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Dear all, I have some problems to install R-2.4.1 on AIX 5.3. Configure string: ./configure --with-readline=no LDFLAGS='-bshared' --with-jpeglib=no --with-libpng=no --with-lapack=no --prefix=/cineca/prod/Bioinf/R-2.4.1 configure .site= #! /bin/sh CC=xlc F77=xlf MAIN_LDFLAGS=-Wl,-brtl SHLIB_LDFLAGS=-Wl,-G CXX=xlc CXXFLAGS=' -g -O' SHLIB_LDFLAGS=-W1, -G MAKE=gmake Configure ends successfully, but the make fails: ---cut de -DHAVE_CONFIG_H -I/usr/local/include -g -c init.c -o init.o xl...

Hi, this is possibly a bug report (I'm not sure if this is a feature). It's related to the --keep-dirlinks option, when combined with --delete . I have the following directory structure on server A: ls -lR software software: total 238 drwxr-xr-x 2 biolord bioinf 1024 Sep 20 10:49 EMBOSS/ lrwxrwxrwx 1 biolord bioinf 6 Feb 5 2003 MSE -> EMBOSS/ lrwxrwxrwx 1 biolord bioinf 6 Feb 5 2003 PHYLIP -> EMBOSS/ ... lrwxrwxrwx 1 biolord bioinf 6 Feb 5 2003 TOPO -> EMBOSS/ ... software/EMBOSS: total 87942 -rw-r--r--...

[cross-posted to R-devel and bioc-devel] Hi, I am trying to implement a 'sort' method in one of the CRAN packages I am maintaining ('apcluster'). I started with using setMethod("sort", ...) in my package, which worked fine. Since many users of my package are from the bioinformatics field, I want to ensure that my package works smoothly with Bioconductor. The problem is that the BiocGenerics package also redefines 'sort' as an S4 generic. If I load BiocGenerics before my package, everything is fine. If I load BiocGeneric after I have loaded my package, my s...

...I get the warning that argument y is present in the code but missing in the documentation , although it is actually NOT in the code. In order to make this reproducible for everybody, I put together a little dummy package in which one of the methods leads to exactly this warning: http://www.bioinf.jku.at/people/bodenhofer/codocMismatchTest_0.0.1.tar.gz Just run 'R CMD check' on this archive and you'll see. You will also see from the code and the corresponding documentation that the warning seems unjustified. I tried the following R versions: 2.12.1, 2.13.0, 2.13.1, 2.14.0, 2....

...nity Propagation in fulfillment of multiple users requests. It should now be much easier to cluster large data sets. Apart from this extension, the interfaces to apcluster() and related functions have been made more comfortable and flexible. For more details, see the following URLs: http://www.bioinf.jku.at/software/apcluster/ <http://www.bioinf.jku.at/software/apcluster/> http://cran.r-project.org/web/packages/apcluster/index.html <http://cran.r-project.org/web/packages/apcluster/index.html> Best regards, Ulrich -----------------------------------------------------------------...

...Maybe someone >> else has a more creative solution, but any sort of conditional/dynamic >> approach would probably be too problematic in comparison. >> >> Michael >> >> >> >> On Wed, Mar 26, 2014 at 4:26 AM, Ulrich Bodenhofer < >> bodenhofer@bioinf.jku.at >> > wrote: >> >> > [cross-posted to R-devel and bioc-devel] >> > >> > Hi, >> > >> > I am trying to implement a 'sort' method in one of the CRAN packages I >> am >> > maintaining ('apcluster'). I start...

...rgot to include the list, sorry. I'm including r-package-devel too this time, as it seems more appropriate for this list. El 22 ene. 2018 10:11, "I?aki ?car" <i.ucar86 at gmail.com> escribi?: > > > El 22 ene. 2018 8:12, "Ulrich Bodenhofer" <bodenhofer at bioinf.jku.at> > escribi?: > > Dear colleagues, dear members of the R Core Team, > > This was an issue raised by Prof. Brian Ripley and sent privately to all > developers of CRAN packages that suggest Bioconductor packages (see > original message below). As mentioned in my message...

...C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" [7] "base" other attached packages: DBI "0.1-12" [root at ws-bioinf-01 MySQL]# ls -l /usr/lib64/R/library/RMySQL/libs/ total 124 -rwxr-xr-x 1 root root 122497 Mar 20 11:49 RMySQL.so [root at ws-bioinf-01 MySQL]# ll /usr/local/lib/mysql/ total 2632 -rw-r--r-- 1 root root 27208 Mar 20 11:47 libdbug.a -rw-r--r-- 1 root root 71144 Mar 20 11:47 libheap.a -rw...

