[Rd] R 2.3.0 (alpha) on FreeBSD 6.1 fails make check-all
Andrew Robinson
A.Robinson at ms.unimelb.edu.au
Tue Mar 28 12:19:48 CEST 2006
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"
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
--
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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