similar to: Non identical numerical results from R code vs C/C++ code?

Hi, this post is about foreach operators, the compiler package and the last update of doMC that includes support for the compiler functionality. I am using a home-made %dopar%-like operator that adds some custom expression to be executed before the foreach loop expression itself (see sample code below). It used to work perfectly with doMC 1.2.1, but with the introduction of the compiler

Hi, is there a way to define a method say '$$' that would behave like '$' and allow calls like 'a$$name'? Thanks. Renaud -- Renaud Gaujoux Computational Biology - University of Cape Town South Africa ### UNIVERSITY OF CAPE TOWN This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at

Hi, in R 2.12.1, R CMD check hangs when building a vignette that uses a foreach loop with the doMC parallel backend. This does not happen in R 2.13.1, nor if I use doSEQ instead of doMC. All versions of multicore, doMC and foreach are the same on both my R installations. Has anybody encountered a similar issue? Thank you. Renaud ### UNIVERSITY OF CAPE TOWN This e-mail is subject to the

Hi, another Rd related issue I encountered is that if an error occurs in an \Sexpr in an Rd file, then on get the following error: * checking for portable compilation flags in Makevars ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking examples ... ERROR Error in paste(before, x, after, sep = "") : object 'exfile' not found Execution halted

Hi, When loading a package that provides the user-supplied RNG hook user_unif_rand, calling getNativeSymbolInfo("user_unif_rand") returns informations about the loaded symbol. I am using this to identify which package currently provides the RNG hook. The results are the same on windows and linux if only one library provides the hook. If one loads a second package that provides this

Hi, I am facing with a strange behaviour of isClass and extends when these are called in .onLoad in both R 2.12.1 and R 2.13.0. This is preventing my package from doing some object initializations at a proper place (i.e. in .onLoad). Suppose one defines two S4 classes in a package, and that one needs to check the inheritance between these two when loading the package (e.g. to validate slots

Hi Henrik (and list), I am interested in a similar feature, and would be happy to see the suggestions you got off-line :) Have you come up with a robust solution, which would work in a variety of situations (in examples, tests, \Sexpr calls, etc..)? Thank you. Bests, Renaud -- Renaud Gaujoux Computational Biology - University of Cape Town South Africa

Hi, when I run R CMD check with flag --as-cran, the process hangs at stage: * checking CRAN incoming feasibility ... I am pretty sure it is a proxy issue. I looked at the check code in the tools package and it seems that the issue is in the local function `.repository_db()` (defined in `tools:::.check_package_CRAN_incoming()`), which eventually calls `url()` with argument

Hi, I am having troubles sourcing a file from our local network from R. It looks like this file are not properly accessed by 'source', even they can be downloaded with download.file. (See below my settings and some tests I did). I ended up with a work around, but I would like to understand what is going on. Doesn't source/readLines uses the same mechanism as download.file to

Hi, is there an easy, robust, and/or recommended way to distinguish a missing argument from an empty argument as in: foo <- function(i, j){ print(missing(j)) print(nargs()) } foo(i) # TRUE, 1 foo(i,) # TRUE, 2 I know I can work around with nargs, the list of arguments and the names of the passed arguments, but I wish there is something already in place for this. This is

Hi again, following my previous post on RCurl, I cannot install Rcpp either: g++ -m32 -I/home/renaud/bin/R/2.15/lib64/R/include -I/home/renaud/bin/R/2.15/lib64/R/include/i386 -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c r_cast.cpp -o r_cast.o g++ -m32 -shared -L/usr/local/lib64 -o Rcpp.so Date.o DateVector.o Datetime.o DatetimeVector.o Dimension.o DottedPair.o

Hi again, following my previous post on RCurl, I cannot install Rcpp either: g++ -m32 -I/home/renaud/bin/R/2.15/lib64/R/include -I/home/renaud/bin/R/2.15/lib64/R/include/i386 -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c r_cast.cpp -o r_cast.o g++ -m32 -shared -L/usr/local/lib64 -o Rcpp.so Date.o DateVector.o Datetime.o DatetimeVector.o Dimension.o DottedPair.o

Hi, I started this post on bioc-devel but this seems to be more general: https://stat.ethz.ch/pipermail/bioc-devel/2013-May/004311.html See reproducible example from Martin below. Thank you. Renaud ---------- Forwarded message ---------- From: Martin Morgan <mtmorgan at fhcrc.org> Date: 7 May 2013 19:55 Subject: Re: [Bioc-devel] ExpressionSet and LumiBatch: inheritance problem in S4

Hi, I want to extend the type list, but it looks like the names are not handled properly (in the show method), not the [ method. See below for code example. I imagine this comes from the S3/S4 mixing, but I would like to understand and the recommended work around (that avoid redefining all the list methods [, $, etc...). Thank you. Bests, Renaud # define S4 class that inherits from list

Hi, running install.packages() to install a package from a local repository (i.e., starts with file:///) appears to delete the PACKAGES file that is in the src/contrib/ directory. This happens on a cluster running Scientific Linux release 6.4 (Carbon), but not on my Ubuntu local machine. Subsequent calls to install.packages() complain about src/contrib/PACKAGES not existing, although there still

Hi, when mixing newline and backspace characters I get the following output (see below). In the second call, the backspace character is simply not applied. Is this normal behaviour? Thank you. > cat("abc\b") ab> cat("abc\b\n") abc > [[alternative HTML version deleted]]

Hi all Apologies if this is a trivial question- I have searched the lists and the online help files etc but have not managed to find anything. I recently downloaded the latest version of R, which has the help type set to htmlhelp as default (according to http://127.0.0.1:18380/library/utils/html/help.html) I would very much like to be able to access the help files when I am offline by typing

Hi, on R version 2.15.1 (2012-06-22) (Platform: i686-pc-linux-gnu (32-bit)) sourced functions have srcref attached as an attribute. Are such data also available for S4 generics and methods? How? (See sample code below) Thank you. Bests, Renaud f <- textConnection( " f <- function(){} setGeneric('myfun', function(x, ...) standardGeneric('myfun'))

Hi, it seems that my proxy settings are not picked up by the R console any longer, although the environment variable http_proxy is set and exported. Is anybody experiencing this issue as well? Thank you. Bests, Renaud # System info (from R --vanilla) > sessionInfo() R version 3.0.3 (2014-03-06) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3]

Hi, from the man page ?methods, I expected to be able to build pairs (class,package) for a given S3 method, e.g., print, using attr(methods(print), 'info'). However all the methods, except the ones defined in base or S4 methods, get the 'from' value "registered S3method for print", instead of the actual package name (see below for the first rows). Is this normal