[Rd] make check-all fails (PR#7784)

[M. Edward (Ed) Borasky]

Peter Dalgaard wrote:

>znmeb at cesmail.net writes:
>
>  
>
>>Full_Name: Ed Borasky
>>Version: R-beta 2.1.0 2005-04-08
>>OS: Linux 2.6.11 GCC 3.3.5
>>Submission from: (NULL) (24.21.57.139)
>>
>>
>>I downloaded the latest R-beta tarball and did a build with the default options.
>>OS is Linux 2.6.11 and compiler is GCC 3.3.5. "make check-all" failed with the
>>following message:
>>
>>make[3]: Entering directory `/home/znmeb/R-beta/tests'
>>running code in 'reg-tests-1.R' ...make[3]: *** [reg-tests-1.Rout] Error 1
>>make[3]: Leaving directory `/home/znmeb/R-beta/tests'
>>make[2]: *** [test-Reg] Error 2
>>make[2]: Leaving directory `/home/znmeb/R-beta/tests'
>>make[1]: *** [test-all-basics] Error 1
>>make[1]: Leaving directory `/home/znmeb/R-beta/tests'
>>make: *** [check-all] Error 2
>>
>>I looked at "tests/reg-tests-1.Rout.fail"; it's 1427 lines long. The error given
>>is
>>
>>    
>>
>>>## Comments:
>>>
>>>
>>>## PR 796 (aic in binomial models is often wrong)
>>>##
>>>a1 <- glm(cbind(ncases, ncontrols) ~ agegp + tobgp * alcgp,
>>>      
>>>
>>+     data = esoph, family = binomial())$aic
>>    
>>
>>>a1
>>>      
>>>
>>[1] 236.9645
>>    
>>
>>>a2 <- glm(ncases/(ncases+ncontrols) ~ agegp + tobgp * alcgp,
>>>      
>>>
>>+     data = esoph, family = binomial(), weights=ncases+ncontrols)$aic
>>    
>>
>>>a2
>>>      
>>>
>>[1] 236.9645
>>    
>>
>>>stopifnot(a1 == a2)
>>>      
>>>
>>Error: a1 == a2 is not TRUE
>>Execution halted
>>
>>I am running on an Athlon Thunderbird with Atlas 3.6.0 installed. If necessary,
>>I can back Atlas out and run this again.
>>    
>>
>
>Hmm, could you replace the a1 == a2 with all.equal(a1, a2) instead?
>(inside reg-tests-1.R of course)
>
>Asking for identity up to machine precision does look a bit optimistic...
>
>  
>
That worked ... it got through reg-tests-1.R fine. However, it failed a 
little further down in the NA handling tests:

running tests of NA handling functions
make[3]: Entering directory `/home/znmeb/R-beta/tests'
running code in 'nafns.R' ...make[3]: *** [nafns.Rout] Error 1
make[3]: Leaving directory `/home/znmeb/R-beta/tests'
make[2]: *** [test-Nafns] Error 2
make[2]: Leaving directory `/home/znmeb/R-beta/tests'
make[1]: *** [test-all-devel] Error 1
make[1]: Leaving directory `/home/znmeb/R-beta/tests'
make: *** [check-all] Error 2

 > sm(fitted(gfit2))
length 153 with 42 NAs
 > sm(resid(gfit2))
length 153 with 42 NAs
 > sm(predict(gfit2))
length 153 with 42 NAs
 > (pp2 <- predict(gfit2, nd))
6 25 26 27
NA -16.177404 1.688479 NA
 > stopifnot(all.equal(pp, pp2))
 >
 > ## more precise tests.
 > f1 <- fitted(gfit)
 > f2 <- fitted(gfit2)
 > common <- match(names(f1), names(f2))
 > stopifnot(max(abs(f1 - f2[common])) < 100*.Machine$double.eps)
Error: max(abs(f1 - f2[common])) < 100 * .Machine$double.eps is not TRUE
Execution halted
"tests/nafns.Rout.fail"