[Rd] Recent and upcoming changes to R-devel

Martin Morgan mtmorgan at fhcrc.org
Mon Jul 4 14:29:12 CEST 2011

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.


> 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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