similar to: S4 Method Signatures

Hello, I've got a DESCRIPTION file with a the first line: Package: Repitools But, when I run R CMD INSTALL Repitools I get: * installing *source* package Repitools ... ** R ** data ** inst ** preparing package for lazy loading Warning in FUN(X[[1L]], ...) : Created a package name, "2011-04-20 09:05:40", when none found ** help *** installing help indices ** building package

I have a confusing error from R CMD check that I don't get when running the example manually by hand. In the \examples section of an Rd file, I create a GRanges object, then I call a function with the GRanges object, whose first 2 lines are require(GenomicRanges) annoDF <- as.data.frame(anno) # anno is the GRanges object. and that second line gives: Error in

Hello, In the documentation for agnes in the package 'cluster', it says that NAs are allowed, and sure enough it works for a small example like : > m <- matrix(c( 1, 1, 1, 2, 1, NA, 1, 1, 1, 2, 2, 2), nrow = 3, byrow = TRUE) > agnes(m) Call: agnes(x = m) Agglomerative coefficient: 0.1614168 Order of objects: [1] 1 2 3 Height (summary): Min. 1st Qu. Median Mean 3rd

Hello, I am using R 2.11.0. I have a curious problem where I get a warning in R CMD check which is seemingly not relevant to my Rd file. The warning says : * checking Rd \usage sections ... WARNING Bad \usage lines found in documentation object 'enrichmentCalc': <unescaped bksl>S4method{enrichmentCalc}{GenomeDataList, BSgenome}(rs, organism, seqLen=NULL, ...) <unescaped

Hello, I am using R 2.11.0. I have a curious problem where I get a warning in R CMD check which is seemingly not relevant to my Rd file. The warning says : * checking Rd \usage sections ... WARNING Bad \usage lines found in documentation object 'enrichmentCalc': <unescaped bksl>S4method{enrichmentCalc}{GenomeDataList, BSgenome}(rs, organism, seqLen=NULL, ...) <unescaped

Hello, In my description file, I have an example data package in Suggests: that I've deleted from my library to test what the user who doesn't have it will experience. However, R CMD check won't even pass my package : * checking package dependencies ... ERROR Package required but not available: RepitoolsExamples Why would it have to be installed, if it's only a data package,

Hi, I have a couple of new errors in our package when I check it on R 2.13-rc (r55310). The first one that's mystifying me is * checking R code for possible problems ... NOTE Error : object normalizePath is not exported by 'namespace:utils' Error : object normalizePath is not exported by 'namespace:utils' Firstly, it's strange to see NOTE and Error being used

Hello, This question is a nightmare to search for, as I get so many irrelevant results. What I'm interested in doing if I have many pages of plots and I want to keep them together in the same document, say a PDF, is there a way to flatten all the dot plots and graphics, so that they don't take a long time to load on a slow computer in Adobe Reader, without using external programs outside

I am using PAM with k = 10 clusters, but I only get one cluster ID for all my observations. I couldn't find any discussion about this in the help file, or mailing lists. Is there a reasonable explanation for this result ? cIDs <- pam(all, 10, cluster.only = TRUE, do.swap = FALSE) > table(cIDs) cIDs 0 16671 The matrix of observations can be found at :

Hello, I've been attempting to make a generic method that dispatches on the first argument, which can be either an S3 or an S4 class. This is as far as I've gotten. Any suggestions about what to try next ? library(aroma.affymetrix) library(GenomicRanges) setGeneric("analyse", function(x, y, ...) standardGeneric("analyse")) setMethodS3("analyse",

Hello, I'm looking for a way to extract objects from what gets created when I Sweave with driver = weaver(). I found where the .Rdata objects are, but when I load one into R, I don't see anything that looks like the objects that were created in that code chunk. > load("/home/darstr/r_env_cache/2.11.0/AbsMeth_5/ac047940aaa9cf1a1ec09f1628b13381.RData") > ls() [1]

Hello, I thought I'd add this to the mailing list, in case it could be handled smoother in a future release of R. > q() Save workspace image? [y/n/c]: n *** caught segfault *** address (nil), cause 'unknown' Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: 3 Error: no graphics

Hello, I'm trying to follow the documentation of how to use gridBase, and I've reached the minimal code example below as my best effort. Can someone explain how to keep the column of boxplots on the same page as the rectangles (even though I've tried new = TRUE) ? Also, would it be hard / possible to match up the middle of each boxplot to the middle of each rectangle ?

Hi, I've got something strange going on. I'm trying to compile a vignette using Sweave("vignette.Rnw"), and in the first code chunk that illustrates an example, I noticed from the output text I have inside the function, that it is running it twice, because the sequence of message() statements is output on screen twice, and takes twice as long to do. e.g. Processing sample 1

Hello, Is it possible to call a graphing function that uses layout() multiple times and layout those outputs ? Here's a minimal example : myplot <- function() { layout(matrix(1:2, nrow=1), widths = c(1, 1)) plot(1:10) plot(10:1) } layout(matrix(1:2), heights = c(1, 2)) myplot() myplot() -------------------------------------- Dario Strbenac Research Assistant Cancer Epigenetics Garvan

Hi, I have this data.frame with two variables in it, > z V1 V2 1 10 8 2 NA 18 3 9 7 4 3 NA 5 NA 10 6 11 12 7 13 9 8 12 11 and a vector of means, > means <- apply(z, 2, function (col) mean(na.omit(col))) > means V1 V2 9.666667 10.714286 My intention was substracting means from z, so instictively I tried > z-means V1 V2 1 0.3333333

Hello, I'm trying to track down the cause of some extreme memory usage and I've been using Dirk Eddelbuettel's lsos() function he posted on stack overflow. There is a large difference between R's RAM usage : PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 6637 darstr 20 0 30.0g 29g 4712 S 0 63.2 10:34.43 R and what objects I have loaded in memory :

Hello I am trying to find a way to find the max value, for only a subset of a dataframe, depending on how the data is grouped for example, How would I find the maxmium responce, for all the GPR119a condition below: responce,mouce,condition 0.105902,KO,con 0.232018561,KO,con 0.335008375,KO,con 0.387025433,KO,GPR119a 0.576769897,KO,GPR119a 0.645120419,KO,GPR119a 0.2538608,KO,GPR119b

I'm in the process of converting some S3 methods to S4 methods. I have this function : setGeneric("enrichmentCalc", function(rs, organism, seqLen, ...){standardGeneric("enrichmentCalc")}) setMethod("enrichmentCalc", c("GenomeDataList", "BSgenome"), function(rs, organism, seqLen, ...) { ... ... ... })

Hello, I have 2 vectors of the same mode and the same contents but I still get FALSE. Any ideas ? > reference <- c(11, 14, 16, 5, 4, 2, 0, 15, 9, 0) > reference [1] 11 14 16 5 4 2 0 15 9 0 > cpgDensity [1] 11 14 16 5 4 2 0 15 9 0 > identical(cpgDensity, reference) [1] FALSE > mode(cpgDensity) [1] "numeric" > mode(reference) [1] "numeric"