend{}\lyxframe{Slide 2}


 Note that your Layout causes a \lyxframeend to be inserted, then a
 \lyxfragileframe, but there is no \lyxfragileframeend, only
 \lyxframeend. Do you think that is related to the trouble?
 
 No - I took the plain frame \lyxframeplain, and changed plain to fragile.
 
 Here are some latex errors I see when I run that through.  I believe
 the first one is superficial, but the second is more serious.

 (/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty)

 Package hyperref Warning: Option `pdfpagelabels' is turned off
 (hyperref)because \thepage is undefined.

 Hyperref stopped early
 )
 *hyperref using default driver hdvips*


 (/usr/share/texmf/tex/latex/beamer/themes/color/beamercolorthemewhale.sty))
 (/usr/share/texmf-texlive/tex/generic/babel/babel.sty
 (/usr/share/texmf-texlive/tex/generic/babel/english.ldf
 (/usr/share/texmf-texlive/tex/generic/babel/babel.def)))
 (/usr/share/texmf/tex/latex/R/Sweave.sty
 (/usr/share/texmf-texlive/tex/latex/base/ifthen.sty)
 (/usr/share/texmf-texlive/tex/latex/fancyvrb/fancyvrb.sty
 Style option: `fancyvrb' v2.6, with DG/SPQR fixes 1998/07/17 (tvz)
 No file fancyvrb.cfg.
 ) (/usr/share/texmf/tex/latex/R/upquote.sty
 (/usr/share/texmf-texlive/tex/latex/base/textcomp.sty
 (/usr/share/texmf-texlive/tex/latex/base/ts1enc.def (./beamertest.aux)
 (/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd)
 (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty
 (/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) 
 (./beamertest.out)
 (./beamertest.out)
 No file beamertest.nav.
 )
 Runaway argument?
 ! File ended while scanning use of \next.
 inserted text
\par
 * beamertest.tex



 I hope you get this working and let us know how you did it.
 
 I got it working, but am not entirely happy.
 
 Thanks for your comments,
 
 Rainer
 



 ###
 ...
 No file BeamerSweaveExample.nav.
 \openout3 = `BeamerSweaveExample.vrb'.

 )
 Runaway argument?
 ! File ended while scanning use of \next.
 ...
 ###

 When I change from Frame (fragile) to Frame, it compiles, but when
 setting one 

Re: Usinr Sweave / noweb in BEamer presentation

[Paul Johnson]

On Tue, Mar 3, 2009 at 3:23 AM, Rainer M Krug r.m.k...@gmail.com wrote:
 On Mon, Mar 2, 2009 at 10:30 PM, Paul Johnson pauljoh...@gmail.com wrote:
 Hello, I don't have any answers, but I have some questions for you.. I
 have an interest because I have been using LyX with Sweave a long
 time, but have not yet needed a beamer Sweave.

 I wanted to use it for lectures, where it would be very nice to have
 the code and the result.



Wow, this is frustrating.  I've hammered on this all night and I've
only succeeded in re-producing the problem as you originally stated
it.

I believe I've gotten down the base of the problem by repeatedly
exporting documents to noweb format and then running them through R.
Recall the transformation from LyX first creates a noweb file *.Rnw
and then it runs R CMD Sweave whatever.Rnw to create the tex file,
which is then processed through latex. It is possible to monitor each
step and see where it goes wrong.

Using ERT in the lyx document can generate a working document. From
the attached example beamerERTSweave.lyx, you should be able to
compile the document even if echo=T.  Processing that into Rnw and
then tex, the working LaTeX is like this:

\begin{frame}[containsverbatim]
\frametitle{Here's a title}

\begin{Schunk}
\begin{Sinput}
 plot(gl(5, 20))
\end{Sinput}
\end{Schunk}
\includegraphics{beamerERTSweave-001}

LaTeX can process that.

All we need to do is create a new Frame environment based on
beamer.layout that will add the right code.   I tried to take the
BeginPlainFrame environment and revise it to create
BeginVerbatimEnvironment.  Like you, I thought this should be a simple
change.

But it fails.  A file you can test is beamertest-1.lyx.

I'm attaching the layout files I was using.

Maybe somebody who writes lots of layout files will take mercy and
tell us how we can modify a frame environment from beamer.layout so
that it creates the proper preamble to create the tex we need.  If we
start with this, which changes are needed?



