[Rd] R Startup configuration file

Henrik Bengtsson hb at stat.berkeley.edu
Fri Feb 12 16:27:35 CET 2010


a while ago I was looking into the "problem" with generic settings
files.  I didn't find an omnibus/perfect solution, but have a look at
the Settings class in the R.utils package (R/Settings.R in the source
code).  It tries to deal with automatic loading and saving of settings
(robust detection of the quiting of an R session etc), finding the
settings file and so.  You can use this to load package specific
settings as well.  (We make use of this in the aroma.* framework
(aroma.core, aroma.affymetrix etc), but I'll leave there for now).

My $.02


On Fri, Feb 12, 2010 at 3:22 PM, Simon Urbanek
<simon.urbanek at r-project.org> wrote:
> On Feb 12, 2010, at 3:50 , Barry Rowlingson wrote:
>> On Wed, Feb 10, 2010 at 3:06 PM, Barry Rowlingson
>> <b.rowlingson at lancaster.ac.uk> wrote:
>>>  But I agree that writing a saveable options package is the first step
>>> - then making that a default in R is the second so people don't have
>>> to edit profiles and R packages and applications can expect an API for
>>> savable state.
>> More thinking about this has turned it into a problem of being able
>> to serialize R objects to XML.
> This is getting OT, but, please, no XML. It's entirely useless in this
> context IMHO (as it is in others, but that's another story) and we already
> have reliable support for storing R objects (more than one in fact). Despite
> the fact that some used to claim human readability of XML in practice it
> turns out to be false, so I don't see any real benefits of XML in this
> context.
> Cheers,
> Simon
>> The most reliable way I can find of
>> doing that is to use serialize, then rawToChar, and put a big old hex
>> string in the XML. Hardly the most user-friendly format, but then
>> users aren't supposed to edit XML anyway. I have also considered
>> having encoding types for objects, something like:
>> <object encoding="raw" name="foo">66f6e.....a7726</object>
>> <object encoding="numeric" name="bar">3.141</object>
>> <object encoding="numeric" size="2"
>> name="baz"><item>3.14</item><item>6.28</item></object>
>> at which point I remembered that R objects can also have attributes
>> which can be any other R objects too. At which point I realized life's
>> too short for this...
>> ..and had a rethink. Lots of software these days has a configuration
>> directory, and runs all the scripts or configs within - think
>> /etc/cron.daily/ or /etc/init.d on a unix system. This has the
>> advantage that components of the system can manage their own startup
>> files there, and not worry about stomping on others. So you'd have a
>> .Rprofile.d/ folder with, say, a cran.R file that could be sourced by
>> anything that used CRAN, for example to set the default mirror. I'd
>> insist that each file in .Rprofile.d/ started with a "# do not edit
>> this file" warning...
>> I'll think some more over coffee until I realise why this is another
>> of my dumb ideas...
>> Barry
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