R 2.3.0 (alpha) on FreeBSD 6.1 fails make check-all

Rhyper <- scan()

Phyper         <- phyper   (Rhyper, m = 40, n = 30, k = 20) 
qhyper(Phyper, m = 40, n = 30, k = 20)                             

Phyper <- phyper (7, m = 40, n = 30, k = 20)
qhyper(Phyper, m = 40, n = 30, k = 20)

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