similar to: Rscript segfaults with lazy loading

The GeneSetCollection class in the Bioconductor package GSEABase extends 'list' > library(GSEABase) > showClass("GeneSetCollection") Slots: Name: .Data Class: list Extends: Class "list", from data part Class "vector", by class "list", distance 2 Class "AssayData", by class "list", distance 2 If I create

Hi, I'm trying to use Frank Harrell's Design:::ols function to do regression of y (numeric) on the interaction of two factors (x1 and x2), but Lapack throws an error: > library(Design) ... > load(url("http://www.csse.unimelb.edu.au/~gabraham/x")) > ols(y ~ x1 * x2, data=x) Error in chol2inv(fit$qr$qr) : 'size' cannot exceed nrow(x) = 20 > traceback()

Hi, I have two example packages, test1 and test2, where the only code in them is: setGeneric("predict", function(object, ...) standardGeneric("predict")) (get them from http://www.cs.mu.oz.au/~gabraham/test1.tar and http://www.cs.mu.oz.au/~gabraham/test2.tar) The difference between them is that first does not have a namespace, and loads fine. The second has a namespace

Hi, Again I'm doing logistic regression using lrm from Harrell's Design package, but on wide matrices (28 observations, 1891 variables) so L2 penalisation is used. I get the following error, although I've tried different penalties and different tolerances. The X matrix is scaled and centred. > library(Design) >

The package 'graph' defines classes graph and graphNEL (extending graph) and a union,graph,graph-method. These are all exported and fully documented. The package 'GSEABase' Imports: graph and importClassesFrom(graph, graphNEL). GSEABase defines methods on union for its own classes (not graph / graphNEL), and has exportMethods(union). union,graph,graph-method is not used in

Dear ALL I want to load "HTSanalyzeR", It 's necessary to load "igraph" package. This time I see this error: library(igraph) library(HTSanalyzeR) Loading required package: GSEABase Loading required package: Biobase Error: package 'Biobase' is not installed for 'arch=i386' > I 'll be glade if you help me [[alternative HTML version deleted]]

Hi, Say I have two packages, test1 and test2, that both define the generic method train (identical definition), and each has a specific train method for a different S4 object (foo and bar, resp.) I want to be able to call train(foo, x, y) and train(bar, x, y), which doesn't work since test2 masks test1, as seen below. The two solutions I can think of are to a) prefix train,

Hi, I'm doing PCA on wide matrices and I don't understand why calling predict.prcomp on it throws an error: > x1 <- matrix(rnorm(100), 5, 20) > x2 <- matrix(rnorm(100), 5, 20) > p <- prcomp(x1) > predict(p, x2) Error in predict.prcomp(p, x2) : 'newdata' does not have the correct number of columns > dim(x2) [1] 5 20 > dim(p$rotation) [1] 20 5

Hi, I'm trying to do PCA on a n by p wide matrix (n < p), and I'd like to get more principal components than there are rows. However, svd() only returns a V matrix of with n columns (instead of p) unless the argument nv=p is set (prcomp calls svd without setting it). Moreover, the eigenvalues returned are always min(n, p) instead of p, even if nv is set: > x <-

Hi, I'm using Ubuntu Hardy i386, and the R 2.7.1 Ubuntu packages from CRAN. The CRAN r-base-dev package depends on refblas3-dev or atlas3-base-dev, but octave3.0-headers depends on libblas-dev. The two blas packages seem to conflict, so r-base-dev and octave3.0-headers can't be installed together. Is this a known issue? Thanks, Gad $ sudo apt-get install octave3.0-headers Reading

Hi, Is this a bug in truehist()? > library(MASS) > x <- rep(1, 10) > truehist(x) Error in pretty(data, nbins) : invalid 'n' value Thanks, Gad > R.version platform i486-pc-linux-gnu arch i486 os linux-gnu system i486, linux-gnu status major 2 minor 4.1 year 2006 month 12 day 18 svn

Hi, Is this a bug in truehist()? > library(MASS) > x <- rep(1, 10) > truehist(x) Error in pretty(data, nbins) : invalid 'n' value Thanks, Gad > R.version platform i486-pc-linux-gnu arch i486 os linux-gnu system i486, linux-gnu status major 2 minor 4.1 year 2006 month 12 day 18 svn

Hi, If I have warnings converted to errors, and if I plot a simple plot and then resize and move the plot's window many times, I eventually get an error "Display list redraw incomplete", and after a while an endlessly repeating error "An unusual circumstance has arisen in the nesting of readline input". I cannot stop it using Ctrl-C (Ctrl-Z works though). I'm

Hi, I'm using Ubuntu 9.10 amd64 with cran2deb packages (I know it's meant for Debian, it's worked fine for me for many months). Recently apt-get update has to started to complain: ... Hit http://debian.cran.r-project.org testing/ Release Get:1 http://debian.cran.r-project.org testing/ Packages [515kB] Fetched 1B in 3s (0B/s) W: Failed to fetch

Hi, I'd like to store large covariance matrices using Matrix classes. dsyMatrix seems like the right one, but I want to specify just the upper/lower triangle and diagonal and not have to instantiate a huge n^2 vector just for the sake of having half of it ignored: Dumb example: M <- new("dsyMatrix", uplo="U", x=rnorm(1e4), Dim=as.integer(c(100, 100))) diag(M) <- 1

Hi, Say x.train is a matrix of covariates that I want to do PCA on, so I can do regression on its principal components, and x.test is a test set of the same covariates on which I want to evaluate the regression fit. I would like the covariates to be centred and scaled: p <- prcomp(x.train, center=TRUE, scale=TRUE) x.train.pc <- predict(p) Now I want to get the PCs from the test set.

Hi, Design isn't strictly an R base package, but maybe someone can explain the following. When lrm is called within a function, it can't find the dataset dd: > library(Design) > age <- rnorm(30, 50, 10) > cholesterol <- rnorm(30, 200, 25) > ch <- cut2(cholesterol, g=5, levels.mean=TRUE) > fit <- function(ch, age) + { + d <- data.frame(ch, age) +

I feel tedious when I define a S4 class and the methods. For each method, I have to call both setMethod and setGeneric (or both setReplaceMethod and setGeneric). I would like a more compact grammar so that I can reduce the key strokes. I'm wondering if there is a better way available. setClass( Class='A', representation=representation( x='numeric' )

Hi, I'm using zoo because it can automatically label the months of a time series composed of daily observations. This works well for certain time series lengths, but not for others, e.g.: While: > library(zoo) > plot(zoo(runif(10), as.Date("2005-06-01") + 0:50)) Shows up the months and day of month, > plot(zoo(runif(10), as.Date("2005-06-01") + 0:380))

Hi, Can anyone explain how the standard error in arima() is calculated? Also, how can I extract it from the Arima object? I don't see it in there. > x <- rnorm(1000) > a <- arima(x, order = c(4, 0, 0)) > a Call: arima(x = x, order = c(4, 0, 0)) Coefficients: ar1 ar2 ar3 ar4 intercept -0.0451 0.0448 0.0139 -0.0688 0.0010 s.e.