Style BeginPlainFrame
  Category  Frames
  TocLevel  4
  KeepEmpty 1
  LatexType Command
  LatexName lyxframeend{}\lyxplainframe
  MarginFirst_Dynamic
  NextNoIndent  1
  ParSkip   0
  TopSep2.5
  BottomSep 0.5
  ParSep0
  Align Center
  LabelType Static
  LabelBottomSep0
  LeftMarginM
  LabelSep  xx
  LabelString   Frame (no head/foot/sidebars)

  Font
Series  Bold
SizeLargest
Color   Blue
  EndFont

  LabelFont
Family  Roman
Color   latex
  EndFont

  Preamble
\makeatletter
\long\def\lyxplainframe#...@lyxplainframe#1\@lyxframestop}%
\d...@lyxplainframe{\@ifnextchar{\@@lyxplainframe}{\@@lyxplainframe*}}%
\long\def\@@lyxplainframe#1#...@lyxframestop#3\lyxframeend{%
  \frame#1[plain]{\frametitle{#2}#3}}
\makeatother
  EndPreamble
End


I tried to change lyxplainframe to lyxverbatimframe everywhere and
then simply replace [plain] with [containsverbatim] but it didn't get
the job done.

Oh, well.

I'm wondering if this will be useful in the end because it appears to
me that the R output does not want to fit itself very nicely onto the
tight pages of the beamer layout.  But, then again, we might find
enthusiasm to fix margins if we could make documents compile when they
have Schunk in them.

-- 
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas


beamertest-1.lyx
Description: application/lyx


beamerERTSweave.lyx
Description: application/lyx


pjbeamer.layout
Description: Binary data


literate-beamer.layout
Description: Binary data

Re: Usinr Sweave / noweb in BEamer presentation

[Rainer M Krug]

On Mon, Mar 2, 2009 at 10:30 PM, Paul Johnson  wrote:
> Hello, I don't have any answers, but I have some questions for you.. I
> have an interest because I have been using LyX with Sweave a long
> time, but have not yet needed a beamer Sweave.

I wanted to use it for lectures, where it would be very nice to have
the code and the result.

>
>  I've only spent 40 minutes looking at your case. I don't know what a
> fragile frame is for, but I'll go read more about it.
>
> The problem is obviously that you have an error in the latex macros in
> your layout file.  Trying to find where those problems might be is,
> well, difficult (since I don't see why you care about changing the
> frame, mainly).

Right - so I decided to use a different approach (see attached file
BeamerSweaveExample3.lyx) which is working.

My question is just: why is "Slide 2" working, but "Slide 1" or "Slide
3" not, when I say "echo=TRUE"?

I don't have a problem usoing ERT boxes, but I know others, who would
prefer the approch used for "Slide 1" or "Slide 3" using the Frame
environment.

>
> On Mon, Mar 2, 2009 at 1:53 AM, Rainer M Krug  wrote:
>> Hi
>>
>> I want to use sweave in a beamer presentation. I found the following article
>> http://ggorjan.blogspot.com/2008/09/using-beamer-with-lyx-sweave.html
>>
>> and I implemented the laypout file as suggested, but changed it, based
>> on the BeamerUserGuide.pdf 3.13 Verbatim Text, tho include a fragile
>> frame and a verbatim environment (see layout file attached).
>>
>> But there must be something wrong: when I try to compile the attached
>> lyx file, it gives an error message ()\\i the LaTeX log:
>>
>
> I've downloaded your test case on my Ubuntu Linux 8.1 system and I can
> confirm that your fragile frame environment causes the compile to
> fail.  Here's one way to try and figure what is going on. Instead of
> using the LyX Layout approach, just write ERT in your lyx document. If
> that DOES work, then  you have good information because it means the
> fragile frame will work.  Then concentrate on the LyX layout.

As I said, I am not using it any more.

