[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 confidential and may be
privileged. It is intended for the addressee(s) only. Access to this E-mail by
anyone else is unauthorized. If you are not an addressee, any disclosure or
copying of the contents of this E-mail or any action taken (or not taken) in
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please inform the sender immediately.
ligges@statistik.uni-dortmund.de
2005-Sep-01 16:23 UTC
[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
>>
>>confidential and may be privileged. It is intended for the
>>addressee(s) only. Access to this E-mail by anyone else is
>>unauthorized. If you are not an addressee, any disclosure or
>>copying of the contents of this E-mail or any action taken
>>(or not taken) in reliance on it is unauthorized and may be
>>unlawful. If you are not an addressee, please inform the
>>sender immediately.
>>
>>>
>>>
>>--------------------------------------------------------------
>>----------
>>
>>>______________________________________________
>>>R-devel at r-project.org mailing list
>>>https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
>>
>
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 > >> > >>confidential and may be privileged. It is intended for the > >>addressee(s) only. Access to this E-mail by anyone else is > >>unauthorized. If you are not an addressee, any disclosure or > >>copying of the contents of this E-mail or any action taken > >>(or not taken) in reliance on it is unauthorized and may be > >>unlawful. If you are not an addressee, please inform the > >>sender immediately. > >> > >>> > >>> > >>-------------------------------------------------------------- > >>---------- > >> > >>>______________________________________________ > >>>R-devel at r-project.org mailing list > >>>https://stat.ethz.ch/mailman/listinfo/r-devel > >> > >> > >> > > > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > >LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}}