similar to: Unexpected side effect of the ":::" operator on the value of isGeneric

Hi, S4 method dispatch can be very slow. Would it be reasonable to cache the most recent dispatch, anticipating the next invocation will be on the same type? This would be very helpful in loops. fun0 <- function(x) sapply(x, paste, collapse="+") fun1 <- function(x) { paste <- selectMethod(paste, class(x[[1]])) sapply(x, paste,

Full_Name: Colin A. Smith Version: 1.8.0 OS: Mac OS X 10.2.6 Submission from: (NULL) (216.102.90.18) Both Biobase and my package annaffy use S4 classes to define methods for "[". Both packages use the save image method of installation. (See annaffy 1.0.3 in BioC CVS.) Depending on how both packages are loaded, the Biobase definitions seem to be getting masked out: >

(a new thread, on purpose) >>>>> "RobG" == Robert Gentleman <rgentlem at fhcrc.org> >>>>> on Mon, 27 Jul 2009 16:55:50 -0700 writes: RobG> Hi, I just committed a change to R-devel so that if RobG> debug is called on an S3 generic function, all methods RobG> will also automatically have debug turned on for them RobG>

I have found a strange "ifelse" behaviour (I think) This works: > ifelse(T,1+1,1+2) [1] 2 > ifelse(F,1+1,1+2) [1] 3 Maybe I missed something about R internals, but why > ifelse(T,print("hello"),print("goodbye")) [1] "hello" [1] "hello" > ifelse(F,print("hello"),print("goodbye")) [1] "goodbye" [1]

I've started to implement checks for package versions on dependencies in install.packages(). However, this is revealing a number of problems/misconceptions. (A) We do not check versions when loading namespaces, ahd the namespace registry does not contain version information. So that for example (rtracklayer) Depends: R (>= 2.7.0), Biobase, methods, RCurl Imports: XML (>=

minimal reproducible example plot(1,1) identify(1,1) # or locator() now, trying to close the window by clicking on the cross of the upper right corner causes Rgui (and Rterm) to crash. I see the same behaviour on 2 different Windows PC (one with Win 8.1 and one with Win 10). I did not see the problem in linux (see below) WINDOWS ************** > sessionInfo() R version 3.3.0 beta

Dear List I'm trying to install a package not present in cran named A2R ( http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=79) After running the demo script I retrieve the following error: cannot change value of locked binding for '._a2r_counter' Please could someone give to me a tip about my error? Thank you very much Here is my sessionInfo() R version 2.15.0

Dear all, I encountered a problem when compiling the source of R patched 2.10.0 r50499 (19-11-2009) linked to ACML single threaded (4.2.0 or 4.3.0) OS: openSuSE 11.0 x86-64 make fails when it comes to installing mgcv with the following [snip] ** R ** inst ** preparing package for lazy loading Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) : non esiste un pacchetto chiamato

If of any help, I can reproduce this (on Windows 7) back to at least R 3.0.3 but it's not there in R 3.0.0. (I have *not* checked with R 3.0.1 and 3.0.2 which I don't have installed). /Henrik On Tue, Apr 5, 2016 at 8:23 AM, Duncan Murdoch <murdoch.duncan at gmail.com> wrote: > Thanks, I'll track this down. > > Duncan Murdoch > > > On 05/04/2016 9:35 AM,

Dea-R community. I'd like to draw your attention to an issue I have recently encountered while doing my current data analysis. I've got an unexpected (to me) result from the command: > augPred(lmList(my.object)), 'my.object' being a grouped data frame of class: > class(my.object) [1] "nfnGroupedData" "nfGroupedData" "groupedData"

Hi, Is there a mean to automatically choose one version of the 'rbind' function ? By default, R chose the 'rbind' from {base}, i would lke to use the one from {IRanges}... Is it possible to set that using 'par' ? > ?rbind Help on topic 'rbind' was found in the following packages: Package Library IRanges

Hi people, I have a text file like this one posted: snp_id gene chromosome distance_from_gene_center position pop1 pop2 pop3 pop4 pop5 pop6 pop7 rs2129081 RAPT2 3 -129993 "upstream" 0.439009 1.169210 NA 0.233020 0.093042 NA -0.902596 rs1202698 RAPT2 3 -128695 "upstream" NA

I recently updated R 2.10.1 Patched (2010-02-20 r51163) This morning I reinstalled biomaRt using biocLite. Now I can no more connect to biomaRt and even the following instruction is hanging for a while until the same error message pops up. > listMarts() Error in value[[3L]](cond) : Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the

Hi, I'm developing in S4 and I wanted to see the methods for a specific class using showMethods but I didn't succed. Can someone help ? See the example below. setClass("myclass", representation( name ="character" ) ) setGeneric("mymeth", function(obj, ...){ standardGeneric("mymeth") } ) setMethod("mymeth",

showMethods isn't reporting inherited methods when it is first called. The methods are there and after calling them, showMethods gives the right output. Here is an example (using R-devel r39647): setClass("A", representation(x="numeric"), prototype=list(x=1)) setClass("B", contains="A", prototype=list(x=2))

Hi How to access the values in the output that is an object of S4 type. I tried to access using subset ( [ ] ) but it is not allowed. Any clue?? Thanks -- Fahim #My code is as follows: require(IRanges); query <- IRanges(c(1, 4, 9), c(5, 7, 10)) subject <- IRanges(c(2, 2, 10), c(2, 3, 12)) findOverlaps(query, subject) Output of find overlap function is: ------------------ 1>

Hi I'm missing something here but I cannot figure out what. What I can see is that the same code works when I load it via source(...) yet fails when I execute it after loading the package I have built (which includes the code. Below is a transcript of my R session. First I load the code from a file, using source(). Then I execute it fine. Then I remove the function object, I load the

Thank you Michael Dewey. Can you please send me the email id for Bioconductor. regards Pijush On Fri, Dec 29, 2017 at 5:20 PM, Michael Dewey <lists at dewey.myzen.co.uk> wrote: > Dear Pijush > > You might do better to ask on the Bioconductor list as IRanges does not > seem to be on CRAN so I deduce it is a Bioconductor package too. > > Michael > > > On

Dear Sir, I have been using R for a long time. But recently I have faced a problem when installing the Bioconductor package named "methyAnalysis". Firstly it was require to update my older R (R version 3.4.3 (2017-11-30)) in to newer version. That time I have also updated the RStudio software. After that when I have tried to install the package named "methyAnalysis". It

Dear Pijush You might do better to ask on the Bioconductor list as IRanges does not seem to be on CRAN so I deduce it is a Bioconductor package too. Michael On 29/12/2017 07:29, Pijush Das wrote: > Dear Sir, > > > > > I have been using R for a long time. But recently I have faced a problem > when installing the Bioconductor package named "methyAnalysis".