...>> list. >> >> >> El 22 ene. 2018 10:11, "I?aki ?car" <i.ucar86 at gmail.com >> <mailto:i.ucar86 at gmail.com>> escribi?: >> >> >> >> ??? El 22 ene. 2018 8:12, "Ulrich Bodenhofer" >> ??? <bodenhofer at bioinf.jku.at <mailto:bodenhofer at bioinf.jku.at>> >> escribi?: >> >> ??????? Dear colleagues, dear members of the R Core Team, >> >> ??????? This was an issue raised by Prof. Brian Ripley and sent >> ??????? privately to all developers of CRAN packages that...

Dear colleagues, This is to inform you that Version 1.3.1 of the R package apcluster has been released on CRAN. We did a major improvement of heatmap and dendrogram plotting, as well as several minor improvements of the package. For more details, see the following URLs: http://www.bioinf.jku.at/software/apcluster/ http://cran.r-project.org/web/packages/apcluster/index.html Best regards, Ulrich ------------------------------------------------------------------------ *Dr. Ulrich Bodenhofer* Associate Professor Institute of Bioinformatics *Johannes Kepler University* Altenberger S...

...e, as it seems more appropriate for this > list. > > > El 22 ene. 2018 10:11, "I?aki ?car" <i.ucar86 at gmail.com > <mailto:i.ucar86 at gmail.com>> escribi?: > > > > El 22 ene. 2018 8:12, "Ulrich Bodenhofer" > <bodenhofer at bioinf.jku.at <mailto:bodenhofer at bioinf.jku.at>> escribi?: > > Dear colleagues, dear members of the R Core Team, > > This was an issue raised by Prof. Brian Ripley and sent > privately to all developers of CRAN packages that suggest > Bioconduc...

Hi, I need to build ROC curve in R, can you please provide data steps / code or guide me through it. Thanks and Regards Rithesh M Mohan [[alternative HTML version deleted]]

Hi, I've been learning how to use R TclTk in Windows over the last few months. I have recently put together a collection of examples of some common widgets and their corresponding R code, at http://bioinf.wehi.edu.au/~wettenhall/RTclTkExamples/ I would be interested in any feedback - Is it useful? Does it contain any significant errors or bad coding style? Does anyone else want to contribute similar examples with screenshots? Regards, James -----------------------------------------------------...

Hello, I'm trying to write a function using tcltk to interactively modify a plot and gather locator() data. I've read Peter's articles in Rnews, the help pages in tcltk, http://bioinf.wehi.edu.au/~wettenhall/RTclTkExamples/, plus a post in R-help sometime ago, but haven't found a solution. The idea goes something like this: require(tcltk) testplot <- function() { getcoords <- function(...) { locator(5) } x <- 1:1000 y <- rnorm(1000) plot(x, y) ba...

...lution, but any sort of >> conditional/dynamic >> approach would probably be too problematic in comparison. >> >> Michael >> >> >> >> On Wed, Mar 26, 2014 at 4:26 AM, Ulrich Bodenhofer >> <bodenhofer at bioinf.jku.at <mailto:bodenhofer at bioinf.jku.at> >> > wrote: >> >> > [cross-posted to R-devel and bioc-devel] >> > >> > Hi, >> > >> > I am trying to implement a 'sort' method in one...

...core on my program. can I compute a roc curve with this? thanks pau -- Pau Marc Muñoz Torres Laboratori de Biologia Computacional Institut de Biotecnologia i Biomedicina Vicent Villar Universitat Autonoma de Barcelona E-08193 Bellaterra (Barcelona) telèfon: 93 5812807 Email : paumarc.munoz@bioinf.uab.cat [[alternative HTML version deleted]]

I would like to display output to a tcltk window from e.g. a call to summary(). I tried to get something else than oneliners into a text window of the kind found at: http://bioinf.wehi.edu.au/~wettenhall/RTclTkExamples/TextWindows.html But without success. Henrik ------------------------------------------------------------- Henrik Andersson Netherlands Institute of Ecology - Centre for Estuarine and Marine Ecology P.O. Box 140 4400 AC Yerseke Phone: +31 113 577473 h.and...

Has anyone written a matrix editor or data.entry() replacement using the Tk table widget? I've been playing around with the examples at http://bioinf.wehi.edu.au/~wettenhall/RTclTkExamples/tktable.html and making some progress, but I'd rather not spend much time on this if someone else has already done it. Jeff

...k CAPITAL letter delta in the mtext() function. I got as far as expression(delta) but this gives me the lowercase version. Can anyone help? I'm using R 2.7 on Windows XP Mick Head of Informatics Institute for Animal Health Compton Berks RG20 7NN 01635 578411 http://www.iah.ac.uk/research/bioinformatics/bioinf.shtml The information contained in this message may be confide...{{dropped:14}}

I'm trying to create an app using TclTk and R Can someone please explain how I bind a click event to the tree widget (http://bioinf.wehi.edu.au/~wettenhall/RTclTkExamples/TreeWidget.html) Ideally I'd like to bind to particular elements in the tree but tkbind doesnt seem to work. thanks tom