Re: [Rd] rc note, etc

From: Peter Dalgaard <p.dalgaard_at_biostat.ku.dk>
Date: Thu, 21 Aug 2008 22:40:44 +0200

Paul Gilbert wrote:
> Are the messages below to be expected from make check-all ?
Yes. They are just that, notes. They occur when a function uses a global variable which is not obviously existent. However, (a) it might be assumed to exist whenever the function is actually used and (b) the function might not actually be using it. As an example of the latter, look at the grid case:

 > grid:::wrap.down
function (x)
{

    recordGrob(downViewport(path), list(path = x)) }

The complaint is that "path" is seemingly used without being defined. However, digging one level further, we have

 > grid:::recordGrob
function (expr, list, name = NULL, gp = NULL, vp = NULL) {

    grob(expr = substitute(expr), list = list, name = name, gp = gp,

        vp = vp, cl = "recordedGrob")
}

and the substitute() contruct shows that "downViewport(path)" is getting treated as an unevaluated expression and might not be evaluated in the global environment at all. Put otherwise, the programmer has outsmarted the code checker... (In some cases, the code predates the code checker, and although it might be rewritten to avoid the message, noone has felt compelled to do so.)

I'm somewhat puzzled by the strange characters in the glm.fit message, though.

    -pd

>
> using the rc today, Aug 21, on
> Red Hat Enterprise Linux AS release 4 (Nahant Update 4)
> Kernel 2.6.9-42.0.8.ELsmp on an x86_64
>
> Paul
> ________
> ....
> checking package 'utils'
> ....
> * checking R code for possible problems ... NOTE
> install.packages: no visible global function definition for
> ‘.install.winbinary’
> install.packages: no visible global function definition for
> ‘.install.macbinary’
>
> ....
> checking package 'stats'
> ....
> * checking R code for possible problems ... NOTE
> glm.fit: no visible binding for global variable ‘n’
> * checking Rd files ... OK
> * checking Rd cross-references ... OK
> * checking for missing documentation entries ... OK
> * checking for code/documentation mismatches ... OK
> * checking Rd \usage sections ... OK
> * checking for portable use of $BLAS_LIBS ... OK
> * checking tests ...
> make[3]: Entering directory
> `/home/mfa/gilp/toolchain/R/src/R-rc/tests/stats.Rcheck/tests'
> Running 'nafns.R'
> Running 'nls.R'
> Comparing 'nls.Rout' to 'nls.Rout.save' ...134c134
> < Achieved convergence tolerance: 2.75e-06
> ---
> > Achieved convergence tolerance: 2.74e-06
> 145c145
> < 3: 0.00060639084: 0.00517051 0.999153
> ---
> > 3: 0.00060639084: 0.00517052 0.999153
> 214c214
> < Achieved convergence tolerance: 1.04e-07
> ---
> > Achieved convergence tolerance: 1.34e-07
> 249c249
> < Achieved convergence tolerance: 1.73e-07
> ---
> > Achieved convergence tolerance: 1.29e-07
> 288c288
> < Achieved convergence tolerance: 3.73e-08
> ---
> > Achieved convergence tolerance: 8.48e-09
> 382c382
> < Achieved convergence tolerance: 2.80e-07
> ---
> > Achieved convergence tolerance: 2.81e-07
> 430c430
> < Achieved convergence tolerance: 3.16e-06
> ---
> > Achieved convergence tolerance: 3.43e-06
> 487c487
> < 11 3.40458 22.42470 1.38476
> ---
> > 11 3.40458 22.42471 1.38476
> 497,498c497,498
> < 7 3.89865 23.13401 1.79455
> < 8 4.52605 166.09148 2.20381
> ---
> > 7 3.89865 23.13399 1.79455
> > 8 4.52605 166.09149 2.20381
> 611c611
> < Achieved convergence tolerance: 7.17e-07
> ---
> > Achieved convergence tolerance: 7.45e-07
> 647c647
> < Achieved convergence tolerance: 2.08e-06
> ---
> > Achieved convergence tolerance: 1.98e-06
> OK
>
> ....
> checking package 'methods'
> ....
> * checking R code for possible problems ... NOTE
> browseAll: no visible binding for global variable ‘.BrowserStack’
> ..dataPartReplace2: no visible binding for global variable ‘THISCLASS’
> ...First.lib: no visible binding for global variable ‘.possibleExtends’
> ...First.lib: no visible binding for global variable ‘.makeGeneric’
> ...First.lib: no visible binding for global variable
> ‘.newClassRepresentation’
> ...First.lib: no visible binding for global variable
> ‘..mergeClassDefSlots’
> ..makeBasicFuns: no visible global function definition for
> ‘.addBasicGeneric’
> ..makeBasicFuns: no visible binding for global variable
> ‘.addBasicGeneric’
> ..oldTestFun: no visible binding for global variable ‘CLASS’
> selectMethod: no visible binding for global variable ‘.SelectMethodOn’
> ....
> checking package 'grid'
> ....
> * checking R code for possible problems ... NOTE
> wrap.down: no visible binding for global variable ‘path’
> wrap.pop: no visible binding for global variable ‘n’
> wrap.up: no visible binding for global variable ‘n’
> wrap.viewport: no visible binding for global variable ‘vp’
> ....
> checking bundle 'VR'
> ....
> ** checking R code for possible problems ... NOTE
> glmmPQL: no visible binding for global variable ‘wts’
> negative.binomial : variance: no visible binding for global variable
> ‘.Theta’
> negative.binomial : dev.resids: no visible binding for global variable
> ‘.Theta’
> negative.binomial : aic: no visible binding for global variable
> ‘.Theta’
> neg.bin : variance: no visible binding for global variable ‘.Theta’
> neg.bin : dev.resids: no visible binding for global variable ‘.Theta’
> neg.bin : aic: no visible binding for global variable ‘.Theta’
> ** checking Rd files ... OK
>
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-- 
   O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark      Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard_at_biostat.ku.dk)              FAX: (+45) 35327907

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