[Rd] R 2.3.0 (alpha) on FreeBSD 6.1 fails make check-all
Andrew Robinson
A.Robinson at ms.unimelb.edu.au
Wed Mar 29 02:05:59 CEST 2006
I tried it. That is, in qhyper.c I replaced
p *= 1 - 64*DBL_EPSILON;
with
p *= 1 - 1000*DBL_EPSILON;
and recompiled. 2.3.0 alpha now passses make check-all and returns
sensible results on both of my FreeBSD 6.1 machines.
> Rhyper <- 1:20
> Phyper <- phyper (Rhyper, m = 40, n = 30, k = 20)
> qhyper(Phyper, m = 40, n = 30, k = 20)
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Thanks very much for your guidance, this has been educational. Is
there anything else that I should check?
On Tue, Mar 28, 2006 at 01:53:09PM +0100, Prof Brian Ripley wrote:
> qgamma.c comtains the line
>
> p *= 1 - 64*DBL_EPSILON;
>
> which seems to be too small nowadays. I find for example
>
> >p <- phyper(7, m = 40, n = 30, k = 20)
> >
> >qhyper(p*(1+5e-16), m = 40, n = 30, k = 20)
> [1] 7
> >qhyper(p*(1+6e-16), m = 40, n = 30, k = 20)
> [1] 8
>
> so it seems far more sensitive than the tolerance indicates is intended.
> Now, phyper has been changed since that tolerance was added, and that
> may be part of the explanation.
>
> Can you try a larger tolerance, e.g 1000?
>
> A better fix is probably not to use a tolerance but rather to do a
> downwards search using phyper.
>
>
> On Tue, 28 Mar 2006, Andrew Robinson wrote:
>
> >This is from 2.2.1:
> >
> >>Phyper <- phyper(7, m = 40, n = 30, k = 20)
> >>print(Phyper, digits=16)
> >[1] 0.01796062766370490
> >
> >This is from 2.3.0:
> >
> >>Phyper <- phyper(7, m = 40, n = 30, k = 20)
> >>print(Phyper, digits=16)
> >[1] 0.01796062766370491
> >
> >>qhyper(Phyper, m = 40, n = 30, k = 20)
> >[1] 8
> >
> >Then if I save Phyper from 2.2.1, and load it in 2.3.0,
> >
> >>qhyper(Phyper, m = 40, n = 30, k = 20)
> >[1] 7
> >
> >so it appears that the difference between 0.01796062766370490 and
> >0.01796062766370491 is important here.
> >
> >(2.3.0)
> >
> >>qhyper(0.01796062766370490, m = 40, n = 30, k = 20)
> >[1] 7
> >>qhyper(0.01796062766370491, m = 40, n = 30, k = 20)
> >[1] 8
> >
> >
> >
> >Comparing the full sample:
> >
> >This is from 2.2.1:
> >
> >>Rhyper <- scan()
> >1: 16 11 11 15 11 13 13 12 13 10 10 7 11 14 13 9 14 13 13 11
> >21:
> >Read 20 items
> >>Phyper <- phyper (Rhyper, m = 40, n = 30, k = 20)
> >>print(Phyper, digits=16)
> >[1] 0.99744478362220412 0.51295659016196715 0.51295659016196715
> >[4] 0.98680472393309626 0.51295659016196715 0.86627412777488222
> >[7] 0.86627412777488222 0.71494883441868140 0.86627412777488222
> >[10] 0.30864259597126753 0.30864259597126753 0.01796062766370490
> >[13] 0.51295659016196715 0.95139460528774533 0.86627412777488222
> >[16] 0.15132082044442866 0.95139460528774533 0.86627412777488222
> >[19] 0.86627412777488222 0.51295659016196715
> >
> >
> >
> >This is from 2.3.0:
> >
> >>print(Phyper, digits=16)
> >[1] 0.99744478362220401 0.51295659016196726 0.51295659016196726
> >[4] 0.98680472393309615 0.51295659016196726 0.86627412777488211
> >[7] 0.86627412777488211 0.71494883441868129 0.86627412777488211
> >[10] 0.30864259597126747 0.30864259597126747 0.01796062766370491
> >[13] 0.51295659016196726 0.95139460528774533 0.86627412777488211
> >[16] 0.15132082044442868 0.95139460528774533 0.86627412777488211
> >[19] 0.86627412777488211 0.51295659016196726
> >
> >
> >The 14's (elements 14 and 17) are identical, everything else is
> >slightly different.