>
> I suppose it would help if we had a tex file with the fragile frame in
> use, so we could compare the working tex against the tex that LyX
> creates.
>
> With the existing Layout file you provide, you can see a bit more
> about where this is going wrong if you export the LyX document to TeX
> format.  Then we could compare that TeX file with a working tex file.
> The file LyX creates will default to batchmode, but you can edit that
> tex file and erase line 1, the  batchmode line.  After that, you can
> run  latex or pdflatex on the tex file to see what happens.
>
> From looking at that tex file, it appears to me there is a mismatch in
> the frame begin and end markers.   Here's a snip
>
>
> \lyxframeend{}\lyxfragileframe{Slide 1}
>
> \includegraphics{beamertest-001}
>
>
> \lyxframeend{}\lyxframe{Slide 2}
>
>
> Note that your Layout causes a \lyxframeend to be inserted, then a
> \lyxfragileframe, but there is no \lyxfragileframeend, only
> \lyxframeend. Do you think that is related to the trouble?

No - I took the plain frame \lyxframeplain, and changed "plain" to "fragile".

>
> Here are some latex errors I see when I run that through.  I believe
> the first one is superficial, but the second is more serious.
>
> (/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty)
>
> Package hyperref Warning: Option `pdfpagelabels' is turned off
> (hyperref)                because \thepage is undefined.
>
> Hyperref stopped early
> )
> *hyperref using default driver hdvips*
>
>
> (/usr/share/texmf/tex/latex/beamer/themes/color/beamercolorthemewhale.sty))
> (/usr/share/texmf-texlive/tex/generic/babel/babel.sty
> (/usr/share/texmf-texlive/tex/generic/babel/english.ldf
> (/usr/share/texmf-texlive/tex/generic/babel/babel.def)))
> (/usr/share/texmf/tex/latex/R/Sweave.sty
> (/usr/share/texmf-texlive/tex/latex/base/ifthen.sty)
> (/usr/share/texmf-texlive/tex/latex/fancyvrb/fancyvrb.sty
> Style option: `fancyvrb' v2.6, with DG/SPQR fixes <1998/07/17> (tvz)
> No file fancyvrb.cfg.
> ) (/usr/share/texmf/tex/latex/R/upquote.sty
> (/usr/share/texmf-texlive/tex/latex/base/textcomp.sty
> (/usr/share/texmf-texlive/tex/latex/base/ts1enc.def (./beamertest.aux)
> (/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd)
> (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty
> (/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) (./beamertest.out)
> (./beamertest.out)
> No file beamertest.nav.
> )
> Runaway argument?
> ! File ended while scanning use of \next.
> 
>                \par
> <*> beamertest.tex
>
>
>
> I hope you get this working and let us know how you did it.

I got it working, but am not entirely happy.

Thanks for your comments,

Rainer

>
>
>
>
>> ###
>> ...
>> No file BeamerSweaveExample.nav.
>> \openout3 = `BeamerSweaveExample.vrb'.
>>
>> )
>> Runaway argument?
>> ! File ended while scanning use of 

Re: Usinr Sweave / noweb in BEamer presentation

[M. Edward (Ed) Borasky]

