[Rd] slight inconsistency in Factorize( logical matrix )
We have a very slight inconsistency in the treatment of logical matrices with our three major factorizations: qr() coerces to numeric , whereas svd() and eigen() give an error. I'm proposing to change svd() and eigen() such that they also treat a logical matrix as if it was 0-1 , analogously to all other arithmetic operations. Martin Maechler, R Core Team ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] tabulate can accept NA values?
tabulate has .C(R_tabulate, as.integer(bin), as.integer(length(bin)), as.integer(nbins), ans = integer(nbins), PACKAGE=base)$ans The implementation of R_tabulate has if(x[i] != R_NaInt x[i] 0 x[i] = *nbin) and so copes with (silently drops) NA. Perhaps the .C could have NAOK=TRUE? This is useful in apply'ing tabulate to the rows or columns of a (large) matrix, where the work-around involves introducing some artificial NA value (and consequently copying the matrix) outside the range of tabulate's nbin argument. Martin -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Rcmd check fails on Windows Samba network path in R 2.9.1
Hi, I have just updated R from version 2.8.1 to version 2.9.1. I am running Windows XP Professional, Service Pack 3. With the update, I decided to update a set of packages that I maintain by compiling them for the new version. Everything worked fine except for one package. This package is unique (among the six I was working on) in that is stored on a UNIX-based file server that is exported to the Windows network via Samba. The root of that network path is mapped to drive N: on the local machine. 'Rcmd check' fails for this package under 2.9.1. The error message in '00install.out' is: Error: ERROR: no permission to install to directory 'N:/krc/Umpire/R-Package/Umpire.Rcheck' 'Rcmd check' works for this package under 2.8.1. 'Rcmd check' works for this package if the directory is copied onto a local hard drive instead of the network drive. 'Rcmd build' and 'Rcmd build --binary' work under both versions. It would be nice if someone could figure out what has changed and fix it Best, Kevin Coombes __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] bug in seq_along
This has now been fixed in R-2.9 and R-devel by Martin Maechler.
Thanks
Kasper
On Jul 13, 2009, at 15:43 , Hervé Pagès 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
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--
Hervé Pagès
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: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax:(206) 667-1319
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Re: [Rd] tabulate can accept NA values?
should be in devel now, NAs are ignored (as are non-integers and things outside the nbin argument) Martin Morgan wrote: tabulate has .C(R_tabulate, as.integer(bin), as.integer(length(bin)), as.integer(nbins), ans = integer(nbins), PACKAGE=base)$ans The implementation of R_tabulate has if(x[i] != R_NaInt x[i] 0 x[i] = *nbin) and so copes with (silently drops) NA. Perhaps the .C could have NAOK=TRUE? This is useful in apply'ing tabulate to the rows or columns of a (large) matrix, where the work-around involves introducing some artificial NA value (and consequently copying the matrix) outside the range of tabulate's nbin argument. Martin -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgent...@fhcrc.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
