similar to: eval and evironments: call local function in a global function

Hi, I'd like to know how estimate the memory actually used by some function call. The function essentially contains a for loop, which stops after a variable number of iterations, depending on the input data. I used Rprof with memory.profiling=TRUE, but the memory results seem to increase with the number of iterations. What I understand is that the reported memory is cumulative and based on

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 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 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, 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 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, 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, 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, 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, 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, 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, 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, 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

Hi, is there a simple way, I mean a utility that converts a windows package (.zip file) to a Linux source package (tar.gz or even simply extract the source code and Rd files needed to run successfully a R CMD check). The windows package doesn't have any external lib, C code, etc..., just plain R code, so in theory it is quite straight forward (extract the code from the functions, and

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, 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, 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 the package hooks .onLoad and its C++ pendant R_unload_mylib are actually not called when R quits, but only when explicitly calling detach('package:mylib', unload = TRUE). Maybe this is platform specific, I'm on Ubuntu 13.10 - R 3.0.2 (see below). * is there a mechanism that a package can use to effectively do some cleanup on standard exit, such as calling

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