From murdoch.duncan at gmail.com  Tue Jul  5 17:21:33 2011
From: murdoch.duncan at gmail.com (Duncan Murdoch)
Date: Tue, 05 Jul 2011 11:21:33 -0400
Subject: [Rd] Recent and upcoming changes to R-devel
In-Reply-To: <4E132BA0.5000003@walware.de>
References: <alpine.OSX.1.00.1107041124460.59432@tystie.local>	<3D59DF35E7CF3E42BA70C23BD5CBE6A85F4C199E22@exvic-mbx04.nexus.csiro.au>
	<4E12ED06.5040603@openanalytics.eu>
	<4E1310D9.6050901@gmail.com> <4E132BA0.5000003@walware.de>
Message-ID: <4E132BFD.5090604@gmail.com>

On 05/07/2011 11:20 AM, Stephan Wahlbrink wrote:
> Dear developers,
>
> Duncan Murdoch wrote [2011-07-05 15:25]:
> >  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.
>
> I don?t know how the new installation works exactly, but would it be
> possible, to simply install both types, the old expression bodies and
> the new byte-compiled, as single package at the same time?

Yes, that's what is done.
>   This would
> allow the R user and developer to simply use the variant which is the
> best at the moment. If he wants to debug code, he can switch of the use
> of byte-compiled code  and use the old R expressions (with attached
> srcrefs). If debugging is not required, he can profit from the
> byte-compiled version. The best would be a toggle, to switch it at
> runtime, but a startup option would be sufficient too.
>
> I think direct access to the code is one big advantage of open source
> software. For developer it makes it easier to find and fix bugs if
> something is wrong. But it can also help users a lot to understand how a
> function or algorithm works and learn from code written by other persons
> ? if the access to the sources is easy.
>
> As long byte-code doesn?t support the debugging features of R, it is
> required for best debugging support to run the functions completely
> without byte-complied code. If I understood it correctly, byte-code
> frames would disable srcrefs as well as features like ?step return? to
> that frames. Therefore I ask for a way that it is easy to switch between
> both execution types.

What gave you that impression?

Duncan Murdoch

> Best,
> Stephan
>
>
> >
> >  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).
>
> --
> Stephan Wahlbrink
> Humboldtstr. 19
> 44137 Dortmund
> Germany
> http://www.walware.de/goto/opensource
>



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