[Rd] Warning: you may need to use R-patched with recent R distros
Dominick Samperi
djsamperi at gmail.com
Wed Feb 2 16:39:37 CET 2011
On Wed, Feb 2, 2011 at 6:03 AM, Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:
> On Wed, 2 Feb 2011, Simone Giannerini wrote:
>
>> I see the problem on my OpenSuse 11.3 box
>>
>> gcc (SUSE Linux) 4.5.0 20100604 [gcc-4_5-branch revision 160292]
>>
>> > sessionInfo()
>> R version 2.12.1 Patched (2011-01-10 r53953)
>
> Please update this and let us know if it persists with current R-patched.
>
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> DS failed to tell us his platform, and maybe it was not x86_64.
It is x86_64, to be precise:
Linux 2.6.35.10-74.fc14.x86_64 #1 SMP Thu Dec 23 16:04:50 UTC 2010
I tested against released R-2.12.1 and R-devel trunk (latest yesterday).
>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> > z <- 0.2853725+0.3927816i
>> > z2 <- z^(1:20)
>> > z3 <- z^-(1:20)
>> > z0 <- cumprod(rep(z, 20))
>> > stopifnot(all.equal(z2, z0), all.equal(z3, 1/z0))
>> Error: all.equal(z2, z0) is not TRUE
>>
>> Simone
>>
>>
>> On Wed, Feb 2, 2011 at 1:45 AM, Dominick Samperi <djsamperi at gmail.com>
>> wrote:
>> On Mon, Jan 31, 2011 at 3:18 PM, Prof Brian Ripley
>> <ripley at stats.ox.ac.uk> wrote:
>> > On Mon, 31 Jan 2011, Ken.Williams at thomsonreuters.com wrote:
>> >
>> >> For the complex-numbers bug, do you know a reliable way (besides
>> looking
>> >> at version numbers) to determine whether the bug is present or
>> absent in a
>> >> given build?
>> >
>> > I know a way: See tests/complex.R in R-devel.
>> >
>> > z <- 0.2853725+0.3927816i
>> > z2 <- z^(1:20)
>> > z3 <- z^-(1:20)
>> > z0 <- cumprod(rep(z, 20))
>> > stopifnot(all.equal(z2, z0), all.equal(z3, 1/z0))
>> > ## z^3 had value z^2 ....
>> >
>>
>> I tried this under Fedora 14 (GCC 4.5.1) using the released R 2.12.1
>> and
>> R-devel (2.13.0 devel) and saw no problems? I compared the numbers
>> with
>> those generated by Octave, took the cube root of z^3 and got z, ran
>> this
>> unit test and stopifnot did not terminate, etc.
>>
>> At build time the optimization level was O2.
>>
>> Dominick
>>
>> >>
>> >> I don't know what version of gcc was used in my build nor the
>> optimization
>> >> flags, so I did a few test exponentiations z^n and the results look
>> okay,
>> >> but maybe I'm not tickling the right bits.
>> >>
>> >>
>> >> --
>> >> Ken Williams
>> >> Senior Research Scientist
>> >> Thomson Reuters
>> >> Phone: 651-848-7712
>> >> ken.williams at thomsonreuters.com
>> >> http://labs.thomsonreuters.com
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> On 1/31/11 1:48 PM, "Prof Brian Ripley" <ripley at stats.ox.ac.uk>
>> wrote:
>> >>
>> >>> Two things have emerged in testing on x86_64 Fedora 14 which mean
>> that
>> >>> a recent R-patched is probably needed.
>> >>>
>> >>> 1) That OS uses zlib 1.2.5: that claims to be binary-compatible
>> with
>> >>> zlib 1.2.3 but is not, as we found (painfully) on Windows. The
>> remedy
>> >>> was to remap _all_ the symbols in R's own copy of zlib (not just
>> those
>> >>> zlib arranged to remap).
>> >>>
>> >>> The symptoms were crashes using packages XML and rgoobi (both of
>> which
>> >>> link to zlib) and incorrect results in RJaCGH (which contains a
>> copy
>> >>> of zlib). There may well be other problems ....
>> >>>
>> >>> 2) Fedora 14 uses gcc 4.5.1. With CFLAGS containing the default
>> -O2
>> >>> or higher, HAVE_C99_COMPLEX was detected as false because there is
>> a
>> >>> (genuine) incompatibility between types Rcomplex and C99's double
>> >>> complex. This means that R's fallback code is used, and
>> regretably
>> >>> that contains a serious bug in an 'optimization' by a colleague,
>> so
>> >>> z^n is incorrect for most complex z and integer n (and has been
>> since
>> >>> 2.10.0). The remedy is to use R-patched or R-devel, or only
>> optimize
>> >>> to -O.
>> >>>
>> >>> We've also seen incorrect results from package mvtnorm when C
>> >>> optimization was -O3.
>> >>>
>> >>> The upshot is that there is likely to be a 2.12.2 to fix these
>> issues.
>> >>>
>> >>> --
>> >>> 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
>> >>>
>> >>> ______________________________________________
>> >>> R-devel at r-project.org mailing list
>> >>> https://stat.ethz.ch/mailman/listinfo/r-devel
>> >>>
>> >>
>> >>
>> >
>> > --
>> > 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
>> >
>> > ______________________________________________
>> > 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
>>
>>
>>
>>
>> --
>> ______________________________________________________
>>
>> Simone Giannerini
>> Dipartimento di Scienze Statistiche "Paolo Fortunati"
>> Universita' di Bologna
>> Via delle belle arti 41 - 40126 Bologna, ITALY
>> Tel: +39 051 2098262 Fax: +39 051 232153
>> http://www2.stat.unibo.it/giannerini/
>> ______________________________________________________
>>
>>
>
> --
> 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
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
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