inst and extdata folders in R Packaging
RPackageR Problem Overview
In the documentation, R suggests that raw data files (not Rdata nor Rda) should be placed in inst/extdata/
From the first paragraph in: http://cran.r-project.org/doc/manuals/R-exts.html#Data-in-packages
> The data subdirectory is for data files, either to be made available > via lazy-loading or for loading using data(). (The choice is made by > the ‘LazyData’ field in the DESCRIPTION file: the default is not to do > so.) It should not be used for other data files needed by the package, > and the convention has grown up to use directory inst/extdata for such > files.
So, I have moved all of my raw data into this folder, but when I build and reload the package and then try to access the data in a function with (for example):
read.csv(file=paste(path.package("my_package"),"/inst/extdata/my_raw_data.csv",sep=""))
# .path.package is now path.package in R 3.0+
I get the "cannot open file" error.
However, it does look like there is a folder called /extdata
in the package directory with the files in it (post-build and install). What's happening to the /inst
folder?
Does everything in the /inst folder get pushed into the /
of the package?
R Solutions
Solution 1 - R
More useful than using file.path
would be to use system.file
. Once your package is installed, you can grab your file like so:
fpath <- system.file("extdata", "my_raw_data.csv", package="my_package")
fpath
will now have the absolute path on your HD to the file.
Solution 2 - R
You were both very close and essentially had this. A formal reference from 'Writing R Extensions' is:
> 1.1.3 Package subdirectories
>
> [...]
>
> The contents of the inst
subdirectory will be copied recursively
> to the installation directory. Subdirectories of inst
should not
> interfere with those used by R (currently, R
, data
, demo
,
> exec
, libs
, man
, help
, html
and Meta
, and earlier versions
> used latex
, R-ex
). The copying of the inst
happens after src
> is built so its Makefile
can create files to be installed. Prior to
> R 2.12.2, the files were installed on POSIX platforms with the permissions in the package sources, so care should be taken to ensure
> these are not too restrictive: R CMD build
will make suitable
> adjustments. To exclude files from being installed, one can specify a
> list of exclude patterns in file .Rinstignore
in the top-level
> source directory. These patterns should be Perl-like regular
> expressions (see the help for regexp
in R for the precise details),
> one per line, to be matched(10) against the file and directory paths,
> e.g. doc/.*[.]png$
will exclude all PNG files in inst/doc
based on
> the (lower-case) extension.