R CMD check example problem (PR#8113)

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

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