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Renaud Gaujoux

2011-Oct-28 14:49 UTC

[Rd] R CMD check and error in an \Sexpr in an Rd file

Hi,

another Rd related issue I encountered is that if an error occurs in an 
\Sexpr in an Rd file, then on get the following error:

* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... ERROR
Error in paste(before, x, after, sep = "") : object 'exfile'
not found
Execution halted

To reproduce, put a call like this in an Rd section:

\Sexpr[results=verbatim, stage=render]{x <- 1; stop("sexpr error")}

The strange thing is that it occurs at the example checking step.
Not sure why it does not break before.

Thank you.

Renaud

PS: I am on R version 2.13.2 (2011-09-30) - x86_64-pc-linux-gnu (64-bit)

-- 
Renaud Gaujoux
Computational Biology - University of Cape Town
South Africa

Duncan Murdoch

2011-Oct-28 14:53 UTC

head link

[Rd] R CMD check and error in an \Sexpr in an Rd file

On 28/10/2011 10:49 AM, Renaud Gaujoux wrote:> Hi,
>
> another Rd related issue I encountered is that if an error occurs in an
> \Sexpr in an Rd file, then on get the following error:
>
> * checking for portable compilation flags in Makevars ... OK
> * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
> * checking examples ... ERROR
> Error in paste(before, x, after, sep = "") : object
'exfile' not found
> Execution halted
>
> To reproduce, put a call like this in an Rd section:
>
> \Sexpr[results=verbatim, stage=render]{x<- 1; stop("sexpr
error")}
>
> The strange thing is that it occurs at the example checking step.
> Not sure why it does not break before.
>
> Thank you.
>
> Renaud
>
> PS: I am on R version 2.13.2 (2011-09-30) - x86_64-pc-linux-gnu (64-bit)
>
I would update to 2.13.2 patched, or the release candidate of 2.14.0.

Duncan Murdoch

Georgi Boshnakov

2011-Nov-01 11:36 UTC

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[Rd] R CMD check and error in an \Sexpr in an Rd file

Dear Renaud,
> Getting back to the \Sexpr issue, I tried with R-2.14.0 and I still see
> the following issues:
>
> - verbatim multiline is not shown properly on PDF
> (\Sexpr[results=verbatim, stage=render]{cat("line\nnext line")})
You probably meant to use `paste', not `cat'. 
The latter sends its output  somewhere and returns NULL, not the string. 

Best,
Georgi



--
Dr Georgi Boshnakov               tel: (+44) (0)161 306 3684
School of Mathematics             fax: (+44) (0)161 306 3669
Alan Turing Building 1.125
The University of Manchester      email: Georgi.Boshnakov at manchester.ac.uk
Oxford Road
Manchester M13 9PL
UK


------------------------------

Message: 18
Date: Tue, 01 Nov 2011 12:22:30 +0200
From: Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>
To: Duncan Murdoch <murdoch.duncan at gmail.com>
Cc: Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>,
        "r-devel at r-project.org" <r-devel at r-project.org>
Subject: Re: [Rd] R CMD check and error in an \Sexpr in an Rd file
Message-ID: <4EAFC866.6040803 at cbio.uct.ac.za>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Getting back to the \Sexpr issue, I tried with R-2.14.0 and I still see
the following issues:

- verbatim multiline is not shown properly on PDF
(\Sexpr[results=verbatim, stage=render]{cat("line\nnext line")})
- verbatim with empty lines breaks PDF generation
(\Sexpr[results=verbatim, stage=render]{cat("line\nnext line\n\nyet
another line")}). Would there be an issue in using a plain Latex
verbatim environment for \Sexpr[results=verbatim]?

- an error in an \Sexpr (\Sexpr[results=verbatim,
stage=render]{stop("error in sexpr")}) gives the following in R CMD
check:

* checking examples ... ERROR
Error in paste(before, x, after, sep = "") : object 'exfile'
not found
Execution halted

The two first issues can be reproduced with a call to R CMD Rd2pdf on
the Rd code below.

Thank you.
Renaud.

%%%%%%%%%%%
\name{Sexpr}
\alias{Sexpr}
\title{Error and verbatim in Sexpr}
\description{
   Testing Sexpr in Rd files

   %\Sexpr[results=verbatim, stage=render]{stop("error in sexpr")}

   \Sexpr[results=verbatim, stage=render]{cat("line\nnext line")}

   %\Sexpr[results=verbatim, stage=render]{cat("line\nnext line\n\nyet
another line")}
}
%%%%%%%%%%%



--
Renaud Gaujoux
Computational Biology - University of Cape Town
South Africa


On 28/10/2011 17:25, Duncan Murdoch wrote:> On 28/10/2011 10:53 AM, Duncan Murdoch wrote:
>> On 28/10/2011 10:49 AM, Renaud Gaujoux wrote:
>> >  Hi,
>> >
>> >  another Rd related issue I encountered is that if an error occurs
>> in an
>> >  \Sexpr in an Rd file, then on get the following error:
>> >
>> >  * checking for portable compilation flags in Makevars ... OK
>> >  * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS)
... OK
>> >  * checking examples ... ERROR
>> >  Error in paste(before, x, after, sep = "") : object
'exfile' not
>> found
>> >  Execution halted
>> >
>> >  To reproduce, put a call like this in an Rd section:
>> >
>> >  \Sexpr[results=verbatim, stage=render]{x<- 1; stop("sexpr
error")}
>> >
>> >  The strange thing is that it occurs at the example checking step.
>> >  Not sure why it does not break before.
>> >
>> >  Thank you.
>> >
>> >  Renaud
>> >
>> >  PS: I am on R version 2.13.2 (2011-09-30) - x86_64-pc-linux-gnu
>> (64-bit)
>> >
>>
>> I would update to 2.13.2 patched, or the release candidate of 2.14.0.
>
> Oops, sorry, 2.13.2 is "final", so I didn't backport the
patch.
> 2.14.0 is what you should get.
>
> Duncan Murdoch


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Renaud Gaujoux

2011-Nov-03 11:58 UTC

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[Rd] R CMD check and error in an \Sexpr in an Rd file

Georgi, I tried with paste() instead of cat(), but I then get the 
following in my PDF manual:

[1] "line\nnext line"

i.e. what would be printed in the R console, which is not what I want.
I would like to get something like this in the Latex code:

\begin{verbatim}
line
next line
\end{verbatim}

Using cat() I get the following in the Latex code:

\AsIs{
line
next line}

which does not render as a new line in the PDF and breaks if empty lines 
are present in the output text.
Besides it will also break on \Sexpr[results=verbatim, 
stage=render]{list("text", 3)}.

But maybe this is not what 'results=verbatim' is supposed to do nor to 
be used for?

Renaud

Another test Rd file.

%%%%%%%%%
\name{Sexpr}
\alias{Sexpr}
\title{Error and verbatim in Sexpr}
\description{
    Testing Sexpr in Rd files

    %\Sexpr[results=verbatim, stage=render]{stop("error in sexpr")}

    Verbatim:

    1: \Sexpr[results=verbatim, stage=render]{cat("line\nnext
line\n")}

    2: \Sexpr[results=verbatim, stage=render]{"line\nnext line\n"}

    3: \Sexpr[results=verbatim, stage=render]{list("line\nnext line",
3)}

    Text:

    1: \Sexpr[results=text, stage=render]{cat("line\nnext line\n")}

    2: \Sexpr[results=text, stage=render]{"line\nnext line\n"}

    3: \Sexpr[results=text, stage=render]{list("line\nnext line", 3)}

}
%%%%%

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