Rainer M Krug wrote:
> On Mon, Mar 2, 2009 at 10:30 PM, Paul Johnson  wrote:
>> Hello, I don't have any answers, but I have some questions for you.. I
>> have an interest because I have been using LyX with Sweave a long
>> time, but have not yet needed a beamer Sweave.
> 
> I wanted to use it for lectures, where it would be very nice to have
> the code and the result.
> 
>>  I've only spent 40 minutes looking at your case. I don't know what a
>> fragile frame is for, but I'll go read more about it.
>>
>> The problem is obviously that you have an error in the latex macros in
>> your layout file.  Trying to find where those problems might be is,
>> well, difficult (since I don't see why you care about changing the
>> frame, mainly).
> 
> Right - so I decided to use a different approach (see attached file
> BeamerSweaveExample3.lyx) which is working.
> 
> My question is just: why is "Slide 2" working, but "Slide 1" or "Slide
> 3" not, when I say "echo=TRUE"?
> 
> I don't have a problem usoing ERT boxes, but I know others, who would
> prefer the approch used for "Slide 1" or "Slide 3" using the Frame
> environment.
> 
>> On Mon, Mar 2, 2009 at 1:53 AM, Rainer M Krug  wrote:
>>> Hi
>>>
>>> I want to use sweave in a beamer presentation. I found the following article
>>> http://ggorjan.blogspot.com/2008/09/using-beamer-with-lyx-sweave.html
>>>
>>> and I implemented the laypout file as suggested, but changed it, based
>>> on the BeamerUserGuide.pdf 3.13 Verbatim Text, tho include a fragile
>>> frame and a verbatim environment (see layout file attached).
>>>
>>> But there must be something wrong: when I try to compile the attached
>>> lyx file, it gives an error message ()\\i the LaTeX log:
>>>
>> I've downloaded your test case on my Ubuntu Linux 8.1 system and I can
>> confirm that your fragile frame environment causes the compile to
>> fail.  Here's one way to try and figure what is going on. Instead of
>> using the LyX Layout approach, just write ERT in your lyx document. If
>> that DOES work, then  you have good information because it means the
>> fragile frame will work.  Then concentrate on the LyX layout.
> 
> As I said, I am not using it any more.
> 
>> I suppose it would help if we had a tex file with the fragile frame in
>> use, so we could compare the working tex against the tex that LyX
>> creates.
>>
>> With the existing Layout file you provide, you can see a bit more
>> about where this is going wrong if you export the LyX document to TeX
>> format.  Then we could compare that TeX file with a working tex file.
>> The file LyX creates will default to batchmode, but you can edit that
>> tex file and erase line 1, the  batchmode line.  After that, you can
>> run  latex or pdflatex on the tex file to see what happens.
>>
>> From looking at that tex file, it appears to me there is a mismatch in
>> the frame begin and end markers.   Here's a snip
>>
>>
>> \lyxframeend{}\lyxfragileframe{Slide 1}
>>
>> \includegraphics{beamertest-001}
>>
>>
>> \lyxframeend{}\lyxframe{Slide 2}
>>
>>
>> Note that your Layout causes a \lyxframeend to be inserted, then a
>> \lyxfragileframe, but there is no \lyxfragileframeend, only
>> \lyxframeend. Do you think that is related to the trouble?
> 
> No - I took the plain frame \lyxframeplain, and changed "plain" to "fragile".
> 
>> Here are some latex errors I see when I run that through.  I believe
>> the first one is superficial, but the second is more serious.
>>
>> (/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty)
>>
>> Package hyperref Warning: Option `pdfpagelabels' is turned off
>> (hyperref)because \thepage is undefined.
>>
>> Hyperref stopped early
>> )
>> *hyperref using default driver hdvips*
>>
>>
>> (/usr/share/texmf/tex/latex/beamer/themes/color/beamercolorthemewhale.sty))
>> (/usr/share/texmf-texlive/tex/generic/babel/babel.sty
>> (/usr/share/texmf-texlive/tex/generic/babel/english.ldf
>> (/usr/share/texmf-texlive/tex/generic/babel/babel.def)))
>> (/usr/share/texmf/tex/latex/R/Sweave.sty
>> (/usr/share/texmf-texlive/tex/latex/base/ifthen.sty)
>> (/usr/share/texmf-texlive/tex/latex/fancyvrb/fancyvrb.sty
>> Style option: `fancyvrb' v2.6, with DG/SPQR fixes <1998/07/17> (tvz)
>> No file fancyvrb.cfg.
>> ) (/usr/share/texmf/tex/latex/R/upquote.sty
>> (/usr/share/texmf-texlive/tex/latex/base/textcomp.sty
>> (/usr/share/texmf-texlive/tex/latex/base/ts1enc.def (./beamertest.aux)
>> (/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd)
>> (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty
>> (/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) 
>> (./beamertest.out)
>> (./beamertest.out)
>> No file beamertest.nav.
>> )
>> Runaway argument?
>> ! File ended while scanning use of \next.
>> 
>>\par
>> <*> beamertest.tex
>>
>>
>>
>> I hope you get this working and let us know how you did it.
> 
> I got it working, but am not entirely happy.
> 
> Thanks for your comments,
> 
> Rainer
> 

Re: Usinr Sweave / noweb in BEamer presentation

[Paul Johnson]

On Tue, Mar 3, 2009 at 3:23 AM, Rainer M Krug  wrote:
> On Mon, Mar 2, 2009 at 10:30 PM, Paul Johnson  wrote:
>> Hello, I don't have any answers, but I have some questions for you.. I
>> have an interest because I have been using LyX with Sweave a long
>> time, but have not yet needed a beamer Sweave.
>
> I wanted to use it for lectures, where it would be very nice to have
> the code and the result.
>
>

Wow, this is frustrating.  I've hammered on this all night and I've
only succeeded in re-producing the problem as you originally stated
it.

