similar to: Ubuntu console weird behaviour

Hi, not sure this is a bug or just an unavoidable undesirable side-effect -- or just me that does not do the right thing. Consider the code and output below. It creates 2 packages: * pkgA * pkgB that creates a method for a generic defined in pkgA Changes in a method for the generic in pkgA (after re-installing pkgA) are not reflected in pkgB, unless pkgB is re-installed against the new

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, 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, I'm wondering if the following behaviour is normal: setClass('A', representation(number='numeric'), validity=function(object){ if( object at number < -1 ) return("Invalid number"); TRUE}) >[1] "A" a <- new('A') a >An object of class ?A? >Slot "number": >numeric(0) a at number <- 0 a at number <- -3 a >An

Hello list, I'm having troubles setting up a basic calss hierarchy with S4. Here is a simplified schema of what I'd like to do: - Two classes: A and B that extends A - Ensure that the slots added by B are consistent with the slots of A - Let A initialize itself (I'm not supposed to know the internal cooking of A) - By default set the slots of B based on the slots that A initialized

Hi, I was trying to get a list of S3 method for a given generic, along with the package in which they are defined, and I came across what looks like an issue in the data.frame returned in attribute 'info'. The column 'from' mostly gets the value "registered S3method for ..." except for visible methods. Is this the expected behavior? See code and output below. Thank you.

Thanks Kevin, this indeed clarifies a bit the S3 method registration universe. On 8 July 2015 at 15:48, Kevin Wright <kw.stat at gmail.com> wrote: > Not sure if this answers your question, but you can't unregister a method. See > > http://tolstoy.newcastle.edu.au/R/help/06/07/30791.html > > Kevin Wright > > > On Wed, Jul 8, 2015 at 5:09 AM, Renaud Gaujoux >

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, 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 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

[we apologize if you receive multiple copies of this announcement] The Storage and Systems Department at IBM''s Haifa Research Lab (HRL), in collaboration with the Technion - Israel Institute of Technology, cordially invite you to a full-day workshop on the subject of virtualization within the SYSTOR 2007 conference. SYSTOR 2007 is the first high-quality refereed systems and storage

[we apologize if you receive multiple copies of this announcement] The Storage and Systems Department at IBM''s Haifa Research Lab (HRL), in collaboration with the Technion - Israel Institute of Technology, cordially invite you to a full-day workshop on the subject of virtualization within the SYSTOR 2007 conference. SYSTOR 2007 is the first high-quality refereed systems and storage

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, 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, for checking purposes, I setup a multiple sub-architecture R installation following this post from Simon Urbanek: https://stat.ethz.ch/pipermail/r-devel/2011-August/061755.html It all went fine. The only change I made to Simon's procedure was to install with: make prefix=~/bin/R/2.15 install instead of sudo make install rhome=/usr/local/R/2.15. I am now trying to install RCurl in

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

Thank you very much Steve. Your suggestion works perfectly -- at least with doSEQ, doMC and doMPI. Bests, Renaud On 28/06/2011 15:35, Stephen Weston wrote: > I think that the result of the concatenation should be a call object, > rather than an expression object. How about something along the > lines of: > > '%dopar2%'<- function(obj, ex) { > ex<-