similar to: Editing a package with a NAMESPACE in place

Hello, assignInNamespace refuses to assign an object to a name that is not already used in the namespace. Something like this would make it possible: --- src/library/utils/R/objects.R (revision 56024) +++ src/library/utils/R/objects.R (working copy) @@ -252,8 +252,9 @@ stop("environment specified is not a package") ns <- asNamespace(substring(nm, 9L))

Hi, On Windows, with last R-devel tarball (r40647) from ftp://ftp.stat.math.ethz.ch/Software/R/R-devel_2007-02-04.tar.gz I get the following build error: E:\biocbld\bbs-2.0-bioc\R\src\gnuwin32> make ... ... ---------- Making package utils ------------ adding build stamp to DESCRIPTION installing NAMESPACE file and metadata installing R files Error in namespaceExport(ns, exports) :

Running R.app on Mac OS X 10.4 > version _ platform powerpc-apple-darwin8.6.0 arch powerpc os darwin8.6.0 system powerpc, darwin8.6.0 status major 2 minor 3.1 year 2006

Running R.app on Mac OS X 10.4 > version _ platform powerpc-apple-darwin8.6.0 arch powerpc os darwin8.6.0 system powerpc, darwin8.6.0 status major 2 minor 3.1 year 2006

First, here's the specific bug I have. Later I'll say why I care. > ls(zappo) Error in try(name) : object "zappo" not found # good. > f = function(zappo) { function(y) zappo + y } > g = f(1) > g(1) [1] 2 > formals(g) $y > formals(g)$y > formals(g)$y = 2 > g function (y = 2) zappo + y > g(1) Error in g(1) : object "zappo" not found

Dear list, I''ve had this a few times now, and wonder if this is possible: I''m using a package, often for plotting something, but I want to tune the way the plotting goes, in a way that was not foreseen by the maker of the package. Now, most of the time, these kinds of R functions (say pkg::plot.something) call into other R functions (say pkg::plot.something.internal), and

I have a data set in which I have 5000 repeated measures on 6 subjects over time (varying intervals, but measurements for all individuals are at the same times). There are two states, a "resting" state (the majority of the time), and a perturbed state. I have a continuous measurement at each time point for each of the individuals. I would like to determine the "state"

if I have.... QQQQ<-priceIts("QQQQ",quote="Close") QQQQ<-priceIts("QQQQ",quote="Close");plot(QQQQ) and then i want to do the same thing but say with IBM instead of QQQQ is there an easy way like replace qqqq/ibm Thanks in advance./Jonathan

I have a function that does some plotting. I then add lines to the plot. If executed one line at a time, there is not a problem. If I execute the function, though, I get: Error in ans[[1]] : subscript out of bounds This always occurs after the second lines command, and doesn't happen with all of my data points (some do not have errors). Any ideas? Thanks, Sean

There are numerous tools like scons, make, ruffus, ant, rake, etc. that can be used to build complex pipelines based on task dependencies. These tools are written in a variety of languages, but I have not seen such a thing for R. Is anyone aware of a package available? The goal is to be able to develop robust bioinformatic pipelines driven by scripts written in R. Thanks, Sean

I have a binary vector and I want to find all "regions" of that vector that are runs of TRUE (or FALSE). > a <- rnorm(10) > b <- a<0.5 > b [1] TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE TRUE TRUE My function would return something like a list: region[[1]] 1,3 region[[2]] 5,5 region[[3]] 7,10 Any ideas besides looping and setting start and ends directly?

Dear helpers Does R have a package that performs projection pursuit density estimation? Or anyone knows code in Matlab or C for example to do this? Thank you all Luis

> Dear expeRts, > > Currently, my colors are as follows: > mycol <- > c("blue1","blue2","blue3","blue4","black","yellow4","yellow3","yellow2","y > ellow1") > heatmap(snp, Rowv=NA, Colv=NA, col=mycol) > > However, I would like to have the following colors: > bright blue ->

Hi When I give the command: > heatmap.2(as.matrix(d),Rowv=as.dendrogram(hc.gene),Colv=FALSE,scale="row ",trace="none",col=greenred.colors(79)) The resulting heatmap has re-ordered my columns! This is time-course data, and I don't want my columns re-ordered! Note from the help: Rowv: determines if and how the _row_ dendrogram should be reordered.

Can anyone share experience with opteron versus the xeon (woodcrest) for R under linux? I am looking at using 16-32Gb of ram in a workstation (as opposed to a server). Thanks in advance.... Sean

Hi, The file I am reading is a text file, whose contents are a matrix that has 15 rows and 58 columns. The first row has column names, and the first column has row names, so the format is correct as far as using read.table is concerned. The other values in the table are all float values (numeric). So when I read in the file using data1 <- read.table("HAL001_HAL0015_Signals.txt"), it

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I have a list of vectors $A "AB" "BC" "CD" $B "GF" "HG" "FH" "FJ" and I want to convert it into a dataframe of form A AB A BC A CD B GF B HG B FH B FJ Just can't quite come up with a nice "R" solution for it. Thanks, Sean

This is hopefully a simple question. I am trying to escape single quotes like so: abc's >> abc\'s However, I cannot find an easy way to do that with gsub: gsub("'","\\\\'","abc's") # returns "abc\\'s" How can I get a single \ in the output? Thanks, Sean

I have a table (output from table(factor1,factor2)). I would like to use write.table to output that table to a file. However, it seems that as.data.frame converts such a table to three columns, Var1, Var2, and Freq rather than converting to the data.frame with equivalent numbers of rows and columns. I can use write.matrix from the MASS package, but then I get no rownames. Any hints here?