From khansen at stat.berkeley.edu  Mon Jul 20 23:02:21 2009
From: khansen at stat.berkeley.edu (Kasper Daniel Hansen)
Date: Mon, 20 Jul 2009 14:02:21 -0700
Subject: [Rd] bug in seq_along
In-Reply-To: <4A5BB888.8020708@fhcrc.org>
References: <7E0D03FE-2742-4442-977F-538AE7DE920A@stat.berkeley.edu>
	<4A5BB888.8020708@fhcrc.org>
Message-ID: <427BCBED-A2DE-464E-B8A7-4FA089CA4BBC@stat.berkeley.edu>

This has now been fixed in R-2.9 and R-devel by Martin Maechler.

Thanks
Kasper

On Jul 13, 2009, at 15:43 , Herv? Pag?s wrote:

> Hi Kasper and R developers,
>
> Kasper Daniel Hansen wrote:
>> Using the IRanges package from Bioconductor and somewhat recent  
>> R-2.9.1.
>> ov = IRanges(1:3, 4:6)
>> length(ov) # 3
>> seq(along = ov) # 1 2 3 as wanted
>> seq_along(ov) # 1!
>> I had expected that the last line would yield 1:3. My guess is that  
>> somehow seq_along don't utilize that ov is an S4 class with a  
>> length method.
>
> I agree, this is not good. seq_along() has always been broken on S4
> objects:
>
>  https://stat.ethz.ch/pipermail/r-devel/2007-July/046337.html
>
> so I prefer to not use it, ever. Even when I deal with S3 objects.
> Because the day I need to extend my code to deal with S4 objects,
> it's too easy to forget to replace 'seq_along(x)' with  
> 'seq_len(length(x))'.
> So I'd rather use the latter all the time and from the very beginning
> (hopefully there is no serious performance penalty for doing this).
>
> Surprisingly, seq_along() diserves its own C implementation (why
> wouldn't seq_along <- function(x) seq_len(length(x)) be just good
> enough?). It's calling length() at the C level which is an inline
> function defined as:
>
> INLINE_FUN R_len_t length(SEXP s)
> {
>    int i;
>    switch (TYPEOF(s)) {
>    case NILSXP:
>        return 0;
>    case LGLSXP:
>    case INTSXP:
>    case REALSXP:
>    case CPLXSXP:
>    case STRSXP:
>    case CHARSXP:
>    case VECSXP:
>    case EXPRSXP:
>    case RAWSXP:
>        return LENGTH(s);
>    case LISTSXP:
>    case LANGSXP:
>    case DOTSXP:
>        i = 0;
>        while (s != NULL && s != R_NilValue) {
>            i++;
>            s = CDR(s);
>        }
>        return i;
>    case ENVSXP:
>        return Rf_envlength(s);
>    default:
>        return 1;
>    }
> }
>
> Hence it will return 1 when 's' is an S4SXP.
>
> If for whatever reason, seq_along() is not able to figure out what
> the *real* length of an S4 object is, then wouldn't it be better to
> make it return an error? Or at least to put a big warning in its
> man page saying: DON'T TRUST ME ON YOUR S4 OBJECTS, I'M BROKEN!
>
> Cheers,
> H.
>
>
>> The last line of the *Details* section of ?seq has a typeo.  
>> Currently it is
>>     'seq.int', 'seq_along' and 'seq.int' are primitive: the latter  
>> two
>>     ignore any argument name.
>> I would guess it ought to be
>>     'seq.int', 'seq_along' and 'seq_len' are primitive: the latter  
>> two
>>     ignore any argument name.
>> Kasper
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
> -- 
> Herv? Pag?s
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319



[Rd] bug in seq_along
Kasper Daniel Hansen