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

From: Duncan Murdoch <murdoch.duncan_at_gmail.com>
Date: Tue, 05 Jul 2011 09:25:45 -0400

On 05/07/2011 6:52 AM, Tobias Verbeke wrote:
> L.S.
>
> On 07/05/2011 02:16 AM, Mark.Bravington@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
> >
>
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