R devel - Mar 2004 - Re: CRAN packages maintained by you (subscripting problem under 1.9.0.alpha?)

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I was notfied that my package ref fails R CMD CHECK under 1.9.0 Alpha.
I downloaded the windows version of 1.9.0 Alpha (dated 2004-03-17) and package
ref passes R CMD CHECK without any complaints.

The daily checks suggest the problem arises in example(optimal.index)

Error in identical(l[i], l[optimal.index(i, n = length(l), strict = FALSE)]) : 
	only 0's may mix with negative subscripts

where negative subscripts are mixed with NAs (which was legal in versions prior
1.9.0).

Is it an intended change not to allow NA mix with negative subscripts any
longer?
(I did not find any hint in NEWS)

Thanks for any hint


Jens Oehlschlägel




library(ref)

# examples from optimal.index

l <- letters
names(l) <- letters
stopifnot({i <- 1:3 ; identical(l[i], l[optimal.index(i, n=length(l))])})
stopifnot({i <- -(4:26) ; identical(l[i], l[optimal.index(i, n=length(l))])})
stopifnot({i <- c(rep(TRUE, 3), rep(FALSE, 23)) ; identical(l[i],
l[optimal.index(i, n=length(l))])})
stopifnot({i <- c("a", "b", "c");
identical(l[i], l[optimal.index(i, i.names=names(l))])})
old.options <- options(show.error.messages=FALSE);
stopifnot(inherits(try(optimal.index(c(1:3, 3), n=length(l))),
"try-error")); options(old.options)
stopifnot({i <- c(1:3, 3, NA);identical(l[i], l[optimal.index(i, n=length(l),
strict=FALSE)])})

# that one triggeres an error ???
stopifnot({i <- c(-(4:26), -26, NA);identical(l[i], l[optimal.index(i,
n=length(l), strict=FALSE)])})

stopifnot({i <- c(rep(TRUE, 3), rep(FALSE, 23), TRUE, FALSE,
NA);identical(l[i], l[optimal.index(i, n=length(l), strict=FALSE)])})
stopifnot({i <- c("a", "b", "c", "a",
NA);identical(l[i], l[optimal.index(i, i.names=names(l), strict=FALSE)])})
rm(l)







> version
         _              
platform i386-pc-mingw32
arch     i386           
os       mingw32        
system   i386, mingw32  
status   alpha          
major    1              
minor    9.0            
year     2004           
month    03             
day      17             
language R  


Kurt.Hornik@wu-wien.ac.at schrieb am 22.03.04 10:27:18:
> 
> Dear maintainers of CRAN packages,
> 
> This concerns the packages
> 
>   gregmisc hdf5 ref
> 
> These packages fail R CMD check for a current version of r-devel, which
> went into ferature freeze on 2004-03-21 and will be released as R 1.9.0
> on 2004-04-04.
> 
> As you know, packages which fail R CMD check at the time of a new
> release will be moved from CRAN's main area into the Devel area. 
Hence,
> it is very important that we receive updates of such packages as soon as
> possible.
> 
> Please have a look at the daily check logs at
> 
>   http://cran.r-project.org/src/contrib/checkSummary.html
> 
> to see what the problem is, and look at the NEWS file in the r-devel
> sources as well as
> 
>   http://developer.r-project.org/190update.txt
> 
> for information on changes in the current development version of R.
> 
> Please note also that binary versions of r-devel for Windows and Mac OS
> X are available via CRAN.
> 
> Keep the fixes coming in!
> 
> Best
> -k
>

>>>>> "JensOe" == Jens Oehlschl?gel
<joehl@web.de>
>>>>>     on Mon, 22 Mar 2004 18:03:08 +0100 writes:
    JensOe> I was notfied that my package ref fails R CMD CHECK
    JensOe> under 1.9.0 Alpha.  I downloaded the windows version
    JensOe> of 1.9.0 Alpha (dated 2004-03-17) and package ref
    JensOe> passes R CMD CHECK without any complaints.

    JensOe> The daily checks suggest the problem arises in
    JensOe> example(optimal.index)

    JensOe> Error in identical(l[i], l[optimal.index(i, n     JensOe>
length(l), strict = FALSE)]) : only 0's may mix with
    JensOe> negative subscripts

    JensOe> where negative subscripts are mixed with NAs (which
    JensOe> was legal in versions prior 1.9.0).

    JensOe> Is it an intended change not to allow NA mix with
    JensOe> negative subscripts any longer?  (I did not find any
    JensOe> hint in NEWS)

A shorter version is

  > x <- 1:9; x[-c(-1,NA,3:5)]
  Error: only 0's may mix with negative subscripts

which used to simply give

  > x <- 1:9; x[-c(1,NA,3:5)]
  [1] 2 6 7 8 9

and is the same if there was no NA in the index -- without a warning;
not necessarily desirable as well.

---------

However, the current NEWS  file does say


    o   Negative subscripts that were out of range or NA were not handled 
        correctly.


R 1.9.0 (beta)'s behavior seems to match the one of S-plus here,
but that alone is not convincing enough IMO.

Regards, Martin