similar to: follow up on "[Rd] NAMESPACE & methods guidance, please" ( http://tolstoy.newcastle.edu.au/R/e4/devel/08/06/1901.html )

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

Just jumping to conclusions since the site is down as I type (7PM EST). What's the news from that part of Australia -- thus showing my complete ignorance of DownUnder geography.

I have encountered a problem with merge() that appears to be a bug. Here's an example to illustrate it. > tmp1 <- data.frame(a=letters[1:3],b=LETTERS[2:4],x=1:3) > tmpa <- expand.grid(a=letters[1:4],b=LETTERS[1:4]) > tmpm.1 <- merge(tmpa,tmp1) > tmpm.2 <- merge(tmp1,tmpa) Error in "names<-.default"(*tmp*, value = vnames) : names attribute must

I'd like to have two packages with S4 classes with the same name but different implementation. To that end I create a package tmpA with setClass("A", representation=representation( x="numeric"), sealed=TRUE) setClass("B", representation=representation( x="numeric")) B <- function(...)

### I got bit again by the same bugs I wrote about a year ago. ### The bugs are related to matrices and arrays of lists. ### 1. There is a clear inconsistency in how R handles two ### functionally equivalent statements. ### array() is able to take a list and create a matrix. ### matrix() is unable to create that matrix. > vector("list", 2) [[1]] NULL [[2]] NULL >

Dear R useRs, i have the following code to compute values needed for a contour plot ############################################################ "myContour" <- function(a, b, plist, veca, vecb, dim) { tmpb <- seq(0.5 * b, 1.5 * b, length=dim) tmpa <- seq(0.5 * a, 1.5 * a, length=dim) z <- matrix(0, nrow=dim, ncol=dim) for(i in 1:dim) { for(j in 1:dim)

Greetings all, I am getting this error that is driving me nuts... (not a long trip, haha) I have a set of files and in these files I want to calculate ttests on rows 'compareA' and 'compareB' (these will change over time there I want a variable here). Also these files are in many different directories so I want a way filter out the junk... Anyway I don't believe that this is

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

You have attempted to send a message to a list to which you are not authorised. Your message has been discarded. QUT Help Desk (Postmaster) helpdesk@qut.edu.au Ph: +61 7 3864 4000 --- Original Message --- Received: from mail-router01.qut.edu.au (IDENT:mirapoint@mail-router01.qut.edu.au [131.181.254.7]) by copperhead.qut.edu.au (8.11.6/8.11.6) with ESMTP id i678hKJ30761 for

Hi, Re: http://optics.ph.unimelb.edu.au/help/samba/findsmb.1.html http://www.cl.cam.ac.uk/~pb/NSLU2/NSLU2.html#S0500 Could you please advise whether or not "findsmb" should work on a WindowsXP machine?. *'findsmb' is not recognized as an internal or external command, operable program or batch file.* ** I'm trying to set-up a Linksys NSLU2 to run Apache, php and MySQL and am

The department of computer science at ANU is looking at networking costs. One big cost is the network traffic charges for samba.anu.edu.au. Currently it is costing about $1000 per month in international traffic charges (at 20c/meg). Note that we only pay for incoming data. To try and reduce the cost we are going to need to put in a mirror of the Samba web pages and ftp site in the US. I'm

I've noticed that after my appeal for mirrors last week several people started mirroring samba.anu.edu.au without asking first. Don't do this! It causes the problem of network costs to go up enormously. For example, today we had about 150k hits on the server. About 60% of these were from web robots mirroring the site! The robots only do a "HEAD" on each page but that costs us

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:

Let us submit http://www.samba.anu.edu.au for FREE on Japanese search engines, German search engines, Hispanic search engines , French search engines , Chinese search engines etc.....! After reviewing http://www.samba.anu.edu.au, we have noticed that your website cannot be found on foreign search engines. Could you please put me in touch with your marketing director or whoever is in charge of web

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 everyone, I have a problem when loading the library: IlluminaHumanMethylation27k.db I installed the package from zip (from the Bioconductor website), and also installed all the packages it asked for. It went all succesfull: "package 'IlluminaHumanMethylation27k.db' successfully unpacked and MD5 sums checked" But when I am trying to load this library I get an error:

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

This bug appears intermittently in R CMD check when reference classes have finalize methods. The problem is that garbage collection can be run after the methods package is no longer available. It affects (periodically) the Bioconductor AnnotationDbi package as well as packages that contain Rcpp classes. To reproduce: library(methods) a = setRefClass("A",

Dear All, maybe this is something obvious, I seem to be incapable of understanding how S4 works. So, in package 'A' I defined a "summary" method for my class: setMethod("summary", signature(object="ListHyperGResult"), function(object, pvalue=pvalueCutoff(object), categorySize=NULL) { "whatever" })