Re: [Rd] R 2.1.1 slated for June 20

From: Martyn Plummer <plummer_at_iarc.fr>
Date: Thu 16 Jun 2005 - 15:46:56 GMT

On Thu, 2005-06-16 at 12:41 +0100, Prof Brian Ripley wrote:
> On Thu, 16 Jun 2005, Martyn Plummer wrote:
>
> > On Tue, 2005-06-14 at 17:07 -0500, Marc Schwartz wrote:
> >> On Tue, 2005-06-14 at 23:52 +0200, Peter Dalgaard wrote:
> >>> Marc Schwartz <MSchwartz@mn.rr.com> writes:
> >>>
> >>>> On Fri, 2005-06-10 at 14:57 +0100, Prof Brian Ripley wrote:
> >>>>> On Fri, 10 Jun 2005, Peter Dalgaard wrote:
> >>>>>
> >>>>>> The next version of R will be released (barring force majeure) on June
> >>>>>> 20th, with beta versions available starting Monday.
> >>>>>>
> >>>>>> Please do check them on your system *before* the release this time...
> >>>>>
> >>>>> Some things which it would be particularly helpful to have tested:
> >>>>
> >>>>
> >>>>> - Bleeding-edge OSes, e.g. anyone running Fedora Core 4 test 3? (These
> >>>>> often show up problems with bugs in the pre-release versions of
> >>>>> components such as X11 and compilers.)
> >>>>
> >>>>
> >>>> Just as a quick heads up, I installed FC4 Release ("Stentz") late
> >>>> yesterday.
> >>>>
> >>>> R (Version 2.1.1 beta (2005-06-14)) compiles fine using:
> >>>>
> >>>> $ gcc --version
> >>>> gcc (GCC) 4.0.0 20050519 (Red Hat 4.0.0-8)
> >>>>
> >>>> and make check-all passes with no problems.
> >>>>
> >>>> I have also installed all CRAN packages that do not require other 3rd
> >>>> party drivers, etc. and there were no observed errors in those cases.
> >>>>
> >>>> So far, so good.
> >>>>
> >>>> If anything comes up, I will post a follow up.
> >>>>
> >>>> Best regards,
> >>>>
> >>>> Marc Schwartz
> >>>
> >>> Yep. Just tried the same on AMD64 (I had a bit of a fight converting
> >>> my SuSE setup -- FC4 is quite unhappy about ReiserFS for some reason).
> >>> A couple of f95 warnings whooshed by during the compile, that was all.
> >>>
> >>> By the way, I noticed that you can now "yum install R R-devel" and get
> >>> everything straight from Fedora Extras.
> >>
> >> Yep. Tom "Spot" Callaway is the FE maintainer for R.
> >
> > I had a look at his RPM last night. It includes a patch for gcc4, which
> > fails to build R with the fairly aggressive optimizations used by
> > rpmbuild. ("-O2 -D_FORTIFY_SOURCE=2" will reproduce the bug, IIRC, but
> > I'm not upgrading my work PC just yet, so I can't be sure). I folded
> > this into R-patched. It's a shame he didn't send a bug report or, if he
> > did, I missed it.
>
> Looks to me that this is bug in gcc4, not in R. (It's not actually an
> optimization.) I've resisted making any such changes until gcc 4.0.1 is
> released - and that is held up on some outstanding bug fixes.
>
> (BTW, it is a really good idea to put a comment in the file as to why
> unnecessary parentheses have been added.)

Mea culpa.

I have asked Tom Callaway whether this was intended as a bug-fix for R or a workaround.

> It's a shame FC4 does not contain a well-tested high-quality compiler like
> 3.4.4 or 3.3.6, especially a well-tested high-quality Fortran compiler.

That's not what Fedora is for, as I was discussing with Marc. Fedora users are willing (although perhaps unthinking) participants in Red Hat's beta testing cycle. By the time the bleeding-edge technology in Fedora gets to Red Hat's paying customers, it is well-tested and highquality.

> > I also note he is using the patch that sets LANG=C, which is obsolete
> > now that R supports utf-8 locales. I'll write to him (cc Marc) to let
> > him know about these changes.
> >
> > The RedHat RPMS also use the shared library version of R. I've been
> > thinking about making this change myself, despite the substantial speed
> > penalty, since I've seen a growing number of people recompiling to get
> > the shared library. The Red Hat choice forces my hand though: I don't
> > want people upgrading from their R 2.1.0 to my R 2.1.1 and finding their
> > installed packages don't work anymore. The $64,000 question is how many
> > people are going to care about that 15-20% decrease in speed. Speak up
> > now if it concerns you.
>
> Well, if they do they will also care about the 5-10% or so that gcc4 costs
> them over 3.4.4 and so will not want your RPM.

That would depend on how I compile it. I'm quite happy to maintain an R-static RPM for people who feel the need for speed. But I don't know if there is a demand. I see that the Debian package uses the shared library.

> BTW, I find 15-20% on i686, 10-15 on x86_64, and I have no idea about PPC.
> (That warning about
>
> dotcode.c:96: warning: ISO C forbids assignment between function pointer and `void *'
>
> is supposed to be serious on PPC64 where a function pointer is really a
> different sort of object. FC4 claims to support 64-bit PPC, but it is not
> clear that this is actually a 64-bit OS.) gcc4 has features we can use to
> narrow the gap but first it has to work reliably.
>
> --
> Brian D. Ripley, ripley@stats.ox.ac.uk
> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
> University of Oxford, Tel: +44 1865 272861 (self)
> 1 South Parks Road, +44 1865 272866 (PA)
> Oxford OX1 3TG, UK Fax: +44 1865 272595



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