Re: [Rd] surprised matrix (1:256, 8, 8) doesn't cause error/warning

0, ncol = 0) >> <0 x 0 matrix> >>> matrix (numeric(0), nrow = 2, ncol = 3) >> [,1] [,2] [,3] >> [1,] NA NA NA >> [2,] NA NA NA > >>> matrix(1:2, ncol = 8) >> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8

Re: [Rd] surprised matrix (1:256, 8, 8) doesn't cause error/warning

ve), but that would require bigger surgery way above my payscale. Kind regards Wolfgang Huber Index: array.c === --- array.c (revision 79951) +++ array.c (working copy) @@ -133,18 +133,19 @@ nc = (int) ceil((d

Re: [Rd] A different error in sample()

FWIW, I suspect this is related to the function R_unif_index that was introduced in src/main/RNG.c around revision 72356, or the way this function is used in do_sample in src/main/random.c. 20.9.18 08:19, Wolfgang Huber scripsit: Besides wording of the documentation re truncating vs rounding

Re: [Rd] A different error in sample()

nteger. round(2.5) [1] 2 -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia -- With thanks in advance- Wolfgang --- Wolfgang Huber Principal Investigator, EMBL Senior Scientist European Molecular Biology Laboratory (EMBL) Heidelberg, Germany wolfgang.hu...@embl.de h

Re: [Rd] Crash after (wrongly) applying product operator on S4 object that derives from list

Dear Hilmar Perhaps this gives an indication of why the infinite recursion happens: ## after calling `*` on ma and a matrix: showMethods(classes=class(ma), includeDefs=TRUE, inherited = TRUE) Function: * (package base) e1="FOOCLASS", e2="matrix" (inherited from: e1="vector", e2="structur

Re: [Rd] R not responding (must force quit) when saving graphic to PDF (bug?)

ll...@leuphana.de > Google Scholar > <https://scholar.google.com.au/citations?hl=en&user=xVdc-dsJ&view_op=list_works&sortby=pubdate> > Ideas for Sustainability <https://ideas4sustainability.wordpress.com> > > [[alternative HTML version deleted]] > &g

Re: [Rd] package vignettes build in the same R process?

t will > see their system state, but at least it gives them a way to get the > identical output. On the other hand, they already have a way to do > that: just build the whole package. Overall I'd say it's probably a > good idea. Let the perfect be the enemy of the good? Marti

Re: [Rd] Revolutions Blog: January 2014 roundup

My apologies. Clicked ‘send’ prematurely with wrong recipient. Il giorno 16 Feb 2014, alle ore 09:46, Wolfgang Huber ha scritto: > > FYI: > > Revolution Analytics staff write about R every weekday at the Revolutions > blog: > http://blog.revol

[Rd] Revolutions Blog: January 2014 roundup

FYI: Revolution Analytics staff write about R every weekday at the Revolutions blog: http://blog.revolutionanalytics.com and every month I post a summary of articles from the previous month of particular interest to readers of r-help. In case you missed them, here are some articles related to R

Re: [Rd] Arrays Partial unserialization

R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-devel<https://stat.ethz.ch/mailman/listinfo/r-devel> -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber __

[Rd] Scripting SVG with R

interactive? I am aware of the excellent packages gridSVG and SVGAnnotation, which facilitate making R-generated SVG plots more interesting either at construction time or by postprocessing; the above question is about employing R at viewing time. Best wishes Wolfgang Huber EMBL http

Re: [Rd] R CMD build cannot create vignettes on Windows if Makefile is used

_ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] as.character on NaN gives "NaN", is that intentional?

haracter NA. Is there an intention behind this behavior? Best, Ulrike __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber _

Re: [Rd] require( "foo (>= 2.1)" )

Hi Romain, not that I have any authority here, but wouldn't your suggestion (which I think could be very useful) be more powerful if it were accompanied by a patch that could be applied to the R sources? Best wishes Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/

Re: [Rd] Strange behavior of assign in a S4 method.

oo2",function(x,...){standardGeneric("foo2")}) setMethod(f="foo2",signature="numeric",definition= function(x,...){ nameX<-deparse(substitute(x)) x <- x^2 assign(nameX,x,envir=parent.frame()) } ) e <- 3 foo2(e,y=5) cat(e) ___

Re: [Rd] Unexpected behaviour of x[i] when i is a matrix, on Windows

e for not trying with 2.11 there. Sorry again for wasting your time, and best wishes Wolfgang Simon Urbanek scripsit 02/12/2010 07:15 PM: On Feb 12, 2010, at 12:50 , Wolfgang Huber wrote: Hi, when running the following on different instances of R (Linux and Windows),

[Rd] Unexpected behaviour of x[i] when i is a matrix, on Windows

packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] fortunes_1.3-7 -- Best wishes Wolfgang -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber/contact

Re: [Rd] "Too many raster images" in devPS.c

Hi Paul from a user perspective, this sounds reasonable. Thank you very much, Wolfgang Il giorno Jan 28, 2010, alle ore 2:44 AM, Paul Murrell ha scritto: Wolfgang Huber wrote: > Hi, > I am finding the recently added [1] functionality of embedding raster images

[Rd] "Too many raster images" in devPS.c

veloper.r-project.org/Raster/raster-RFC.html [2] http://www.ebi.ac.uk/~huber/pub/Druggable_ratio_1_before.pdf Thank you and best wishes, Wolfgang -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber/contact __ R-dev

