Re: [Rd] Recent and upcoming changes to R-devel

From: Duncan Murdoch <murdoch.duncan_at_gmail.com>
Date: Tue, 05 Jul 2011 11:21:33 -0400

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
>



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