From murdoch.duncan at gmail.com  Tue Jul  5 15:25:45 2011
From: murdoch.duncan at gmail.com (Duncan Murdoch)
Date: Tue, 05 Jul 2011 09:25:45 -0400
Subject: [Rd] Recent and upcoming changes to R-devel
In-Reply-To: <4E12ED06.5040603@openanalytics.eu>
References: <alpine.OSX.1.00.1107041124460.59432@tystie.local>	<3D59DF35E7CF3E42BA70C23BD5CBE6A85F4C199E22@exvic-mbx04.nexus.csiro.au>
	<4E12ED06.5040603@openanalytics.eu>
Message-ID: <4E1310D9.6050901@gmail.com>

On 05/07/2011 6:52 AM, Tobias Verbeke wrote:
> L.S.
>
> On 07/05/2011 02:16 AM, Mark.Bravington at csiro.au wrote:
> >  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.
>
> I completely second this request. All speed improvements and the byte
> compiler in particular are leaps forward and I am very grateful and
> admiring towards the people that make this happen.
>
> That being said, 'moving away' from the sources (with the lazy loading
> files and byte-compilation) may be a step back for R package developers
> that (during development and maybe on separate development installations
> [as opposed to production installations of R]) require
> the sources of all packages to be efficient in their work.
>
> As many of you know there is an open source Eclipse/StatET visual
> debugger ready and for that application as well (similar to Mark's
> request) presence of non-compiled code is highly desirable.
>
> For the particular purpose of debugging R packages, I would even plead
> to go beyond the current options and support the addition of an
> R package install option that allows to include the sources (e.g. in
> a standard folder Rsrc/) in installed packages.
>
> I am fully aware that one can always fetch the source tarballs from
> CRAN for that purpose, but it would be much more easy if a simple
> installation option could put the R sources of a package in a separate
> folder [or archive inside an existing folder] such that R development
> tools (such as the Eclipse/StatET IDE) can offer inspection of sources
> or display them (e.g. during debugging) out of the box.
>
> If one has the srcref, one can always load the absolutely correct source
> code this way, even if one doesn't know the parent function with
> the source attribute.
>
> Any comments?

I think these requests have already been met.  If you modify the body of 
a closure (as trace() does), then the byte compiled version is 
discarded, and you go back to the regular interpreted code.  If you 
install packages with the R_KEEP_PKG_SOURCE=yes environment variable 
set, the you keep all source for all functions.  (It's attached to the 
function itself, not as a file that may be out of date.)  It's possible 
that byte compiling turns off R_KEEP_PKG_SOURCE, but that is something 
that is either easily fixed, or avoided by re-installing without byte 
compiling.

Duncan Murdoch

> Best,
> Tobias
>
> P.S. One could even consider a post-install option e.g. to add 'real'
> R sources (and source references) to Windows packages (which are by
> definition already 'installed' and for which such information is not
> by default included in the CRAN binaries of these packages).
>
> >>  >  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).
> >  ______________________________________________
> >  R-devel at r-project.org  mailing list
> >  https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



[Rd] Recent and upcoming changes to R-devel
Duncan Murdoch