> >
> >
> >I also got this interesting result from 2.2.1:
> >
> >
> >>Rhyper <- 1:20
> >>Phyper <- phyper (Rhyper, m = 40, n = 30, k = 20)
> >>qhyper(Phyper, m = 40, n = 30, k = 20)
> >[1] 1 2 3 4 6 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
> >
> >
> >Repeating the operation for 2.3.0:
> >
> >
> >>Rhyper <- 1:20
> >>Phyper <- phyper (Rhyper, m = 40, n = 30, k = 20)
> >>qhyper(Phyper, m = 40, n = 30, k = 20)
> >[1] 1 2 3 4 6 6 8 8 9 10 11 12 13 14 15 16 17 18 19 20
> >
> >
> >(I also tried on WinXP R 2.2.1, and got the expected 1:20 back.)
> >
> >
> >On Tue, Mar 28, 2006 at 12:02:11PM +0100, Prof Brian Ripley wrote:
> >>Then we need you to dig in to find out why. I'd start by seeing if Phyper
> >>had changed (either by printing it to 16dp or by saving it from 2.2.1 and
> >>reloading into 2.3.0).
> >>
> >>On Tue, 28 Mar 2006, Andrew Robinson wrote:
> >>
> >>>I get:
> >>>
> >>>>Rhyper <- scan()
> >>>1: 16 11 11 15 11 13 13 12 13 10 10 7 11 14 13 9 14 13 13 11
> >>>21:
> >>>Read 20 items
> >>>>Phyper <- phyper (Rhyper, m = 40, n = 30, k = 20)
> >>>>qhyper(Phyper, m = 40, n = 30, k = 20)
> >>>[1] 16 11 11 15 11 13 13 12 13 10 10 8 11 14 13 9 14 13 13 11
> >>>
> >>>
> >>>The 12th element (8) differs from the input (7).
> >>>
> >>>
> >>>>Phyper <- phyper (7, m = 40, n = 30, k = 20)
> >>>>qhyper(Phyper, m = 40, n = 30, k = 20)
> >>>[1] 8
> >>>
> >>>
> >>>If I do this using 2.2.1 then the input and the output are identical.
> >>>
> >>>
> >>>
> >>>
> >>>On Tue, Mar 28, 2006 at 10:27:08AM +0100, Prof Brian Ripley wrote:
> >>>>On Tue, 28 Mar 2006, Andrew Robinson wrote:
> >>>>
> >>>>>You're welcome. You are correct. d-p-q-r-tests.Rout.fail
> >>>>>shows:
> >>>>>
> >>>>>>All.eq(Rhyper, qhyper (Phyper, m = 40, n = 30, k = 20))
> >>>>>[1] "Mean scaled difference: 0.08333333"
> >>>>
> >>>>Yes, please run the lines below, e.g.
> >>>>
> >>>>Rhyper <- scan()
> >>>>16 11 11 15 11 13 13 12 13 10 10 7 11 14 13 9 14 13 13 11
> >>>>
> >>>>Phyper <- phyper (Rhyper, m = 40, n = 30, k = 20)
> >>>>qhyper(Phyper, m = 40, n = 30, k = 20)
> >>>>
> >>>>and tell us what answer you get.
> >>>>
> >>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>Let me know if/how I can further assist.
> >>>>>
> >>>>>Andrew
> >>>>>
> >>>>>
> >>>>>
> >>>>>On Tue, Mar 28, 2006 at 09:03:48AM +0100, Prof Brian Ripley wrote:
> >>>>>>Thanks for checking.
> >>>>>>
> >>>>>>Please look in d-p-q-r-tests.Rout.fail and see what immediately
> >>>>>>preceeds
> >>>>>>the line
> >>>>>>
> >>>>>>[1] "Mean scaled difference: 0.08333333"
> >>>>>>
> >>>>>>Some experimentation suggests it is
> >>>>>>
> >>>>>>>All.eq(Rhyper, qhyper (Phyper, m = 40, n = 30, k = 20))
> >>>>>>
> >>>>>>If so, we have
> >>>>>>
> >>>>>>Rhyper <- scan()
> >>>>>>16 11 11 15 11 13 13 12 13 10 10 7 11 14 13 9 14 13 13 11
> >>>>>>
> >>>>>>Phyper <- phyper (Rhyper, m = 40, n = 30, k = 20)
> >>>>>>
> >>>>>>and those have been checked. So the error would appear to be in
> >>>>>>
> >>>>>>qhyper(Phyper, m = 40, n = 30, k = 20)
> >>>>>>
> >>>>>>and indeed a mean scaled difference of 1/12 is plausible, since the
> >>>>>>mean
> >>>>>>of Rhyper is 12. So I deduce that your platform has a problem in
> >>>>>>qhyper,
> >>>>>>but please cross-check.
