similar to: NMF package for Nonnegative Matrix Factorization

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

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<-

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, 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, 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

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 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, 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, 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, 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'))

I am reading the Mining of Massive Datasets Book by Rajaraman and Ullman. It has a good explanation of Recommendation System at Chapter 9. But what are the relationship between 1) SVD (Singular Decomposition) 2) UV-Decomposition 3) NMF (Non-negative Matrix Factorization) In particular, it seems 2) and 3) can be very similar. Is it right? Thanks. -- View this message in context:

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, 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, 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, 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

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 >

Is there a way to force certain formula parameters to be nonnegative? What I want to do is to estimate student capacity over time, namely by > capacity ~ Student + Student:Day I add this formula to a glm call and obtain negative learning slope estimates (Student:Day) in some cases. However, I don't want to allow for that. In such a case, glm should solve > capacity ~ Student and

Dear all, Is there any method in R to find all possible nonnegative integer solutions to the linear equation with unit coefficients as follow: X1+X2+...+Xk=N Thank you, Amin Zollanvari

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