From hpages at fhcrc.org  Mon Apr 11 02:47:06 2011
From: hpages at fhcrc.org (=?ISO-8859-1?Q?Herv=E9_Pag=E8s?=)
Date: Sun, 10 Apr 2011 17:47:06 -0700
Subject: [Rd] R CMD build --resave-data
Message-ID: <4DA24F8A.7030405@fhcrc.org>

Hi,

More about the new --resave-data option

As mentioned previously here

   https://stat.ethz.ch/pipermail/r-devel/2011-April/060511.html

'R CMD build' and 'R CMD INSTALL' handle this new option
inconsistently. The former does --resave-data="gzip" by default.
The latter doesn't seem to support the --resave-data= syntax:
the --resave-data flag must either be present or not. And by
default 'R CMD INSTALL' won't resave the data.

Also, because now 'R CMD build' is resaving the data, shouldn't it
reinstall the package in order to be able to do this correctly?

Here is why. There is this new warning in 'R CMD check' that complains
about files not of a type allowed in a 'data' directory:

 
http://bioconductor.org/checkResults/2.8/bioc-LATEST/Icens/lamb1-checksrc.html

The Icens package also has .R files under data/ with things like:

   bet <- matrix(scan("CMVdata", quiet=TRUE),nc=5,byr=TRUE)

i.e. the R code needs to access some of the text files located
in the data/ folder. So in order to get rid of this warning I
tried to move those text files to inst/extdata/ and I modified
the code in the .R file so it does:

   CMVdata_filepath <- system.file("extdata", "CMVdata", package="Icens")
   bet <- matrix(scan(CMVdata_filepath, quiet=TRUE),nc=5,byr=TRUE)

But now 'R CMD build' fails to resave the data because the package
was not installed first and the CMVdata file could not be found.

Unfortunately, for a lot of people that means that the safe way to
build a source tarball now is with

   R CMD build --keep-empty-dirs --no-resave-data

I hope the list of options/flags that we need to use to "fix" 'R CMD
build' (and make it consistent with R CMD INSTALL) is not going to
grow too much ;-)

Thanks,
H.


-- 
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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P.O. Box 19024
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E-mail: hpages at fhcrc.org
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[Rd] R CMD build --resave-data
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