From ripley at stats.ox.ac.uk  Tue Mar 28 11:27:08 2006
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Tue, 28 Mar 2006 10:27:08 +0100 (BST)
Subject: [Rd] R 2.3.0 (alpha) on FreeBSD 6.1 fails make check-all
In-Reply-To: <20060328101948.GJ53476@ms.unimelb.edu.au>
References: <20060328075537.GD53476@ms.unimelb.edu.au>
	<Pine.LNX.4.64.0603280846340.25281@gannet.stats.ox.ac.uk>
	<20060328101948.GJ53476@ms.unimelb.edu.au>
Message-ID: <Pine.LNX.4.64.0603281025470.26448@gannet.stats.ox.ac.uk>

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



[Rd] R 2.3.0 (alpha) on FreeBSD 6.1 fails make check-all
Prof Brian Ripley