similar to: Error: package/namespace load failed for 'IlluminaHumanMethylation27k.db'

Hello All R-Gurus: ISSUE: Cannot view R vignettes due in Ubuntu Linux (a debian variant). note: this issue has been posted to this list before with no responses given see https://stat.ethz.ch/pipermail/r-help/2007-September/141178.html DETAILS: I am trying to view an R vignette. Here is the situation: I issue the openvignette(), then select the vignette I wish to view...and the system returns:

Dear all, I am a PhD student working with Affymetrix HGU133atag array for analyzing the Latin square experiment. I was trying to generate gene expression index for hgu133atag array for PDNN model. While extracting the chiptype specific data structure, I got the following error- > library(affypdnn) Loading required package: affy Loading required package: Biobase Welcome to Bioconductor

Hi, I'm trying to get this library working under R2.10.0. I downloaded it and installed it from zip file. i get the following output. > library(hgu133a2.db) Error in library(hgu133a2.db) : there is no package called 'hgu133a2.db' > utils:::menuInstallLocal() package 'hgu133a2.db' successfully unpacked and MD5 sums checked > library(hgu133a2.db) Loading required

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

(re-sending after confirming list subscription; apologies if this ends up being sent to the list twice) Is the expected behavior from cat(), as used below, a hanging space before \n at the end of the emitted line? firstheader = gsub("\\s+$", "", paste(c("Hybridization REF", s, s), collapse = "\t")) cat(firstheader, "\n", file = filename) When

Hi, I am a Ph.D. student from Québec, Canada. I’m a beginner with R and Bioconductor. Until now the only experience I have is in analyzing microarray data using affy and limma packages. Now I am trying to analyze Rat Gene 10 st arrays and I would like to run RMA analysis and Smyth moderated t test on those arrays. Since no cdf official package is available for those arrays, after reading many

Hi, This is a follow-up to the problem reported here: https://stat.ethz.ch/pipermail/r-devel/2010-September/058460.html After I updated R-2.12 to 2010-09-13 r52905 on the Bioc build system, some of the packages that have a Makefile in <pkg>/inst/doc still don't build on Windows. For example, 'R\bin\R.exe CMD build adSplit' gives: * checking for file

Say I have a FOR-loop for computing powers (just a trivial example) for(i in 1:5) { x<-i^2 y<-i^3 } How can I create a data.frame and a 3D plot of (i,x(i),y(i)), i.e. for each iteration Thanks, Serguei Kaniovski -- ___________________________________________________________________ ??sterreichisches Institut f??r Wirtschaftsforschung (WIFO) Name: Serguei Kaniovski

Hi All, I tried to install AnnotationDBI like so: source("http://bioconductor.org/biocLite.R") biocLite("AnnotationDbi") and got this error: .... Loading required package: RSQLite Error in dyn.load(file, ...) : unable to load shared library '/RHEL3/local/lib64/R/library/ RSQLite/libs/RSQLite.so': /RHEL3/local/lib64/R/library/RSQLite/libs/RSQLite.so: undefined

This is a follow-up on the discussion originally posted on the R-devel list ( http://tolstoy.newcastle.edu.au/R/e4/devel/08/06/1901.html ), as I have encountered the exact same issue mentioned in Martin's email. Here is a simplified version of my problem: ##================================================================= ## I created a package, say, "tmpA", with a NAMESPACE with

Dear all, I like to extract row names & column names from the named matrix...... like...... a<-matrix(1:6,2) ro<-c("aa","bb") co<-c("dd","ee","ff") dimnames(a)<-list(ro,co) a > dd ee ff aa 1 3 5 bb 2 4 6 from the above matrix "a" I like to extract rownames separately like

Hello R-users! My (simple?) doubt: How to reverse the sequence of axis Y ?? the diagram below illustrate my idea... (default) | | . | . | . | 3 | 2 | 1 | 0 +---------------------------- 0 1 2 3 ... like I want... 0 | 1 | 2 | 3 | . | . | . | | +---------------------------- 0 1 2 3 ... thanks in advance klebyn

My conception of how NAMESPACE and methods in R-2.7.0 resolved a generic 'func' to a func-method was to search as follows: In 2.7.0: func --> NAMESPACE, including Imports: (and other details) --> .GlobalEnv, and eventually Depends: since these are on search() In R-devel it seems like func --> NAMESPACE, including Imports: (and other details) --> ?? but not

Hi, I have an RData file containing a GeneSetCollection object (Bioconductor), http://www.cs.mu.oz.au/~gabraham/c2.RData. I think it uses lazy loading because packages are only loaded when I access the object (see below) in the R console. When I try the same with Rscript, it segfaults. This happens on 2.9.0 both on Linux and Mac: Rscript -e 'load("c2.RData"); c2[1]' ***

Hello, I'm a new user... I have a function : calculate <- function(x,y) { z <- x + y } I would like to use the result (z) with another function : recalculate <- function(...) { a <- z^2 } But R says that z does not exist... How can I use z in an another function ? Thank you for your answer... -- David [[alternative HTML version deleted]]

Hello R - users, This may sound simple to may people: I have a list of data as follows type value y 7 y 7 y 8 y 8 y 8 y 9 y 9 y 9 y 9 y 10 y 10 y 10 y 10 y 11 y 11 y 12 y 12 y 14 y 14 y 14 y 15 y 17 y 20 y 20 y 20 y 20 y 25

Hi, First a bit of disclaimer... I haven't isolated this problem into an easy to reproduce case, and I won't be surprised if the root cause is a fault in my code's use of name spaces or some such. The error I'm seeing is one in which the desired method is not found. What worries me in terms of my expectations of how to debug the problem is that showMethods and selectMethod both

Dear all, We have developed our own Affymetrix chip (Custom Express Array, PM-only with two species). I want to analyse the data with the limma package, but for that I need to built my own CDF package, probe package and built the filters to analyse one specie or another. I'm using the makeProbePackage available in the AnnotationDbi (for a R-2.13.0) but I got the following error message:

Hello there, I would like to simulate X --Normal (20, 5) Y-- Normal (40, 10) and the correlation between X and Y is 0.6. How do I do it in R? Thank you very much Lisa Wang Msc. Princess Margaret Hospital Toronto, Ca

Hi, It's unfortunate that with recent revisions of R 2.13 (this appeared in revision 54640, March 2), 'R CMD build' now removes empty dirs in the package. People might have good reasons for having empty dirs in their packages. For example, in Bioconductor, we have some tools to automatically generate annotation packages and those tools are implemented in software packages that use