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...argh')), warning = function(w) { stop('got warning:', w) }) # this does not catch the warning It seems that the warnings emitted during the evaluation of the arguments of S4 methods can not get caught using withCallingHandlers(). Is this expected ? Is there a work-around ? Best, Karl Forner

...;Interrupted system call' in select 2: In selectChildren(ac, 1) : error 'Interrupted system call' in select Then, just remove library(tcltk), or uncomment unloadNamespace("tcltk"), and it works fine again. I guess there's a bug somewhere, but where exactly ? Best, Karl Forner Further info: R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-unknown-linux-gnu (64-bit) ubuntu 12.04 and 12.10 ubuntu package tk8.5

Hi all, I have a problem with a package that imports two other packages which both export a method for the `[` primitive function. I set up a reproducible example here: https://github.com/kforner/namespaceImportFrom_problem.git Basically, the testPrimitiveImport package imports testPrimitiveExport1 and testPrimitiveExport2, which both export a S4 class and a `[` method for the class. Then: R CMD INSTALL -l lib testPrimitiveExport1 R CMD INSTALL -l lib testPrimitiveExport2 The command: R C...

...ame: >parent.env(getNamespace('data.table')) <environment: 0x7f6ce4d04040> attr(,"name") [1] "imports:data.table" This namespace has a name that might be used to generate the package name. My question is: what should be done ? Thanks for your attention. Karl Forner [[alternative HTML version deleted]]

Dear all, I got an issue trying to parse excel files in parallel using XLConnect, the process hangs forever. Martin Studer, the maintainer of XLConnect kindly investigated the issue, identified rJava as a possible cause of the problem: This does not work (hangs): library(parallel) require(rJava) .jinit() res <- mclapply(1:2, function(i) {

Hi R developers, I am new to this forum and hope someone can help me with .Call in R. Greatly appreciate any help! Say, I have a vector called "vecA" of length 10000, I generate a vector called "vecR" with elements randomly generated from Uniform[0,1]. Both vecA and vecR are of double type. I want to replace elements vecA by elements in vecR only if sum of elements in

I encountered very weird behavior of the dir() function, that I just can not understand. Reproducible example: docker run -ti rocker/r-base R version 3.3.1 (2016-06-21) -- "Bug in Your Hair" Copyright (C) 2016 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) > # setup > tmp <- tempfile() > dir.create(tmp) > setwd(tmp) >

Hello, >From the doc, it says: "isOpen returns a logical value, whether the connection is currently open." But actually it seems to die on closed connections: > con <- file() > isOpen(con) [1] TRUE > close(con) > isOpen(con) Error in isOpen(con) : invalid connection Is it expected ? Tested on R-3.0.2 and R version 3.1.0 Patched (2014-06-11 r65921) on linux x86_64

Hello, I have a package with a namespace. Because I use Roxygen that overwrites the NAMESPACE file each time it is run, I use a R/zzz.R file with an .onLoad() and .onUnload() functions to take care of loading and unloading my shared library. The problem: if I load my library from a local directory, then the unloading of the package fails, e.g: # loads fine >library(Foo,

...ome insight on a problem we encountered using grid, lattice and gridExtra. I tried to reduce the problem, so the plot make no sense. we have a package: gridextrabug with: DESCRIPTION ------------------ Package: gridextrabug Title: gridextrabug Version: 0.1 Author: toto Maintainer: toto <karl.forner at quartzbio.com> Description: gridextrabug Imports: grid, gridExtra, lattice, latticeExtra, reshape, Depends: R (>= 2.15), methods Suggests: testthat, devtools License: GPL (>= 3) Collate: 'zzz.R' 'plotFDR.R' R/plotFDR.R -------...

...tput something like: $`.../testthat/R/auto-test.r` [,1] [,2] [1,] 33 1 [2,] 80 1 $`.../testthat/R/colour-text.r` [,1] [,2] [1,] 18 1 [2,] 19 106 [3,] 20 106 [4,] 22 106 [5,] 23 106 [6,] 40 1 [7,] 59 1 [8,] 70 1 [9,] 71 106 ... Karl Forner Disclaimer ------------- There are probably bugs and ugly statements, but this is just a proof of concept. This is untested and only run on a linux x86_64 -------------- next part -------------- diff -ruN R-devel/src/library/utils/man/Rcov_start.Rd R-devel-cov/src/library/utils/man/Rcov_start.Rd...

Hi, I'm aware that the language definition states "R objects are often coerced to different types during computations". Two questions: 1. Is it possible to configure the R environment so that, for example, coercion from (say) numeric to integer will throw a warning or an error? I realize that in the base R code alone, there are thousands of calls to as.integer() which would

...LLs()))' gives 28 loaded DLLs. I am currently trying to work-around that by putting external packages in Suggests: instead of Imports:, and lazy-load them, but still I am wondering if that threshold value of 100 is still relevant nowadays, or would it be possible to increase it. Thanks, Karl Forner [[alternative HTML version deleted]]

Hello, I've written a package that may use OpenMP to speed up computations. OpenMP is supported in recent Gcc versions by using the -fopenmp flag. The problem is that flag crashed gcc versions that do not support OpenMP. So what is the best way for a package to handle this issue. Has someone a configure script that deals with this ? Thanks, Karl [[alternative HTML version deleted]]

Hello, It seems that the plot function for dendrograms does not draw labels when they are too long. > hc <- hclust(dist(USArrests), "ave") > dend1 <- as.dendrogram(hc) > dend2 <- cut(dend1, h=70) > dd <- dend2$lower[[1]] > plot(dd) # first label is drawn > attr(dd[[1]], "label") <- "aaaaaaaaaaaaaaaaaa" > plot(dd) # first label is

...} } I provided two small R test functions so that you can see how it looks, please see the doc. I would be extremely grateful if you could give me comments, criticisms and other suggestions. I try to release this in order to reuse this functionality in my other packages. Best regards, Karl Forner [[alternative HTML version deleted]]

...There's also a typo in the doc: The sentence: > Otherwise list defaults to the non-hidden **files** in environment (those whose name does not start with .) should be > Otherwise list defaults to the non-hidden **objects** in environment (those whose name does not start with .) Best, Karl Forner > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8...

...tomic [1:8] 1 1 1 3 1 3 1 1 # .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f42951f3b00> # NULL I suppose that the line "for (i in exprs) eval(i, envir)" could be replaced by "eval(exprs, envir)" ? Best, Karl Forner P.S > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-unknown-linux-gnu (64-bit) ... [[alternative HTML version deleted]]

Hi, With R-3.1.0 I get: > getParseData(parse(text = "{1}", keep.source = TRUE)) line1 col1 line2 col2 id parent token terminal text 7 1 1 1 3 7 9 expr FALSE 1 1 1 1 1 1 7 '{' TRUE { 2 1 2 1 2 2 3 NUM_CONST TRUE 1 3 1 2 1 2 3 5 expr FALSE 4 1 3 1

Hello, My problem is that I have an extension in C++ that can be quite time-consuming. I'd like to make it interruptible. The problem is that if I use the recommended R_CheckUserInterrupt() method I have no possibility to cleanup (e.g. free the memory). I've seen an old thread about this, but I wonder if there's a new and definitive answer. I just do not understand why a simple