From plummer at iarc.fr  Thu Jun 16 17:46:56 2005
From: plummer at iarc.fr (Martyn Plummer)
Date: Thu, 16 Jun 2005 17:46:56 +0200
Subject: [Rd] R 2.1.1 slated for June 20
In-Reply-To: <Pine.LNX.4.61.0506161224300.25129@gannet.stats>
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Message-ID: <1118936816.3651.91.camel@seurat>

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 at 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 high-
quality.

> > 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 at 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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[Rd] R 2.1.1 slated for June 20
Martyn Plummer