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
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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