Re: [Rd] RFC: Proposal to make NROW() and NCOL() slightly more general
> Martin Maechler
> on Mon, 6 Feb 2012 15:35:36 +0100 writes:
>> On Sat, Feb 4, 2012 at 10:38 AM, Martin Maechler
>> wrote:
>> > The help has
>> >
>> >> Description:
>> >
>> >> 'nrow' and 'ncol' return the number of rows or columns present in
'x'.
>> >> 'NCOL' and 'NROW' do the same treating a vector as 1-column matrix.
>> >
>> > and
>> >
>> >> x: a vector, array or data frame
>> >
>> > I'm proposing to extend these two convenience functions
>> > to also work ``correctly'' for generalized versions of matrices.
>> >
>> >
>> > The current implementation :
>> >
>> > NROW <- function(x) if(is.array(x)||is.data.frame(x)) nrow(x) else
length(x)
>> > NCOL <- function(x) if(is.array(x) && length(dim(x)) > 1L ||
is.data.frame(x)) ncol(x) else 1L
>> >
>> > only treats something as matrix when is.array(.) is true,
>> > which is not the case, e.g., for multiprecision matrices from
>> > package 'gmp' or for matrices from packages SparseM, Matrix or similar.
>> >
>> > Of course, all these packages could write methods for NROW, NCOL
>> > for their specific matrix class, but given that the current
>> > definition is so simple,
>> > I'd find it an unnecessary complication.
>> >
>> > Rather I propose the following new version
>> >
>> > NROW <- function(x) if(length(dim(x)) || is.data.frame(x)) nrow(x)
else length(x)
>> > NCOL <- function(x) if(length(dim(x)) > 1L || is.data.frame(x))
ncol(x) else 1L
>> That makes me wonder about:
>> DIM <- function(x) if (length(dim(x)) > 1L) dim(x) else c(length(x), 1L)
>> or maybe more efficiently:
>> DIM <- function(x) {
>> d <- dim(x)
>> if (length(d) > 1L) dim(x) else c(length(x), 1L)
>> }
>> given that dim() is not always trivial to compute (e.g. for data
>> frames it can be rather slow if you're doing it for hundreds of data
>> frames)
>> then NROW and NCOL could be exact equivalents to nrow and ncol.
>> Hadley
> Thank you, Hadley.
> Indeed, your suggestion seems to make sense
> {as far as it makes sense to have such simple functions to
> exist in base at all, but as we already have NROW and NCOL ..}
> So, I propose to adopt Hadley's DIM() proposal, modified to
> DIM <- function(x) if(length(d <- dim(x))) d else c(length(x), 1L)
> and wait a day or so (or longer for reasons of vacation!) before
> committing it, so the public can raise opinions.
Actually, the above --- building NROW() and NCOL() ond DIM() is
not quite correct:
NCOL <- function(x) DIM(x)[2L]
will fail for x <- array(1:3, 3)
so I think I'll stick for now with the generalizations to NROW()
and NCOL(), using
NROW <- function(x) if(length(d <- dim(x))) d[1L] else length(x)
NCOL <- function(x) if(length(d <- dim(x)) > 1L) d[2L] else 1L
which incorporates Hadley's note that there are case where
dim(.) is ``relatively expensive''.
Note that the above are also (very slightly) more efficient than
basing them on DIM(.).
Martin
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[Rd] Using custom R_LIBS with R CMD install
Hi all, Am I using the correct syntax to set a custom R_LIBS when running R CMD INSTALL from the command line? I get: R_LIBS=/Users/hadley/R-dev R CMD INSTALL aL3xa-rapport-08e68ca/ # Desktop : R_LIBS=/Users/hadley/R-dev R CMD INSTALL aL3xa-rapport-08e68ca/ # * installing to library ‘/Users/hadley/R’ # ERROR: dependency ‘ascii’ is not available for package ‘rapport’ But: ls /Users/hadley/R-dev/ # HandyStuff animation biOps mcmcTools mvbutils quantreg testthat # SparseMascii ggplot2mturkr nstest scales whisker (I'm actually running this from inside R using system2, but I think this is the essence of my misunderstanding) Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Canonical package directory name for JAR files?
We have an R package which needs to include a JAR file. Is there a canonical directory for it? __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Canonical package directory name for JAR files?
On Feb 7, 2012, at 4:34 PM, Roebuck,Paul L wrote: > We have an R package which needs to include a JAR file. > Is there a canonical directory for it? > rJava defines "java" for that purpose (see ?.jpackage). How canonical that is may be open for debate ;) Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] capture.output() is trying to allocate 17179869182.6 Gb on my not so big data.frame
Hi, This is what I get with recent R devel on a 64-bit Ubuntu laptop: > mydf <- data.frame(a=1:2080, b=1001:2040, c=letters, d=LETTERS, e=1:1040) > mydf_in_a_character_vector <- capture.output(mydf) Error in print.default(m, ..., quote = quote, right = right) : cannot allocate memory block of size 17179869182.6 Gb I get something similar with R 2.14.1. Cheers, H. > sessionInfo() R Under development (unstable) (2012-01-16 r58124) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] capture.output() is trying to allocate 17179869182.6 Gb on my not so big data.frame
On 02/07/2012 04:08 PM, Hervé Pagès wrote:
Hi,
This is what I get with recent R devel on a 64-bit Ubuntu laptop:
> mydf <- data.frame(a=1:2080, b=1001:2040, c=letters, d=LETTERS,
e=1:1040)
> mydf_in_a_character_vector <- capture.output(mydf)
Error in print.default(m, ..., quote = quote, right = right) :
cannot allocate memory block of size 17179869182.6 Gb
The error is thrown inside src/main/printarray.c:425
Rprintf("%*s%s", R_print.gap, "",
EncodeString(x[i + j * r], w[j], quote, right));
where the array w is the result of an unPROTECTed allocation earlier in
the function, and a garbage collection triggered in MatrixRowLabel (in
this case; allocation also occurs in MatrixColLabel, Rprintf).
