From ripley at stats.ox.ac.uk  Mon Jul  4 14:48:35 2011
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Mon, 4 Jul 2011 13:48:35 +0100 (BST)
Subject: [Rd] Recent and upcoming changes to R-devel
In-Reply-To: <4E11B218.1020600@fhcrc.org>
References: <alpine.OSX.1.00.1107041124460.59432@tystie.local>
	<4E11B218.1020600@fhcrc.org>
Message-ID: <alpine.LFD.2.02.1107041344290.25381@gannet.stats.ox.ac.uk>

On Mon, 4 Jul 2011, Martin Morgan wrote:

> On 07/04/2011 05:08 AM, Prof Brian Ripley wrote:
>> There was an R-core meeting the week before last, and various planned
>> changes will appear in R-devel over the next few weeks.
>> 
>> These are changes planned for R 2.14.0 scheduled for Oct 31. As we are
>> sick of people referring to R-devel as '2.14' or '2.14.0', that version
>> number will not be used until we reach 2.14.0 alpha. You will be able to
>> have a package depend on an svn version number when referring to R-devel
>> rather than using R (>= 2.14.0).
>> 
>> All packages are installed with lazy-loading (there were 72 CRAN
>> packages and 8 BioC packages which opted out). This means that the code
>> is always parsed at install time which inter alia simplifies the
>> descriptions. R 2.13.1 RC warns on installation about packages which ask
>> not to be lazy-loaded, and R-devel ignores such requests (with a warning).
>> 
>> In the near future all packages will have a name space. If the sources
>> do not contain one, a default NAMESPACE file will be added. This again
>> will simplify the descriptions and also a lot of internal code.
>> Maintainers of packages without name spaces (currently 42% of CRAN) are
>> encouraged to add one themselves.
>> 
>> R-devel is installed with the base and recommended packages
>> byte-compiled (the equivalent of 'make bytecode' in R 2.13.x, but done
>> less inefficiently). There is a new option
>> R CMD INSTALL --byte-compile
>> to byte-compile contributed packages, but that remains optional.
>
> Anticipating the future, contributed package byte-compilation will have large 
> effects on CRAN and especially Bioconductor build systems. For instance, a 
> moderate-sized package like Biobase built without vignettes installs in about 
> 19s with byte compilation, 9s with, while a more complicated package IRanges 
> is 1m25s, vs. 29s.

I presume the first is 'with' the second 'without'.  Yes, as I did say
'byte compilation is quite expensive', and it is not clear if it will 
ever become the default for contributed packages.

> For Bioconductor this will certainly require new hardware across all 
> supported platforms, and almost certainly significant effort to improve build 
> system efficiencies.
>
> Martin
>
>> Byte-compilation is quite expensive (so you definitely want to do it at
>> install time, which requires lazy-loading), and relatively few packages
>> benefit appreciably from byte-compilation. A larger number of packages
>> benefit from byte-compilation of R itself: for example AER runs its
>> checks 10% faster. The byte-compiler technology is thanks to Luke Tierney.
>> 
>> There is support for figures in Rd files: currently with a first-pass
>> implementation (thanks to Duncan Murdoch).
>> 
>
>
> -- 
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595



[Rd] Recent and upcoming changes to R-devel
Prof Brian Ripley