Re: [R] knitr error with Lyx

2012-11-29 Thread Mark Lamias
Hi, Yihui,

Attached is an HTML Diff report of the two files.  The left pane contains the 
R-2.15.0 file. 

Thanks.

--Mark





 From: Yihui Xie 
To: Mark Lamias  
Cc: "r-help@r-project.org"  
Sent: Thursday, November 29, 2012 2:43 PM
Subject: Re: [R] knitr error with Lyx
 
That is very helpful! Just to continue debugging, can you save the two
versions of the tex files produced from LyX with different versions of
R and do a diff on them? It sounds like something has changed from R
2.15.0 to 2.15.2.

Regards,
Yihui
--
Yihui Xie 
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA


On Thu, Nov 29, 2012 at 1:26 PM, Mark Lamias  wrote:
> Thanks, Yihui!
>
> Luckily I kept R-2.15.0 and left it untouched (so I can continue to use that
> for now).  If it helps any, I was able to go back into Lyx and change the
> path to point to R-2.15.0 and I also changed the windows path environment
> variable to point to the old version.  After doing this, LyX worked fine
> with no problem on the code below.  Changing the paths back to the new
> version  R-2.15.2, generates the error below.
>
> If anyone else has any idea how to resolve this, either through R or a
> Lyx/LaTeX fix, I'd be all ears.
>
> Thanks, again for your response, Yihui!
>
>
> Sincerely yours,
>
> Mark J. Lamias
   C:\Users\Mark\Desktop\Test\2.15.0.tex C:\Users\Mark\Desktop\Test\2.15.2.tex
   \batchmode \batchmode
   \makeatletter \makeatletter
   \def\input@path{{C:/Users/Mark/Desktop//}}
   \def\input@path{{C:/Users/Mark/Desktop//}}
   \makeatother \makeatother
   \documentclass{article}   \documentclass{article}\usepackage{graphicx,
   color}
   \usepackage{graphicx, color}  %% maxwidth is the original width if it is
   less than linewidth
 %% otherwise use linewidth (to make sure the graphics do not exceed the
   margin)
 \makeatletter
 \def\maxwidth{ %
  \ifdim\Gin@nat@width>\linewidth
\linewidth
  \else
\Gin@nat@width
  \fi
 }
 \makeatother

 \IfFileExists{upquote.sty}{\usepackage{upquote}}{}
 \definecolor{fgcolor}{rgb}{0.2, 0.2, 0.2}
   \newcommand{\hlnumber}[1]{\textcolor[rgb]{0,0,0}{#1}}%
   \newcommand{\hlnumber}[1]{\textcolor[rgb]{0,0,0}{#1}}%
   \newcommand{\hlfunctioncall}[1]{\textcolor[rgb]{.5,0,.33}{\textbf{#1}}}%
   \newcommand{\hlfunctioncall}[1]{\textcolor[rgb]{0.501960784
   313725,0,0.329411764705882}{\textbf{#1}}}%
   \newcommand{\hlstring}[1]{\textcolor[rgb]{.6,.6,1}{#1}}%
   \newcommand{\hlstring}[1]{\textcolor[rgb]{0.6,0.6,1}{#1}}%
   \newcommand{\hlkeyword}[1]{\textbf{#1}}%
   \newcommand{\hlkeyword}[1]{\textcolor[rgb]{0,0,0}{\textbf{#1}}}%
   \newcommand{\hlargument}[1]{\textcolor[rgb]{.69,.25,.02}{#1}}%
   \newcommand{\hlargument}[1]{\textcolor[rgb]{0.6901960784313
   73,0.250980392156863,0.0196078431372549}{#1}}%
   \newcommand{\hlcomment}[1]{\textcolor[rgb]{.18,.6,.34}{#1}}%
   \newcommand{\hlcomment}[1]{\textcolor[rgb]{0.18039215686274
   5,0.6,0.341176470588235}{#1}}%
   \newcommand{\hlroxygencomment}[1]{\textcolor[rgb]{.44,.48,.7}{#1}}%
   \newcommand{\hlroxygencomment}[1]{\textcolor[rgb]{0.4392156
   8627451,0.47843137254902,0.701960784313725}{#1}}%
   \newcommand{\hlformalargs}[1]{\hlargument{#1}}%
   \newcommand{\hlformalargs}[1]{\textcolor[rgb]{0.69019607843
   1373,0.250980392156863,0.0196078431372549}{#1}}%
   \newcommand{\hleqformalargs}[1]{\hlargument{#1}}%
   \newcommand{\hleqformalargs}[1]{\textcolor[rgb]{0.690196078
   431373,0.250980392156863,0.0196078431372549}{#1}}%
   \newcommand{\hlassignement}[1]{\textbf{#1}}%
   \newcommand{\hlassignement}[1]{\textcolor[rgb]{0,0,0}{\textbf{#1}}}%
   \newcommand{\hlpackage}[1]{\textcolor[rgb]{.59,.71,.145}{#1}}%
   \newcommand{\hlpackage}[1]{\textcolor[rgb]{0.58823529411764
   7,0.709803921568627,0.145098039215686}{#1}}%
   \newcommand{\hlslot}[1]{\textit{#1}}% \newcommand{\hlslot}[1]{\textit{#1}}%
   \newcommand{\hlsymbol}[1]{#1}%
   \newcommand{\hlsymbol}[1]{\textcolor[rgb]{0,0,0}{#1}}%
   \newcommand{\hlprompt}[1]{\textcolor[rgb]{.5,.5,.5}{#1}}%
   \newcommand{\hlprompt}[1]{\textcolor[rgb]{0.2,0.2,0.2}{#1}}%

