From gregory.r.warnes at pfizer.com  Thu Sep  1 18:47:22 2005
From: gregory.r.warnes at pfizer.com (Warnes, Gregory R)
Date: Thu, 1 Sep 2005 12:47:22 -0400 
Subject: [Rd] R CMD check example problem (PR#8113)
Message-ID: <915D2D65A9986440A277AC5C98AA466F01863258@groamrexm02.amer.pfizer.com>

Ahh.  I didn't notice that my fingers had used \code() inside of the example
section.  I've removed them, and everything seems to be working properly
now.  

-G

> -----Original Message-----
> From: r-devel-bounces at r-project.org
> [mailto:r-devel-bounces at r-project.org]On Behalf Of
> ligges at statistik.uni-dortmund.de
> Sent: Thursday, September 01, 2005 12:23 PM
> To: r-devel at stat.math.ethz.ch
> Cc: R-bugs at biostat.ku.dk
> Subject: Re: [Rd] R CMD check example problem (PR#8113)
> 
> 
> [CCing to r-bugs to inform people that we have looked at it.]
> 
> Greg,
> 
> you sent me the example which can be reduced to an example.Rd 
> file that 
> contains the following Example section:
> 
> 
> ############################
> \examples{
> # \code{} \code{}
> foo <- function()
> {
> }
> }
> ############################
> 
> calling now
>     R CMD Rdconv -t example example.Rd
> results in:
> 
> 
> 
> ############################
> ### ** Examples
> 
> # this-is-escaped-code{ 
> this-is-escaped-codenormal-bracket9bracket-normal
> foo <- function()
> normal-bracket10bracket-normal
> normal-bracket10bracket-normal
> ############################
> 
> 
> I do not know whether this qualifies as a bug, but for 
> simplicity let's say:
> "Don't use \code{} in an Example section where it does not make sense 
> anyway."
> 
> Best,
> Uwe
> 
> 
> 
> 
> 
> 
> Warnes, Gregory R wrote:
> 
> > 
> >>-----Original Message-----
> >>From: Uwe Ligges [mailto:ligges at statistik.uni-dortmund.de]
> >>Sent: Thursday, September 01, 2005 8:57 AM
> >>To: Warnes, Gregory R
> >>Subject: Re: [Rd] R CMD check example problem (PR#8113)
> >>
> >>
> >>Greg,
> >>
> >>the attachment is not appended on the forwarded message to 
> >>R-devel, and 
> >>I would like to take a look, can you send it in a private 
> >>message, please?
> >>
> >>Best,
> >>Uwe
> >>
> >>Warnes, Gregory R wrote:
> >>
> >>
> >>>[Automatic forwarding from R-bugs failed.  This message has 
> >>
> >>been manually
> >>
> >>>forwarded.]
> >>>
> >>>Hi all!
> >>>
> >>>I'm trying to add Thomas Lumley's defmacro() function  Lumley T.
> >>>"Programmer's Niche: Macros in {R}", R News, 2001, Vol 1,
> >>>  No. 3, pp 11--13, 
> >>
> >>\url{http://CRAN.R-project.org/doc/Rnews/} to the gtools
> >>
> >>>package (provided that Thomas gives his OK). And I've 
> >>
> >>encountered an error
> >>
> >>>in how R CMD check is extracting the example code I have in 
> >>
> >>the .Rd file.
> >>
> >>>The example section contains the lines 
> >>>
> >>>  # An equivalent function is somewhat messier, since it 
> must either
> >>>explicitly
> >>>  # construct the y axis label, duplicating some of the 
> >>
> >>work of the plot
> >>
> >>>  # function:
> >>>  plotit <- function( df, var, col="red", title="" )
> >>>  {
> >>>      dname <- deparse(substitute(df))
> >>>      vname <- deparse(substitute(var))
> >>>      plot( df[[vname]] ~ df$Grp, type="b", col=col, title=title,
> >>>            ylab=paste( dname, "$", vname, sep='' ) )
> >>>  }
> >>>  # or we explicitly construct the call and then call eval. 
> >>
> >> The code for
> >>
> >>>  # the latter approach is # omiited since this is quite messy and
> >>>  # requires a lot of work.
> >>>  
> >>>which is getting extracted for testing into 
> >>
> >>gtools.Rcheck/gtools-Ex.R as
> >>
> >>>  # An equivalent function is somewhat messier, since it 
> must either
> >>>explicitly
> >>>  # construct the y axis label, duplicating some of the 
> >>
> >>work of the plot
> >>
> >>>  # function:
> >>>  plotit <- function( df, var, col="red", title=""
> >>>)normal-bracket43bracket-normal
> >>>      dname <- deparse(substitute(df))
> >>>      vname <- deparse(substitute(var))
> >>>      plot( df[[vname]] ~ df$Grp, type="b", col=col, title=title,
> >>>            ylab=paste( dname, "$", vname, sep='' ) )
> >>>  normal-bracket43bracket-normal
> >>>  # or we explicitly construct the call and then call eval. 
> >>
> >> The code for
> >>
> >>>  # the latter approach is # omiited since this is quite messy and
> >>>  # requires a lot of work.
> >>>
> >>>Note that the opening and closing curly brakkets are 
> >>
> >>converted to the string
> >>
> >>>"normal-bracket43bracket-normal".   [I assume that this is happeing
> >>>somewhere to check for brace-matches, and isn't being 
> >>
> >>properly undone.]  As
> >>
> >>>a consequence, R CMD check is failing:
> >>>
> >>>  > # An equivalent function is somewhat messier, since it 
> >>
> >>must either
> >>
> >>>explicitly
> >>>  > # construct the y axis label, duplicating some of the 
> >>
> >>work of the plot
> >>
> >>>  > # function:
> >>>  > plotit <- function( df, var, col="red", title=""
> >>>)normal-bracket43bracket-normal
> >>>  >     dname <- deparse(substitute(df))
> >>>  >     vname <- deparse(substitute(var))
> >>>  >     plot( df[[vname]] ~ df$Grp, type="b", col=col, title=title,
> >>>  +           ylab=paste( dname, "$", vname, sep='' ) )
> >>>  Error in df[[vname]] : object is not subsettable
> >>>  Execution halted
> >>>
> >>>I've checked, and this occurs under R-2.1.0, R-2.1.1, and today's
> >>>R-2.2.0-devel on my
> >>>
> >>>  platform i686-pc-linux-gnu
> >>>  arch     i686             
> >>>  os       linux-gnu        
> >>>  system   i686, linux-gnu  
> >>>
> >>>I'm attaching the probelmatic .Rd file to this email.  
> >>>
> >>>  <<defmacro.Rd>> 
> >>>
> >>>(For the record, I've simply enclosed the problematic 
> >>
> >>section in \dontrun as
> >>
> >>>a workaround.)
> >>>
> >>>-Greg
> >>>
> >>>
> >>>
> >>>Gregory R. Warnes, Ph.D.
> >>>Associate Director, Non-Clinical Statistics
> >>>Pfizer Global Research and Development
> >>>
> >>>
> >>>
> >>>LEGAL NOTICE
> >>>Unless expressly stated otherwise, this message is 
> >>
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> >>
> >>>
> >>>
> >>--------------------------------------------------------------
> >>----------
> >>
> >>>______________________________________________
> >>>R-devel at r-project.org mailing list
> >>>https://stat.ethz.ch/mailman/listinfo/r-devel
> >>
> >>
> >>
> >
> 
> ______________________________________________
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> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
> 


LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}}



[Rd] R CMD check example problem (PR#8113)
Warnes, Gregory R