I believe I've gotten down the base of the problem by repeatedly
exporting documents to noweb format and then running them through R.
Recall the transformation from LyX first creates a noweb file *.Rnw
and then it runs "R CMD Sweave whatever.Rnw" to create the tex file,
which is then processed through latex. It is possible to monitor each
step and see where it goes wrong.

Using ERT in the lyx document can generate a working document. From
the attached example "beamerERTSweave.lyx", you should be able to
compile the document even if echo=T.  Processing that into Rnw and
then tex, the working LaTeX is like this:

\begin{frame}[containsverbatim]
\frametitle{Here's a title}

\begin{Schunk}
\begin{Sinput}
> plot(gl(5, 20))
\end{Sinput}
\end{Schunk}
\includegraphics{beamerERTSweave-001}

LaTeX can process that.

All we need to do is create a new Frame environment based on
beamer.layout that will add the right code.   I tried to take the
BeginPlainFrame environment and revise it to create
BeginVerbatimEnvironment.  Like you, I thought this should be a simple
change.

But it fails.  A file you can test is "beamertest-1.lyx".

I'm attaching the layout files I was using.

Maybe somebody who writes lots of layout files will take mercy and
tell us how we can modify a frame environment from beamer.layout so
that it creates the proper preamble to create the tex we need.  If we
start with this, which changes are needed?



Style BeginPlainFrame
  Category  Frames
  TocLevel  4
  KeepEmpty 1
  LatexType Command
  LatexName lyxframeend{}\lyxplainframe
  MarginFirst_Dynamic
  NextNoIndent  1
  ParSkip   0
  TopSep2.5
  BottomSep 0.5
  ParSep0
  Align Center
  LabelType Static
  LabelBottomSep0
  LeftMarginM
  LabelSep  xx
  LabelString   "Frame (no head/foot/sidebars)"

  Font
Series  Bold
SizeLargest
Color   Blue
  EndFont

  LabelFont
Family  Roman
Color   latex
  EndFont

  Preamble
\makeatletter
\long\def\lyxplainframe#...@lyxplainframe#1\@lyxframestop}%
\d...@lyxplainframe{\@ifnextchar<{\@@lyxplainframe}{\@@lyxplainframe<*>}}%
\long\def\@@lyxplainframe<#1>#...@lyxframestop#3\lyxframeend{%
  \frame<#1>[plain]{\frametitle{#2}#3}}
\makeatother
  EndPreamble
End


I tried to change "lyxplainframe" to "lyxverbatimframe" everywhere and
then simply replace [plain] with [containsverbatim] but it didn't get
the job done.

Oh, well.

I'm wondering if this will be useful in the end because it appears to
me that the R output does not want to fit itself very nicely onto the
tight pages of the beamer layout.  But, then again, we might find
enthusiasm to fix margins if we could make documents compile when they
have Schunk in them.

-- 
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas


beamertest-1.lyx
Description: application/lyx


beamerERTSweave.lyx
Description: application/lyx


pjbeamer.layout
Description: Binary data


literate-beamer.layout
Description: Binary data

Re: Usinr Sweave / noweb in BEamer presentation

[Paul Johnson]

Hello, I don't have any answers, but I have some questions for you.. I
have an interest because I have been using LyX with Sweave a long
time, but have not yet needed a beamer Sweave.

  I've only spent 40 minutes looking at your case. I don't know what a
fragile frame is for, but I'll go read more about it.

The problem is obviously that you have an error in the latex macros in
your layout file.  Trying to find where those problems might be is,
well, difficult (since I don't see why you care about changing the
frame, mainly).

On Mon, Mar 2, 2009 at 1:53 AM, Rainer M Krug r.m.k...@gmail.com wrote:
 Hi

 I want to use sweave in a beamer presentation. I found the following article
 http://ggorjan.blogspot.com/2008/09/using-beamer-with-lyx-sweave.html

 and I implemented the laypout file as suggested, but changed it, based
 on the BeamerUserGuide.pdf 3.13 Verbatim Text, tho include a fragile
 frame and a verbatim environment (see layout file attached).