   \usepackage{color}%

   \newsavebox{\hlnormalsizeboxclosebrace}%
   \newsavebox{\hlnormalsizeboxopenbrace}%
   \newsavebox{\hlnormalsizeboxbackslash}%
   \newsavebox{\hlnormalsizeboxlessthan}%
   \newsavebox{\hlnormalsizeboxgreaterthan}%
   \newsavebox{\hlnormalsizeboxdollar}%
   \newsavebox{\hlnormalsizeboxunderscore}%
   \newsavebox{\hlnormalsizeboxand}%
   \newsavebox{\hlnormalsizeboxhash}%
   \newsavebox{\hlnormalsizeboxat}%
   \newsavebox{\hlnormalsizeboxpercent}%
   \newsavebox{\hlnormalsizeboxhat}%
   \newsavebox{\hlnormalsizeboxsinglequote}%
   \newsavebox{\hlnormalsizeboxbacktick}%

   \setbox\hlnormalsizeboxopenbrace=\hbox{\begin{normalsize}\v
   erb.{.\end{normalsize}}%
   \setbox\hlnormalsizeboxclosebrace=\hbox{\begin{norm

Re: [R] knitr error with Lyx

2012-11-29 Thread Yihui Xie
That is very helpful! Just to continue debugging, can you save the two
versions of the tex files produced from LyX with different versions of
R and do a diff on them? It sounds like something has changed from R
2.15.0 to 2.15.2.

Regards,
Yihui
--
Yihui Xie 
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA


On Thu, Nov 29, 2012 at 1:26 PM, Mark Lamias  wrote:
> Thanks, Yihui!
>
> Luckily I kept R-2.15.0 and left it untouched (so I can continue to use that
> for now).  If it helps any, I was able to go back into Lyx and change the
> path to point to R-2.15.0 and I also changed the windows path environment
> variable to point to the old version.  After doing this, LyX worked fine
> with no problem on the code below.  Changing the paths back to the new
> version  R-2.15.2, generates the error below.
>
> If anyone else has any idea how to resolve this, either through R or a
> Lyx/LaTeX fix, I'd be all ears.
>
> Thanks, again for your response, Yihui!
>
>
> Sincerely yours,
>
> Mark J. Lamias

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


Re: [R] knitr error with Lyx

2012-11-29 Thread Mark Lamias
Thanks, Yihui!

Luckily I kept R-2.15.0 and left it untouched (so I can continue to use that 
for now).  If it helps any, I was able to go back into Lyx and change the path 
to point to R-2.15.0 and I also changed the windows path environment variable 
to point to the old version.  After doing this, LyX worked fine with no problem 
on the code below.  Changing the paths back to the new version  R-2.15.2, 
generates the error below.

If anyone else has any idea how to resolve this, either through R or a 
Lyx/LaTeX fix, I'd be all ears.

Thanks, again for your response, Yihui!

Sincerely yours,

Mark J. Lamias





 From: Yihui Xie 

Cc: "r-help@r-project.org"  
Sent: Thursday, November 29, 2012 2:02 PM
Subject: Re: [R] knitr error with Lyx

Quite a few people have had this problem, but since I'm unable to
reproduce it, I'm not exactly sure how to fix it either. A few
references that might be helpful to you:

http://stackoverflow.com/q/12448507/559676
https://github.com/yihui/knitr/issues/413

It is very likely to be a pure LaTeX problem. Letting MikTeX install
the missing LaTeX packages on the fly might solve the problem.

