From A.Robinson at ms.unimelb.edu.au  Tue Mar 28 12:19:48 2006
From: A.Robinson at ms.unimelb.edu.au (Andrew Robinson)
Date: Tue, 28 Mar 2006 20:19:48 +1000
Subject: [Rd] R 2.3.0 (alpha) on FreeBSD 6.1 fails make check-all
In-Reply-To: <Pine.LNX.4.64.0603280846340.25281@gannet.stats.ox.ac.uk>
References: <20060328075537.GD53476@ms.unimelb.edu.au>
	<Pine.LNX.4.64.0603280846340.25281@gannet.stats.ox.ac.uk>
Message-ID: <20060328101948.GJ53476@ms.unimelb.edu.au>

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



[Rd] R 2.3.0 (alpha) on FreeBSD 6.1 fails make check-all
Andrew Robinson