 But there must be something wrong: when I try to compile the attached
 lyx file, it gives an error message ()\\i the LaTeX log:


I've downloaded your test case on my Ubuntu Linux 8.1 system and I can
confirm that your fragile frame environment causes the compile to
fail.  Here's one way to try and figure what is going on. Instead of
using the LyX Layout approach, just write ERT in your lyx document. If
that DOES work, then  you have good information because it means the
fragile frame will work.  Then concentrate on the LyX layout.

I suppose it would help if we had a tex file with the fragile frame in
use, so we could compare the working tex against the tex that LyX
creates.

With the existing Layout file you provide, you can see a bit more
about where this is going wrong if you export the LyX document to TeX
format.  Then we could compare that TeX file with a working tex file.
The file LyX creates will default to batchmode, but you can edit that
tex file and erase line 1, the  batchmode line.  After that, you can
run  latex or pdflatex on the tex file to see what happens.

From looking at that tex file, it appears to me there is a mismatch in
the frame begin and end markers.   Here's a snip


\lyxframeend{}\lyxfragileframe{Slide 1}

\includegraphics{beamertest-001}


\lyxframeend{}\lyxframe{Slide 2}


Note that your Layout causes a \lyxframeend to be inserted, then a
\lyxfragileframe, but there is no \lyxfragileframeend, only
\lyxframeend. Do you think that is related to the trouble?

Here are some latex errors I see when I run that through.  I believe
the first one is superficial, but the second is more serious.

(/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty)

Package hyperref Warning: Option `pdfpagelabels' is turned off
(hyperref)because \thepage is undefined.

Hyperref stopped early
)
*hyperref using default driver hdvips*


(/usr/share/texmf/tex/latex/beamer/themes/color/beamercolorthemewhale.sty))
(/usr/share/texmf-texlive/tex/generic/babel/babel.sty
(/usr/share/texmf-texlive/tex/generic/babel/english.ldf
(/usr/share/texmf-texlive/tex/generic/babel/babel.def)))
(/usr/share/texmf/tex/latex/R/Sweave.sty
(/usr/share/texmf-texlive/tex/latex/base/ifthen.sty)
(/usr/share/texmf-texlive/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.6, with DG/SPQR fixes 1998/07/17 (tvz)
No file fancyvrb.cfg.
) (/usr/share/texmf/tex/latex/R/upquote.sty
(/usr/share/texmf-texlive/tex/latex/base/textcomp.sty
(/usr/share/texmf-texlive/tex/latex/base/ts1enc.def (./beamertest.aux)
(/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd)
(/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty
(/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) (./beamertest.out)
(./beamertest.out)
No file beamertest.nav.
)
Runaway argument?
! File ended while scanning use of \next.
inserted text
\par
* beamertest.tex



I hope you get this working and let us know how you did it.




 ###
 ...
 No file BeamerSweaveExample.nav.
 \openout3 = `BeamerSweaveExample.vrb'.

 )
 Runaway argument?
 ! File ended while scanning use of \next.
 ...
 ###

 When I change from Frame (fragile) to Frame, it compiles, but when
 setting one echo=TRUE, it does not as it is not in verbtim. If I
 set the environment of the ERT to Verbatim, it still does not compile.

 What am I missing?

 Thanks,

 Rainer


 --
 Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
 Biology, UCT), Dipl. Phys. (Germany)

 Centre of Excellence for Invasion Biology
 Faculty of Science
 Natural Sciences Building
 Private Bag X1
 University of Stellenbosch
 Matieland 7602
 South Africa




-- 
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas

Re: Usinr Sweave / noweb in BEamer presentation

[Paul Johnson]

Hello, I don't have any answers, but I have some questions for you.. I
have an interest because I have been using LyX with Sweave a long
time, but have not yet needed a beamer Sweave.

  I've only spent 40 minutes looking at your case. I don't know what a
fragile frame is for, but I'll go read more about it.

The problem is obviously that you have an error in the latex macros in
your layout file.  Trying to find where those problems might be is,
well, difficult (since I don't see why you care about changing the
frame, mainly).

