[Rd] R 2.3.0 (alpha) on FreeBSD 6.1 fails make check-all
Prof Brian Ripley
ripley at stats.ox.ac.uk
Tue Mar 28 10:03:48 CEST 2006
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
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