PROTECTion seems to have been implemented in the file assuming that the
only allocations are at the head of the function; the return in the
_PRINT_DEAL_c_eq_0 macro makes it difficult to balance the protection
stack, and R_alloc seems to be a better solution anyway. diff attached.
Martin Morgan
I get something similar with R 2.14.1.
Cheers,
H.
> sessionInfo()
R Under development (unstable) (2012-01-16 r58124)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
Index: src/main/printarray.c
===
--- src/main/printarray.c (revision 58290)
+++ src/main/printarray.c (working copy)
@@ -137,7 +137,6 @@
/* initialization; particularly of row labels, rl= dimnames(.)[[1]] and
* rn = names(dimnames(.))[1] : */
#define _PRINT_INIT_rl_rn\
-SEXP sw; \
int *w; \
int width, rlabw = -1, clabw = -1; /* -Wall */ \
int i, j, jmin = 0, jmax = 0, lbloff = 0; \
@@ -159,9 +158,8 @@
_PRINT_INIT_rl_rn;
-sw = allocVector(INTSXP, c);
x = LOGICAL(sx) + offset;
-w = INTEGER(sw);
+w = (int *) R_alloc(c, sizeof(int));
/* compute w[j] = column-width of j(+1)-th column : */
for (j = 0; j < c; j++) {
formatLogical(&x[j * r], r, &w[j]);
@@ -234,9 +232,8 @@
_PRINT_INIT_rl_rn;
-sw = allocVector(INTSXP, c);
x = INTEGER(sx) + offset;
-w = INTEGER(sw);
+w = (int *) R_alloc(c, sizeof(int));
for (j = 0; j < c; j++) {
formatInteger(&x[j * r], r, &w[j]);
_PRINT_SET_clabw;
@@ -271,19 +268,14 @@
static void printRealMatrix(SEXP sx, int offset, int r_pr, int r, int c,
SEXP rl, SEXP cl, const char *rn, const char *cn)
{
-SEXP sd, se;
double *x;
int *d, *e;
_PRINT_INIT_rl_rn;
-PROTECT(sd = allocVector(INTSXP, c));
-PROTECT(se = allocVector(INTSXP, c));
-sw = allocVector(INTSXP, c);
-UNPROTECT(2);
x = REAL(sx) + offset;
-d = INTEGER(sd);
-e = INTEGER(se);
-w = INTEGER(sw);
+d = (int *) R_alloc(c, sizeof(int));
+e = (int *) R_alloc(c, sizeof(int));
+w = (int *) R_alloc(c, sizeof(int));
for (j = 0; j < c; j++) {
formatReal(&x[j * r], r, &w[j], &d[j], &e[j], 0);
@@ -319,27 +311,18 @@
static void printComplexMatrix(SEXP sx, int offset, int r_pr, int r, int c,
SEXP rl, SEXP cl, const char *rn, const char *cn)
{
-SEXP sdr, ser, swr, sdi, sei, swi;
Rcomplex *x;
int *dr, *er, *wr, *di, *ei, *wi;
_PRINT_INIT_rl_rn;
-PROTECT(sdr = allocVector(INTSXP, c));
-PROTECT(ser = allocVector(INTSXP, c));
-PROTECT(swr = allocVector(INTSXP, c));
-PROTECT(sdi = allocVector(INTSXP, c));
-PROTECT(sei = allocVector(INTSXP, c));
-PROTECT(swi = allocVector(INTSXP, c));
-PROTECT(sw = allocVector(INTSXP, c));
-UNPROTECT(7);
x = COMPLEX(sx) + offset;
-dr = INTEGER(sdr);
-er = INTEGER(ser);
-wr = INTEGER(swr);
-di = INTEGER(sdi);
-ei = INTEGER(sei);
-wi = INTEGER(swi);
-w = INTEGER(sw);
+dr = (int *) R_alloc(c, sizeof(int));
+er = (int *) R_alloc(c, sizeof(int));
+wr = (int *) R_alloc(c, sizeof(int));
+di = (int *) R_alloc(c, sizeof(int));
+ei = (int *) R_alloc(c, sizeof(int));
+wi = (int *) R_alloc(c, sizeof(int));
+w = (int *) R_alloc(c, sizeof(int));
/* Determine the column widths */
@@ -391,9 +374,8 @@
SEXP *x;
_PRINT_INIT_rl_rn;
-sw = allocVector(INTSXP, c);
x = STRING_PTR(sx)+offset;
-w = INTEGER(sw);
+w = (int *) R_alloc(c, sizeof(int));
for (j = 0; j < c; j++) {
formatString(&x[j * r], r, &w[j], quote);
_PRINT_SET_clabw;
@@ -437,9 +419,8 @@
Rbyte *x;
_PRINT_INIT_rl_rn;
-sw = allocVector(INTSXP, c);
x