On Mon, Mar 2, 2009 at 1:53 AM, Rainer M Krug r.m.k...@gmail.com wrote:
 Hi

 I want to use sweave in a beamer presentation. I found the following article
 http://ggorjan.blogspot.com/2008/09/using-beamer-with-lyx-sweave.html

 and I implemented the laypout file as suggested, but changed it, based
 on the BeamerUserGuide.pdf 3.13 Verbatim Text, tho include a fragile
 frame and a verbatim environment (see layout file attached).

 But there must be something wrong: when I try to compile the attached
 lyx file, it gives an error message ()\\i the LaTeX log:


I've downloaded your test case on my Ubuntu Linux 8.1 system and I can
confirm that your fragile frame environment causes the compile to
fail.  Here's one way to try and figure what is going on. Instead of
using the LyX Layout approach, just write ERT in your lyx document. If
that DOES work, then  you have good information because it means the
fragile frame will work.  Then concentrate on the LyX layout.

I suppose it would help if we had a tex file with the fragile frame in
use, so we could compare the working tex against the tex that LyX
creates.

With the existing Layout file you provide, you can see a bit more
about where this is going wrong if you export the LyX document to TeX
format.  Then we could compare that TeX file with a working tex file.
The file LyX creates will default to batchmode, but you can edit that
tex file and erase line 1, the  batchmode line.  After that, you can
run  latex or pdflatex on the tex file to see what happens.

From looking at that tex file, it appears to me there is a mismatch in
the frame begin and end markers.   Here's a snip


\lyxframeend{}\lyxfragileframe{Slide 1}

\includegraphics{beamertest-001}


\lyxframeend{}\lyxframe{Slide 2}


Note that your Layout causes a \lyxframeend to be inserted, then a
\lyxfragileframe, but there is no \lyxfragileframeend, only
\lyxframeend. Do you think that is related to the trouble?

Here are some latex errors I see when I run that through.  I believe
the first one is superficial, but the second is more serious.

(/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty)

Package hyperref Warning: Option `pdfpagelabels' is turned off
(hyperref)because \thepage is undefined.

Hyperref stopped early
)
*hyperref using default driver hdvips*


(/usr/share/texmf/tex/latex/beamer/themes/color/beamercolorthemewhale.sty))
(/usr/share/texmf-texlive/tex/generic/babel/babel.sty
(/usr/share/texmf-texlive/tex/generic/babel/english.ldf
(/usr/share/texmf-texlive/tex/generic/babel/babel.def)))
(/usr/share/texmf/tex/latex/R/Sweave.sty
(/usr/share/texmf-texlive/tex/latex/base/ifthen.sty)
(/usr/share/texmf-texlive/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.6, with DG/SPQR fixes 1998/07/17 (tvz)
No file fancyvrb.cfg.
) (/usr/share/texmf/tex/latex/R/upquote.sty
(/usr/share/texmf-texlive/tex/latex/base/textcomp.sty
(/usr/share/texmf-texlive/tex/latex/base/ts1enc.def (./beamertest.aux)
(/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd)
(/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty
(/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) (./beamertest.out)
(./beamertest.out)
No file beamertest.nav.
)
Runaway argument?
! File ended while scanning use of \next.
inserted text
\par
* beamertest.tex



I hope you get this working and let us know how you did it.




 ###
 ...
 No file BeamerSweaveExample.nav.
 \openout3 = `BeamerSweaveExample.vrb'.

 )
 Runaway argument?
 ! File ended while scanning use of \next.
 ...
 ###

 When I change from Frame (fragile) to Frame, it compiles, but when
 setting one echo=TRUE, it does not as it is not in verbtim. If I
 set the environment of the ERT to Verbatim, it still does not compile.

 What am I missing?

 Thanks,

 Rainer


 --
 Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
 Biology, UCT), Dipl. Phys. (Germany)

 Centre of Excellence for Invasion Biology
 Faculty of Science
 Natural Sciences Building
 Private Bag X1
 University of Stellenbosch
 Matieland 7602
 South Africa




-- 
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas

Re: Usinr Sweave / noweb in BEamer presentation

[Paul Johnson]

Hello, I don't have any answers, but I have some questions for you.. I
have an interest because I have been using LyX with Sweave a long
time, but have not yet needed a beamer Sweave.

  I've only spent 40 minutes looking at your case. I don't know what a
fragile frame is for, but I'll go read more about it.

