similar to: mem.limits deprecated

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

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, when running the following on a fresh R, library("IRanges") annotation showMethods("annotation") Biobase:::annotation showMethods("annotation") I get (see the "^^^^^" marked output at the bottom): > library("IRanges") Carico il pacchetto richiesto: 'IRanges' The following object(s) are masked from package:base :

Hello, Suppose in the following code, PROTECT(sr = R_tryEval( .... )) sr is a RAWSXP vector. I wish to return another RAWSXP starting at position 13 onwards (base=0). I could create another RAWSXP of the correct length and then memcpy the required bytes and length to this new one. However is there a more efficient method? Regards Saptarshi Guha

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

Hello everyone, I am trying to fit the following model All X. variables are continuous, while the conditions are categoricals. model <- lm(X2

The following code results in a seg fault. > sessionInfo() R version 2.6.0 Under development (unstable) (2007-06-21 r42013) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C attached base packages: [1] stats graphics

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

R CMD build fails with recent R-devel because it is looking for texi2dvi in /usr/local/bin, but on this system, MacTex has installed it in /usr/bin. $ R CMD build IRanges * checking for file 'IRanges/DESCRIPTION' ... OK * preparing 'IRanges': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes * creating vignettes ... ERROR

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

Hi: I have a two large files (over 300K lines). file 1: Name X UK 199 UK 230 UK 139 ...... UAE 194 UAE 94 File 2: Name X Y UK 140 180 UK 195 240 UK 304 340 .... I want to select X of File 1 and search if it falls in range of X and Y of File 2 and Print only those lines of File 1 that are in range of File 2 X and Y How can it be done it

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, 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,

Dear all, I had a R segmentation fault, and then invoked debug mode and ran step by step. When I reached "terms(Y~X1*X2*...*X16)", I would then have "segmentation" fault. However, if I just ran this under regular "R interactive" mode, it would be fine though taking long time. My questions are: 1. Is there a known limit of terms for a formula? 2. Why does the

Dear all, I had a R segmentation fault, and then invoked debug mode and ran step by step. When I reached "terms(Y~X1*X2*...*X16)", I would then have "segmentation" fault. However, if I just ran this under regular "R interactive" mode, it would be fine though taking long time. My questions are: 1. Is there a known limit of terms for a formula? 2. Why does the

R experts, Hello, I am trying to sample a vector 1:40 without replacement such that no element in the new vector is within 7 units of either of its immediate neighbors. This is part of a larger program I am working on. The following code works well about 65 % of the time (14/40). The problem I encounter happens when the last element remaining to be sampled from the vector STRATA is within 7

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".

On 11/29/2017 04:15 PM, T?th D?nes wrote: > Hi, > > A benchmarking study with an additional (data.table-based) solution. I don't think speed is the right benchmark (I do agree that correctness is!). For the R-help list, maybe something about least specialized R knowledge required would be appropriate? I'd say there were some 'hard' solutions -- Michael (deep

as.factor / as.ordered is not written as a generic. This differs from as.numeric, as.matrix, and other as.*. The following seems to address this and does not break make check-all. FWIW, the patch is against r55563, because with r55564 I see /home/mtmorgan/src/R-devel/src/main/dounzip.c:75:15: error: storage size of ?dt? isn?t known /home/mtmorgan/src/R-devel/src/main/dounzip.c:88:5: warning:

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 (>=