Regards,
Yihui
--
Yihui Xie 
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA



> R Users,
>
>
> I just upgraded my version of R from R-2.15.0 to R-2.15.2 and installed the 
> latest versions of LyX and MikTex running Windows 7 Ultimate, 64-bit OS.  
> Prior to the upgrade, I was using Lyx with knitr to generate a document with 
> no problems.  However, after the upgrade, and using the same LyX document, 
> I'm receiving the following error when I attempt to compile the document:
>
> \end{verbatim}
> The control sequence at the end of the top line
> of your error message was never \def'ed. If you have
> misspelled it (e.g., `\hobx'), type `I' and the correct
> spelling (e.g., `I\hbox'). Otherwise just continue,
> and I'll forget about whatever was undefined.
>
> I have determined that the error is caused when printing the anova results 
> from the anova statement in my R source code, but can't seem to resolve the 
> issue.  Here is an example code chunk that creates the error:
>
> <>=
> #Read in data
> y=c( 67, 73, 83, 89, 65, 91, 87, 86, 155, 127, 147, 212, 108, 100, 90, 153, 
> 140, 142, 121, 150, 33, 8, 46, 54 )
> temp=as.factor(c(rep(seq(360, 380, 10), each=4), rep(seq(380, 360, -10), 
> each=4)))
> coat=as.factor(rep(seq(1, 4), 6))
> replicate=as.factor(rep(seq(1, 6), each=4))
> #Obtain Factorial/Incorrect Model
> o=lm(y~temp*coat)
> ano=anova(o)
> ano
> @
>
>
> Removing the ano=anova(o) or ano lines in the code chunk allows the document 
> to compile with no problem.  Does anyone else have this problem or did I do 
> something wrong when I migrated to the newer versions?
>
[[elided Yahoo spam]]
>
> Sincerely yours,
>
> Mark J. Lamias
>         [[alternative HTML version deleted]]
>
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


Re: [R] knitr error with Lyx

2012-11-29 Thread Yihui Xie
Quite a few people have had this problem, but since I'm unable to
reproduce it, I'm not exactly sure how to fix it either. A few
references that might be helpful to you:

http://stackoverflow.com/q/12448507/559676
https://github.com/yihui/knitr/issues/413

It is very likely to be a pure LaTeX problem. Letting MikTeX install
the missing LaTeX packages on the fly might solve the problem.

Regards,
Yihui
--
Yihui Xie 
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA


On Thu, Nov 29, 2012 at 10:53 AM, Mark Lamias  wrote:
> R Users,
>
>
> I just upgraded my version of R from R-2.15.0 to R-2.15.2 and installed the 
> latest versions of LyX and MikTex running Windows 7 Ultimate, 64-bit OS.  
> Prior to the upgrade, I was using Lyx with knitr to generate a document with 
> no problems.  However, after the upgrade, and using the same LyX document, 
> I'm receiving the following error when I attempt to compile the document:
>
> \end{verbatim}
> The control sequence at the end of the top line
> of your error message was never \def'ed. If you have
> misspelled it (e.g., `\hobx'), type `I' and the correct
> spelling (e.g., `I\hbox'). Otherwise just continue,
> and I'll forget about whatever was undefined.
>
> I have determined that the error is caused when printing the anova results 
> from the anova statement in my R source code, but can't seem to resolve the 
> issue.  Here is an example code chunk that creates the error:
>
> <>=
> #Read in data
> y=c( 67, 73, 83, 89, 65, 91, 87, 86, 155, 127, 147, 212, 108, 100, 90, 153, 
> 140, 142, 121, 150, 33, 8, 46, 54 )
> temp=as.factor(c(rep(seq(360, 380, 10), each=4), rep(seq(380, 360, -10), 
> each=4)))
> coat=as.factor(rep(seq(1, 4), 6))
> replicate=as.factor(rep(seq(1, 6), each=4))
> #Obtain Factorial/Incorrect Model
> o=lm(y~temp*coat)
> ano=anova(o)
> ano
> @
>
>
> Removing the ano=anova(o) or ano lines in the code chunk allows the document 
> to compile with no problem.  Does anyone else have this problem or did I do 
> something wrong when I migrated to the newer versions?
>
> Thanks, in advance for any help!
>
> Sincerely yours,
>
> Mark J. Lamias
> [[alternative HTML version deleted]]
>
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.