The problem is obviously that you have an error in the latex macros in
your layout file.  Trying to find where those problems might be is,
well, difficult (since I don't see why you care about changing the
frame, mainly).

On Mon, Mar 2, 2009 at 1:53 AM, Rainer M Krug  wrote:
> Hi
>
> I want to use sweave in a beamer presentation. I found the following article
> http://ggorjan.blogspot.com/2008/09/using-beamer-with-lyx-sweave.html
>
> and I implemented the laypout file as suggested, but changed it, based
> on the BeamerUserGuide.pdf 3.13 Verbatim Text, tho include a fragile
> frame and a verbatim environment (see layout file attached).
>
> But there must be something wrong: when I try to compile the attached
> lyx file, it gives an error message ()\\i the LaTeX log:
>

I've downloaded your test case on my Ubuntu Linux 8.1 system and I can
confirm that your fragile frame environment causes the compile to
fail.  Here's one way to try and figure what is going on. Instead of
using the LyX Layout approach, just write ERT in your lyx document. If
that DOES work, then  you have good information because it means the
fragile frame will work.  Then concentrate on the LyX layout.

I suppose it would help if we had a tex file with the fragile frame in
use, so we could compare the working tex against the tex that LyX
creates.

With the existing Layout file you provide, you can see a bit more
about where this is going wrong if you export the LyX document to TeX
format.  Then we could compare that TeX file with a working tex file.
The file LyX creates will default to batchmode, but you can edit that
tex file and erase line 1, the  batchmode line.  After that, you can
run  latex or pdflatex on the tex file to see what happens.

>From looking at that tex file, it appears to me there is a mismatch in
the frame begin and end markers.   Here's a snip


\lyxframeend{}\lyxfragileframe{Slide 1}

\includegraphics{beamertest-001}


\lyxframeend{}\lyxframe{Slide 2}


Note that your Layout causes a \lyxframeend to be inserted, then a
\lyxfragileframe, but there is no \lyxfragileframeend, only
\lyxframeend. Do you think that is related to the trouble?

Here are some latex errors I see when I run that through.  I believe
the first one is superficial, but the second is more serious.

(/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty)

Package hyperref Warning: Option `pdfpagelabels' is turned off
(hyperref)because \thepage is undefined.

Hyperref stopped early
)
*hyperref using default driver hdvips*


(/usr/share/texmf/tex/latex/beamer/themes/color/beamercolorthemewhale.sty))
(/usr/share/texmf-texlive/tex/generic/babel/babel.sty
(/usr/share/texmf-texlive/tex/generic/babel/english.ldf
(/usr/share/texmf-texlive/tex/generic/babel/babel.def)))
(/usr/share/texmf/tex/latex/R/Sweave.sty
(/usr/share/texmf-texlive/tex/latex/base/ifthen.sty)
(/usr/share/texmf-texlive/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.6, with DG/SPQR fixes <1998/07/17> (tvz)
No file fancyvrb.cfg.
) (/usr/share/texmf/tex/latex/R/upquote.sty
(/usr/share/texmf-texlive/tex/latex/base/textcomp.sty
(/usr/share/texmf-texlive/tex/latex/base/ts1enc.def (./beamertest.aux)
(/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd)
(/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty
(/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) (./beamertest.out)
(./beamertest.out)
No file beamertest.nav.
)
Runaway argument?
! File ended while scanning use of \next.

\par
<*> beamertest.tex



I hope you get this working and let us know how you did it.




> ###
> ...
> No file BeamerSweaveExample.nav.
> \openout3 = `BeamerSweaveExample.vrb'.
>
> )
> Runaway argument?
> ! File ended while scanning use of \next.
> ...
> ###
>
> When I change from "Frame (fragile)" to "Frame", it compiles, but when
> setting one "echo=TRUE", it does not as it is not in "verbtim". If I
> set the environment of the ERT to Verbatim, it still does not compile.
>
> What am I missing?
>
> Thanks,
>
> Rainer
>
>
> --
> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
> Biology, UCT), Dipl. Phys. (Germany)
>
> Centre of Excellence for Invasion Biology
> Faculty of Science
> Natural Sciences Building
> Private Bag X1
> University of Stellenbosch
> Matieland 7602
> South Africa
>



-- 
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas