similar to: Advanced course R programming and Bioconductor in Cambridge UK 30.3.+1.4.

Dear R developers, I am writing some C code that loads multiple images into a list of R matrices. The whole R object is created within the C code. To simplify coding, elements of the list are first created as vectors and then converted to corresponding matrices using setAttrib(x, R_DimSymbol, s). Generally the code works fine except for one detail. Applying setAttrib sets ALL elements

Dear community, I am writing a wrapper for '[' operator, which is a generic method declared as function(x, i, j, ..., drop). It turns out that I need to parse the '...' argument and this is where I am stuck. Generally what I need is the following. Say the call is obj[1, 1, 1:10, 3] - here '1:10, 3' is passed into '...'. What I need to evaluate that '...'

Hello, I have come across some unexpected behaviour of the function heatmap in the stats package. This looks like a bug to me, but I might have misunderstood something. When calling the function in symmetric mode, the ColSideColors are plotted correctly, but RowSideColors appear in reverse order. This code (modified from the example on the help page) demonstrates the problem: cU <-

Dear all, I am trying represent a matrix of discrete values. At the moment I am using levelplot from the lattice package, but it seems to only work with numerical values. Is there an option in levelplot that will allow me to assign a color to a discrete value, or another package that will do the same? To clarify, with levelplot I can represent a matrix such as: [,1] [,2] [,3] [,4] [1,]

Dear community, this is just a suggestion, but might be useful for the following R releases. I was programming some C code for R and my compiler constantly showed me some crazy messages that a stdc++ macro length() was supplied with 4 arguments whereas only one was required. The problem could be partially resolved by changing the order of includes. However as soon as the file was used from

Dear R developers, I've just encountered one "feature" of R-C extensions. If it is known, I would be thankful for any hints why it works this way (I found the way around, which is also mentioned here, but maybe it is not the best one). If it is however unknown, it might be considered for a "wish list". Consider a simple "aka" C function (the original

Hi Community, I have a question about how to pass command line parameters to R script running in the batch mode. The problem is: there is a banch of data files which are to be processed by R script called from a web-server, i.e. in the batch mode. The web server generates data files and passes their names calling 'R CMD BATCH' one by one for every file. Now the question is how to

Hello Please find bug report attached. Thanks Matthew -- Matthew Gillman Team 105: Variation Informatics Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK Tel: 01223 834244 Ext. 4922 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered

Hi The cor function in the stats package calculates the correlation between columns of data, does anyone know if it is at all possible to calculate the correlation between rows instead ? Or is there an appropriate package or function that is more appropriate I'd like to calculate spearman & pearson correlations between rows. Many thanks Jason -- --------------------------------

Hi, I would like some extra information on the 'cgh' package in R. I noticed that there isn't much activity regarding this package on the R and BioC mailing list (I googled it). I started using this package and I have few questions: 1/ As I have a custom tiling like array @8um features resolution (affy), I have a lot of probes to work with. I'm assuming it is correct to

Hi Community, here is the problem, Linux problem (reported to work on Windows). I need to generate graphical output in any of bitmap format under the 'R CMD BATCH'. Whereas the script generating png-s works perfectly in the R session, such things as X11, png and jpeg are not usable in BATCH (they cannot be switched on by --gui-X11 etc) and X11 is prompted to be required for png. At

Hi Community, here is the problem, Linux problem (reported to work on Windows). I need to generate graphical output in any of bitmap format under the 'R CMD BATCH'. Whereas the script generating png-s works perfectly in the R session, such things as X11, png and jpeg are not usable in BATCH (they cannot be switched on by --gui-X11 etc) and X11 is prompted to be required for png. At

Hi further to my upgrade question thanks for pointing me in the right direction any ideas how I get round the following problem: I'm trying to install on a Tru64 alpha ecs1h[jps]69: make `Makedeps' is up to date. `libappl.a' is up to date. `Makedeps' is up to date. `libnmath.a' is up to date. `Makedeps' is up to date. `libunix.a' is up to date. `Makedeps' is up

Hi All Not sure if this a bioconductor question or general R mailing list so apologies if this has gone to the wrong one................. When plotting dendrograms created by hclust you can "identify" clusters by clicking on the graphics and returning a list of what is contained in each cluster. However I'd like to be able to "zoom in" on specific clusters and plot

HI All sorry if this question has already been asked but I couldn't find anything that answered my question I have 24 columns of data that I'm trying to plot in heatmap.2 (gregmisc) and I'm having difficulty ordering them except in numerical sequence: I have transposed my matrix so it will appear with the dendrogram I want appearing at the top of the heatmap If I use either of

Hi, I'm a sysadmin who's been tasked with installing R on our 1000-node compute cluster. I have licences for the Intel C and FORTRAN compilers, so I'm using the following to compile: CFLAGS="-O2 -axWK" FFLAGS=$CFLAGS CXXFLAGS=$CFLAGS CC=icc F77=ifort CXX=icc FPICFLAGS=-fpic ./configure --without-x --without-tcltk The compilation seems to go OK, with a few warnings.

Dear Prof. Ripley I noted a change in the behaviour of "cov", which is very reasonable: ## R version 2.7.0 Under development (unstable) (2007-11-30 r43565) > cov(as.numeric(NA), as.numeric(NA), use="complete.obs") Error in cov(as.numeric(NA), as.numeric(NA), use = "complete.obs") : no complete element pairs whereas earlier behavior was, for example: ## R

Hi, I am finding the recently added [1] functionality of embedding raster images into plots on R devices very useful! Thanks to Paul Murrell and others for providing that. I noted that in https://svn.r-project.org/R/trunk/src/library/grDevices/src/devPS.c a macro is defined: #define MAX_RASTERS 64, and consequently, I get Error in grid.Call.graphics("L_raster", x$raster, x$x, x$y,

Dear all, is there a good way to create SVG plots with R whose elements have titles (tooltips) or act as hyperlinks? I am using the RSvgDevice package, which works great - but it doesn't seem to support the notion that plot objects have titles or are act as hyperlinks, so I am helping myself by giving the objects funny unique colors and then postprocessing the .svg file. I wonder

Dear Tony, thanks for the tip with "nargs", when suitably applied, this answers the problem. The behaviour of "nargs" in S4 methods has some subtleties compared to that in normal functions, as shown in the example below. I admit that this is what had earlier created some confusion about the semantics of "nargs". From the perspective of "nargs" and its