[R] R CMD build error with data files

[Uwe Ligges]

Christian,

my late answer on this one:


On 21.08.2012 22:28, Christian Hennig wrote:
> Dear list,
>
> I want to update my prabclus package which I haven't done for quite a
> while.
>
> In the previous version, I had .dat files in my data subdirectory, which
> I read using .R files. Now R CMD check gives me a warning that .dat
> files are no longer accepted there.
>
> So I changed my filenames to .txt, but actually some of these files are
> only there in order to be read by .R, not in order to be read
> independetly by read.table, which produces an error (something like
> "scan error: line 5 does not have 2 elements", which I'd guess comes
> from the fact that R tries to automatically read the file with
> read.table that should be read in a different way as specified in my
> .R-file).
>
> So I decided, following the advice in "Writing R extensions", to put
> these files into a directory called inst/extdata.
> The data directory now only has .R-files that read stuff from files in
> inst/extdata.
> This, unfortunately, doesn't seem to work.
> For example,
> kykladspecreg.R in data has one line reading
> kykladspecreg <-
> read.table(system.file("extdata","kykladspecreg.txt",package="prabclus")).


Not sure why that worked before, at least I am surprised it did; You 
have to have the package already installed before building it so that R 
can find the mentioned files.

I's suggest to generate .RData files anyway.



> R CMD build gives
> Warning in file(file, "rt") :
>    file("") only supports open = "w+" and open = "w+b": using the former
> Error in read.table(system.file("extdata", "kykladspecreg.txt", package
> = "prabclus")) :
>    no lines available in input
>
> Same if I use
> read.table(system.file("inst","extdata","kykladspecreg.txt",package="prabclus"))
>
>
> What's wrong here?
> Now what to do with the files to be read by the R-files?
> In the old days all was fine having them as dat files in the data
> directory. :-(
>
> By the way, R CMD check also produces a warning
> "* checking PDF version of manual ... WARNING
> LaTeX errors when creating PDF version.
> This typically indicates Rd problems."
> ...with no useful hint what the problemn may be whatsoever. If anyone
> has an idea how to find the problem, please tell me!



Not sure why this fails for you. We need the LaTeX output for further 
analysis of the problem.

Best,
Uwe



> Thanks,
> Christian
>
>
>
> *** --- ***
> Christian Hennig
> University College London, Department of Statistical Science
> Gower St., London WC1E 6BT, phone +44 207 679 1698
> chrish at stats.ucl.ac.uk, www.homepages.ucl.ac.uk/~ucakche
>
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