From stephan.wahlbrink at walware.de  Wed Jul  6 09:46:25 2011
From: stephan.wahlbrink at walware.de (Stephan Wahlbrink)
Date: Wed, 06 Jul 2011 09:46:25 +0200
Subject: [Rd] Recent and upcoming changes to R-devel
In-Reply-To: <4E132BFD.5090604@gmail.com>
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>
	<4E132BFD.5090604@gmail.com>
Message-ID: <4E1412D1.2040700@walware.de>

Duncan Murdoch wrote [2011-07-05 17:21]:
> 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.

Perfect! And which version (byte-compiled or expressions) is used at 
runtime under which condition?

Thanks,
Stephan


>> 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
Stephan Wahlbrink