search for: mancala

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, 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

...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 methods for union class To: Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> Cc: bioc-devel at r-project.org, dupan.mail at gmail.com I can replicate this with a simpler example, where PkgA has setClass("A", representation(x="numeric")) with NAMESPACE import(methods) exportClasses("A") PkgB has setClass("B&...

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 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, 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, I get the following error when trying to remove a union class: > setClassUnion('a', c('matrix', 'numeric')) > removeClass('a') > sessionInfo() R version 2.15.3 (2013-03-01) Platform: i686-pc-linux-gnu (32-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

...quote({ a<- i; message("Custom ", a) }), > substitute(ex))) > do.call('%dopar%', list(obj, ex), envir=parent.frame()) > } > > - Steve > > > On Tue, Jun 28, 2011 at 8:26 AM, Renaud Gaujoux > <renaud at mancala.cbio.uct.ac.za> wrote: >> 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 >&g...

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

...ight <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 > <renaud at mancala.cbio.uct.ac.za> wrote: >> Thank you for your reply Martin. >> Your code made me realize that S3 methods are added to the >> .__S3MethodsTable__. of the package that defines the generic, not to >> the ones defining the method itself. >> How does things work in the ca...

Hi list, I've got a class B that contains a slot obj of class A. I'd like to be able to call all the methods of class A directly on objects of class B as if I had called the method on slot obj. This without overloading all methods of class A to work on class B. I don't define B as an extension of A, because I want class B to also work with objects of classes that inherit from

Hi, is there a way to retrieve the line number of where en error occurred when sourcing a file in a tryCatch statement? Is it stored somewhere accessible? It is not found in the error object. Consider the following code/output and note the difference in the traceback between source (has line number) and sys.source (has no line number). Thank you, Renaud ######## # code ######## codefile <-

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 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, suppose you have two versions of the same algorithm: one in pure R, the other one in C/C++ called via .Call(). Assuming there is no bug in the implementations (i.e. they both do the same thing), is there any well known reason why the C/C++ implementation could return numerical results non identical to the one obtained from the pure R code? (e.g. could it be rounding errors? please

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, 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

The 'NMF' package implements a number of standard algorithms to perform Nonnegative Matrix Factorization. It also provides a flexible framework to easily test and develop new methods, as well as a layer to work with Bioconductor objects. The package is available from CRAN. Feedbacks are welcome. -- Renaud Gaujoux Computational Biology - University of Cape Town South Africa

Hi, I've got a microarray dataset (Illumina) coming from a blood assay with a case-control factor of interest. I also have several other covariates (gender, weight, etc...). I know that the experimental design is highly unbalanced with respect to Gender: female male control 12 7 case 7 17 Therefore, if there is a Gender effect, then it really