Re: [Rd] Locating code that is outside of functions in R scripts

__ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Best wishes Wolfgang -- Wo

Re: [Rd] Unexpected side effect of the ":::" operator on the value of isGeneric

quot; is "dangerous". The problem also occurs with "::". ------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber 28/02/2009 11:34 Martin Maechler scripsit >>>>>> "Wolfi" == Wolfgang

[Rd] Unexpected side effect of the ":::" operator on the value of isGeneric

MENT=it_IT.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] IRanges_1.1.40 loaded via a namespace (and not attached): [1] Biobase_2.3.10 Best wishes Wolfgang -

Re: [Rd] How to add a slot to S4 class of an existing package?

t/doc/BiobaseDevelopment.pdf Best wishes Wolfgang Wolfgang Huber EMBL-EBI http://www.ebi.ac.uk/huber cstrato wrote: Dear all, Since my package is based on S4 classes, I would like to know how to add a slot to an existing S4 class wi

Re: [Rd] Adding .PDF files to a package

Wolfgang Huber wrote: Rense Nieuwenhuis wrote: Deal all, new as I am to developing packages for R-Project, I apologize on beforehand for questions that are too obvious. I am trying to 'add' a PDF document containing some detailed information to a package. The way I unde

Re: [Rd] Adding .PDF files to a package

dflatex bar foo: foo.tex cp -p ../pdfs/foo.pdf . --- Bw Wolfgang ---- Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] Surprising behaviour of levelplot in lattice package

uot;, "y", "z") print(levelplot(m)) Best wishes Wolfgang -- Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber > sessionInfo() R version 2.7.0 Under development (unstable) (2008-02-13 r44450) x86_64-unknown-linux-gnu locale: LC_CTYPE=it_IT.UT

[Rd] Error from wilcox.test

-- Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] sd(NA)

## R version 2.7.0 Under development (unstable) (2007-11-30 r43565) > sd(NA, na.rm=TRUE) Error in var(x, na.rm = na.rm) : no complete element pairs ## R version 2.6.0 Patched (2007-10-23 r43258) > sd(NA, na.rm=TRUE) [1] NA Best wishes Wolfgang Huber -----

Re: [Rd] Carriage returns and Sweave output

ly if the user calls your function with, say, "verbose=TRUE", and furthermore set the default value of the 'verbose' argument to "verbose=interactive()". Best wishes Wolfgang > On 19 Mar 2007, at 14:49, Wolfgang Huber wrote: > >> Dear Ernest, >

Re: [Rd] Carriage returns and Sweave output

Dear Ernest, this may not be exactly what you asked for, but how about setting "results=hide" in the options of your code chunk? Best wishes Wolfgang -- Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/hub

Re: [Rd] bug: sticky symbol refs? (PR#9555)

-- Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber [EMAIL PROTECTED] wrote: > > Hello. What happens in the following is that I create two simple functions, f > and g, on the workspace. Then I > replace g. When I then call f, it uses the old versi

[Rd] SVG and tooltips, hyperlinks

yself by giving the objects funny unique colors and then postprocessing the .svg file. I wonder whether somebody has already implemented this in a more elegant way. Best wishes Wolfgang -- Wolfgang Huber EBI/EMBL Cambridge UK

Re: [Rd] extracting rows from a data frame by looping over the row names: performance issues

>> LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C >> >> attached base packages: >> [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" >> [7] "base" >> >> __ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> > -- Best wishes Wolfgang -- Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] "[", .local and S4 methods (was: "[" operator and indexing ambiguity)

nInfo() R version 2.5.0 Under development (unstable) (2007-01-28 r40602) i686-pc-linux-gnu locale: LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=e

Re: [Rd] combn implementation

Dear Giampiero, > storage.mode(1) [1] "double" > storage.mode(1:1) [1] "integer" as.integer(1) would perhaps be the more pedagogical way to program this. Best wishes Wolfgang ------ Wolfgang Huber EB

Re: [Rd] Suggestion for read.table()

Hi Giles, x = "x y z\n1 2 3\n4 5 6" res = read.table(textConnection(x), header=TRUE) will do. See also http://cran.r-project.org/doc/manuals/R-data.html Best wishes Wolfgang Huber EMBL-EBI, Cambridge UK [EMAIL PROTECTED] wrote: > First, I compliment you all > for such

Re: [Rd] png() and image()

MS Visual C++ (in which ImageMagick is provided) and MinGW. If anyone is interested in helping with this, they could have a look at the source package on Bioconductor, and contact us for details. Best wishes Wolfgang > On 7/21/06, Wolfgang Huber <[EMAIL PROTECTED]> wrote: >> >>

Re: [Rd] png() and image()

ishes Wolfgang -- Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber Henrik Bengtsson wrote: > Hi, > > I try to create PNG images of a certain size where each pixel > intensity corresponds to exactly one p

Re: [Rd] Unexpected difference in Bounding Box of PDF graphics between 2.3.1p and 2.4 (PR#9070)

nguage, I don't understand much of PDF, just noted the different appearance of the plots. Thanks for the quick fix (and all the other contributions), this really helps. Best wishes Wolfgang Huber -- Wolfgang Huber EBI/EMB

Re: [Rd] pixmaps and R

image processing functions. Cheers Wolfgang - Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Fax: +44 1223 494486 Http: www.ebi.ac.uk/huber -