From mtmorgan at fhcrc.org  Mon Jul  4 14:29:12 2011
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Mon, 04 Jul 2011 05:29:12 -0700
Subject: [Rd] Recent and upcoming changes to R-devel
In-Reply-To: <alpine.OSX.1.00.1107041124460.59432@tystie.local>
References: <alpine.OSX.1.00.1107041124460.59432@tystie.local>
Message-ID: <4E11B218.1020600@fhcrc.org>

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.

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).
>


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[Rd] Recent and upcoming changes to R-devel
Martin Morgan