> >>>>>>
> >>>>>>If so, this is strange as the only recent change to qhyper.c (or
> >>>>>>things
> >>>>>>I
> >>>>>>can see it uses such as lfastchoose) is cosmetic.
> >>>>>>
> >>>>>>Can you confirm the diagnosis is correct so far?
> >>>>>>
> >>>>>>
> >>>>>>On Tue, 28 Mar 2006, Andrew Robinson wrote:
> >>>>>>
> >>>>>>>Hi Developers,
> >>>>>>>
> >>>>>>>The alpha, compiles successfully, but it is failing make check-all
> >>>>>>>(on
> >>>>>>>two seperate machines, both FreeBSD 6.1).
> >>>>>>>
> >>>>>>>Here is the version string:
> >>>>>>>
> >>>>>>>platform i386-unknown-freebsd6.1
> >>>>>>>arch i386
> >>>>>>>os freebsd6.1
> >>>>>>>system i386, freebsd6.1
> >>>>>>>status alpha
> >>>>>>>major 2
> >>>>>>>minor 3.0
> >>>>>>>year 2006
> >>>>>>>month 03
> >>>>>>>day 27
> >>>>>>>svn rev 37584
> >>>>>>>language R
> >>>>>>>version.string Version 2.3.0 alpha (2006-03-27 r37584)
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>Here is the error message from make check-all
> >>>>>>>
> >>>>>>>comparing 'd-p-q-r-tests.Rout' to './d-p-q-r-tests.Rout.save'
> >>>>>>>...706c706
> >>>>>>>< [1] "Mean scaled difference: 0.08333333"
> >>>>>>>---
> >>>>>>>>[1] TRUE
> >>>>>>>gmake[3]: *** [d-p-q-r-tests.Rout] Error 1
> >>>>>>>gmake[3]: Leaving directory `/usr/local/beta/R-alpha/tests'
> >>>>>>>gmake[2]: *** [test-Specific] Error 2
> >>>>>>>gmake[2]: Leaving directory `/usr/local/beta/R-alpha/tests'
> >>>>>>>gmake[1]: *** [test-all-basics] Error 1
> >>>>>>>gmake[1]: Leaving directory `/usr/local/beta/R-alpha/tests'
> >>>>>>>gmake: *** [check-all] Error 2
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>I have checked d-p-q-r-tests.Rout.fail for any obvious problems - I
> >>>>>>>found some warnings, viz.
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>>pgamma(1,Inf,scale=Inf) == 0
> >>>>>>>[1] TRUE
> >>>>>>>>## Also pgamma(Inf,Inf) == 1 for which NaN was slightly more
> >>>>>>>appropriate
> >>>>>>>>all(is.nan(c(pgamma(Inf, 1,scale=Inf),
> >>>>>>>+ pgamma(Inf,Inf,scale=Inf))))
> >>>>>>>[1] TRUE
> >>>>>>>Warning messages:
> >>>>>>>1: NaNs produced in: pgamma(q, shape, scale, lower.tail, log.p)
> >>>>>>>2: NaNs produced in: pgamma(q, shape, scale, lower.tail, log.p)
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>>x0 <- -2 * 10^-c(22,10,7,5)
> >>>>>>>>stopifnot(pbinom(x0, size = 3, prob = 0.1) == 0,
> >>>>>>>+ dbinom(x0, 3, 0.1) == 0) # d*() warns about non-integer
> >>>>>>>Warning messages:
> >>>>>>>1: non-integer x = -0.000000
> >>>>>>>2: non-integer x = -0.000020
> >>>>>>>>## very small negatives were rounded to 0 in R 2.2.1 and earlier
> >>>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>I hope that this is helpful. Thanks are due to Peter Dalgaard for
> >>>>>>>guidance. So, thanks Peter :).
> >>>>>>>
> >>>>>>>Cheers
> >>>>>>>
> >>>>>>>Andrew
> >>>>>>>
> >>>>>>
> >>>>>>--
> >>>>>>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
> >>>>>
> >>>>>
> >>>>
> >>>>--
> >>>>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
> >>>
> >>>
> >>
> >>--
> >>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
> >
> >
>
> --
> 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
--
Andrew Robinson
Department of Mathematics and Statistics Tel: +61-3-8344-9763
University of Melbourne, VIC 3010 Australia Fax: +61-3-8344-4599
Email: a.robinson at ms.unimelb.edu.au http://www.ms.unimelb.edu.au
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