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

From: Duncan Murdoch <murdoch.duncan_at_gmail.com>
Date: Tue, 05 Jul 2011 10:21:51 -0400

On 05/07/2011 10:17 AM, Tobias Verbeke wrote:
> Dear Duncan,
>
> On 07/05/2011 03:25 PM, Duncan Murdoch wrote:
> > 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.
>
> Many thanks for your reaction. Is the R_KEEP_PKG_SOURCE=yes environment
> variable also supported during R installation ?

Yes, other than the error you saw below, which is a temporary problem. Not sure which function exceeded the length limit, but the length limit is going away before 2.14.0 is released.

Duncan Murdoch

> I hope I'm not overlooking anything, but when compiling
>
>
ftp://ftp.stat.math.ethz.ch/Software/R/R-devel.tar.gz
>
> a few minutes ago I encountered the following issue:
>
> [...]
>
> building package 'tools'
> mkdir -p -- ../../../library/tools
> make[4]: Entering directory `/home/tobias/rAdmin/R-devel/src/library/tools'
> mkdir -p -- ../../../library/tools/R
> mkdir -p -- ../../../library/tools/po
> make[4]: Leaving directory `/home/tobias/rAdmin/R-devel/src/library/tools'
> make[4]: Entering directory `/home/tobias/rAdmin/R-devel/src/library/tools'
> make[5]: Entering directory
> `/home/tobias/rAdmin/R-devel/src/library/tools/src'
> making text.d from text.c
> making init.d from init.c
> making Rmd5.d from Rmd5.c
> making md5.d from md5.c
> gcc -std=gnu99 -I../../../../include -I/usr/local/include
> -fvisibility=hidden -fpic -g -O2 -c text.c -o text.o
> gcc -std=gnu99 -I../../../../include -I/usr/local/include
> -fvisibility=hidden -fpic -g -O2 -c init.c -o init.o
> gcc -std=gnu99 -I../../../../include -I/usr/local/include
> -fvisibility=hidden -fpic -g -O2 -c Rmd5.c -o Rmd5.o
> gcc -std=gnu99 -I../../../../include -I/usr/local/include
> -fvisibility=hidden -fpic -g -O2 -c md5.c -o md5.o
> gcc -std=gnu99 -shared -L/usr/local/lib64 -o tools.so text.o init.o
> Rmd5.o md5.o -L../../../../lib -lR
> make[6]: Entering directory
> `/home/tobias/rAdmin/R-devel/src/library/tools/src'
> make[6]: `Makedeps' is up to date.
> make[6]: Leaving directory
> `/home/tobias/rAdmin/R-devel/src/library/tools/src'
> make[6]: Entering directory
> `/home/tobias/rAdmin/R-devel/src/library/tools/src'
> mkdir -p -- ../../../../library/tools/libs
> make[6]: Leaving directory
> `/home/tobias/rAdmin/R-devel/src/library/tools/src'
> make[5]: Leaving directory
> `/home/tobias/rAdmin/R-devel/src/library/tools/src'
> make[4]: Leaving directory `/home/tobias/rAdmin/R-devel/src/library/tools'
> Error in parse(n = -1, file = file) :
> function is too long to keep source (at line 2967)
> Error: unable to load R code in package ‘tools’
> Execution halted
>
> [...]
>
> tobias_at_openanalytics:~/rAdmin$ echo $R_KEEP_PKG_SOURCE
> yes
>
> I do not have this issue when R_KEEP_PKG_SOURCE is set
> to 'false' during compilation.
>
> 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
> >
>



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https://stat.ethz.ch/mailman/listinfo/r-devel Received on Tue 05 Jul 2011 - 14:24:32 GMT

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