R devel - Jul 2011 - Recent and upcoming changes to R-devel

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. 
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).

-- 
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

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).
>

-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793

I may have misunderstood, but: 

Please could we have an optional installation that does not *not* byte-compile
base and recommended?

Reason: it's not possible to debug byte-compiled code-- at least not with
the 'debug' package, which is quite widely used. I quite often end up
using 'mtrace' on functions in base/recommended packages to figure out
what they are doing. And sometimes I (and others) experiment with changing
functions in base/recommended to improve functionality. That seems to be harder
with BC versions, and might even be impossible, as best I can tell from hints in
the documentation of 'compile').

Personally, if I had to choose only one, I'd rather live with the speed
penalty from not byte-compiling. But of course, if both are available, I could
install both.

Thanks

Mark

-- 
Mark Bravington
CSIRO Mathematical & Information Sciences
Marine Laboratory
Castray Esplanade
Hobart 7001
TAS

ph (+61) 3 6232 5118
fax (+61) 3 6232 5012
mob (+61) 438 315 623

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.    
> 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).

On Mon, Jul 4, 2011 at 8:08 AM, Prof Brian Ripley <ripley at
stats.ox.ac.uk> wrote:
> 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.
This is great.  However, it would also be great if a user could
disable this for a given package at install time, for example with a
command line argument to R CMD INSTALL.  Use case: in the early stages
of package development I find it incredible useful to not have a
NAMESPACE.  This is of course before I release it to anyone else;
purely for development.

My guess is that this has already been anticipated, but in case not, I
wanted to raise the issue.

Kasper

Hi,

On 11-07-04 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.
Now with R-devel r56301:

   > R.version.string
   [1] "R Under development (unstable) (2011-07-06 r56301)"

But:

   > R.Version()[c("major", "minor")]
   $major
   [1] "2"

   $minor
   [1] "14.0"

   > R.version[c("major", "minor")]
       _
   major 2
   minor 14.0

Not sure what's the benefit...
> 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).
Isn't it that R 2.13 patched and R devel share the same svn version
numbers? So using something like R (>= r56301) doesn't actually mean
anything.

Cheers,
H.
>
> 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.
> 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).
>

-- 
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319