R devel - Mar 2011 - system.file() to read a text file from a vignette

[Env: R 2.12.2, WinXp]

In a vignette for the vcdExtra package, I had a text file, tv.dat under 
data/, that I used in the vignette as

<<tv1,results=verbatim>>tv.data<-read.table(system.file("data","tv.dat",package="vcdExtra"))
head(tv.data,5)
@

I was told that this now generates a warning for non-Rdata files in R 
CMD check. But I'm now confused about
where to put this and how to use system.file() in the vignette to read 
it. The R-exts.pdf says

The R working directory for all vignette tests in R CMD
check is the installed version of the ?doc? subdirectory. Make sure all 
files needed by the vignette
(data sets, . . . ) are accessible by either placing them in the 
?inst/doc? hierarchy of the source
package, or using calls to system.file().

So, I moved this file to inst/doc/extdata/tv.dat, and changed the 
vignette to

<<tv1,results=verbatim>>tv.data<-read.table(system.file("inst","doc","extdata","tv.dat",package="vcdExtra"))
head(tv.data,5)
@

But I get the error:
Error: processing vignette 'vcd-tutorial.Rnw' failed with diagnostics:
chunk 23 (label=tv1)
Error in read.table(system.file("inst", "doc",
"extdata", "tv.dat",
package = "vcdExtra")) :
no lines available in input

How can I fix this?

-- 
Michael Friendly     Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University      Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Street    Web:   http://www.datavis.ca
Toronto, ONT  M3J 1P3 CANADA

Hi Michael,

On 03/23/2011 03:03 PM, Michael Friendly wrote:
> [Env: R 2.12.2, WinXp]
>
> In a vignette for the vcdExtra package, I had a text file, tv.dat under
> data/, that I used in the vignette as
>
> <<tv1,results=verbatim>>>
tv.data<-read.table(system.file("data","tv.dat",package="vcdExtra"))
> head(tv.data,5)
> @
>
> I was told that this now generates a warning for non-Rdata files in R
> CMD check. But I'm now confused about
> where to put this and how to use system.file() in the vignette to read
> it. The R-exts.pdf says
>
> The R working directory for all vignette tests in R CMD
> check is the installed version of the ?doc? subdirectory. Make sure all
> files needed by the vignette
> (data sets, . . . ) are accessible by either placing them in the
> ?inst/doc? hierarchy of the source
> package, or using calls to system.file().
>
> So, I moved this file to inst/doc/extdata/tv.dat, and changed the
> vignette to
>
> <<tv1,results=verbatim>>>
tv.data<-read.table(system.file("inst","doc","extdata","tv.dat",package="vcdExtra"))
>
> head(tv.data,5)
> @
>
> But I get the error:
> Error: processing vignette 'vcd-tutorial.Rnw' failed with
diagnostics:
> chunk 23 (label=tv1)
> Error in read.table(system.file("inst", "doc",
"extdata", "tv.dat",
> package = "vcdExtra")) :
> no lines available in input
>
> How can I fix this?
The inst/ will be removed once the package is installed, so you
would need

system.file("doc", "extdata", "tv.dat", package =
"vcdExtra")

The warning on non Rdata files is probably due to the fact that
.dat is not supported, see Section 1.1.5 of Writing R Extensions
and ?data

Best,
Tobias

On 23/03/2011 10:03 AM, Michael Friendly wrote:
> [Env: R 2.12.2, WinXp]
>
> In a vignette for the vcdExtra package, I had a text file, tv.dat under
> data/, that I used in the vignette as
>
> <<tv1,results=verbatim>>>
tv.data<-read.table(system.file("data","tv.dat",package="vcdExtra"))
> head(tv.data,5)
> @
>
> I was told that this now generates a warning for non-Rdata files in R
> CMD check. But I'm now confused about
> where to put this and how to use system.file() in the vignette to read
> it. The R-exts.pdf says
>
> The R working directory for all vignette tests in R CMD
> check is the installed version of the ?doc? subdirectory. Make sure all
> files needed by the vignette
> (data sets, . . . ) are accessible by either placing them in the
> ?inst/doc? hierarchy of the source
> package, or using calls to system.file().
>
> So, I moved this file to inst/doc/extdata/tv.dat, and changed the
> vignette to
>
> <<tv1,results=verbatim>>>
tv.data<-read.table(system.file("inst","doc","extdata","tv.dat",package="vcdExtra"))
> head(tv.data,5)
> @
>
> But I get the error:
> Error: processing vignette 'vcd-tutorial.Rnw' failed with
diagnostics:
> chunk 23 (label=tv1)
> Error in read.table(system.file("inst", "doc",
"extdata", "tv.dat",
> package = "vcdExtra")) :
> no lines available in input
>
> How can I fix this?
Everything in the "inst" directory is moved up a level when it is 
installed.  So you shouldn't mention "inst" in its path.

Duncan Murdoch