similar to: bug in R environments? Was: [BioC] 'recursive default argument' error...

I noticed something recently that I thought was odd: delayedAssign("x", { Sys.sleep(5); 1 }) x ## Hit Ctrl-C within the first second or 2 gives me: > delayedAssign("x", { Sys.sleep(5); 1 }) > x ## Hit Ctrl-C within the first second or two > x Error: recursive default argument reference > My only problem here is that now I'm stuck---there's no way

Dear lists: I am somewhat puzzled by the use of texi2dvi/pdflatex in R2.7.0. When building EBImage (bioconductor) with 2.7.0 I get the same error both in Windows and Linux, which reads the following: ** building package indices ... * DONE (EBImage) * creating vignettes ... ERROR /usr/bin/texi2dvi: pdflatex exited with bad status, quitting. Error in texi2dvi(file = bft, pdf = TRUE, clean =

Hi Jiefei and Duncan, I suspect what is likely happening is that one of ENSURE_NAMEDMAX or MARK_NOT_MUTABLE are being hit for x. These used to set named to 3, but now set it to 7 (ie the previous and current NAMEDMAX value, respectively). Because these are macros rather than C functions, its not easy to figure out why one of them is being invoked from do_isvector (a cursory exploration

Dear all, this is my first message to this list. I hope it is not off topic (and should have been posted to R-help for example). I have R-2.3.0 installed on a couple of systems, including powermac G5, iBook G4 (both with MacOSX 10.4.6), windows xp and linux (kubuntu 5.10). When trying to install package aroma from authors web site I found that R for macosx crashes with segfault. This

I have recently upgraded to Ubuntu Gutsy and, for the first time, am using a 64-bit installation. After failing miserably to install R from source, not a problem for me in the past with a 32-bit install, I went the route of using the Debian Etch build. This went smoothly, but I am unable to update my numerous R and BioConductor packages, getting non-zero exit status errors on each package. Is

Hola: Si codificas "col1" como un factor, lo puedes cambiar todo de una vez renombrando los niveles correspondientes: > df$col1<-as.factor(df$col1) > df$col1  [1] uno   dos   3     4     cinco 6     siete 8     9     diez Levels: 3 4 6 8 9 cinco diez dos siete uno > levels(df$col1)[1:5] <-

I have just finished a graduate introductory R & BioC class, and found them very interesting. At this moment, I am not doing any R & BioC related-work, which might end up with "use it or lose it". My plan is to get into bioinformatics fields shortly after the completion of master's degree in bioinformatics that I am studying. Considering being very new to R & BioC, I

[BioC] ANN: Introductory R and Bioconductor Mini Course , Seattle, April 12-14 We will present a short course on using Bioconductor, primarily aimed at analyzing microarray data, over 2 1/2 days in April. The course will be a mix of lectures and practical labs. Instructors: Robert Gentleman, Seth Falcon, Martin Morgan, and Nolwenn Le Meur Topics: Introduction to R Preprocessing of

Hi everybody, I tried to analyze a custom Affymetrix 3'-biased Array. So I wanted to make a cdf package. (My CDF file size is 1.12Go). I tried several methods but the same error occured Method 1 > #Set the working directory > setwd("D:/Analyse R/Cel files") > #library to create cdf env > library("makecdfenv") >#Create cdf environment >pkgpath

Hello all, There is still space available for the upcoming BioC Advanced Course being held in Seattle January 10th-12th. For details and registration, please visit: https://secure.bioconductor.org/biocadv/ Best Wishes, + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org

"Gerard Tromp" <gerard.tromp at sanger.med.wayne.edu> writes: > Greetings, > > this is a follow-up to the mailing below. Seth Falcon replied and indicated > that he and several others were unable to replicate the problem. > Specifically he requested: > > ============ > We are not able to reproduce this issue. If you reinstall the > annotation packages

David Henderson <DNADave@u.arizona.edu> writes: > > Now that both PC and Mac have 64-bit CPU capable of addressing several > > gigabytes of RAM, will bioconductor be able to take advantage of this > > new feature without a major revision? I remember having a trouble > > trying to process 100+ chips at once due to limitation in addressable > > memory, so

On Wed, Aug 13, 2008 at 6:56 AM, Laurent Gautier <lgautier@gmail.com> wrote: > There is a chance that further changes in the handling of plotting > devices event appear; > I think that there is an ongoing effort to bring new features for R-2.8. > > What about bumping that to r-devel ? (Sorry if you already did and I missed > it). > The solution you came up with could be

[CC:ing package maintainer of 'impute' package and crossposting to r-devel and bioc-devel because this affects both audiences] Hi, the 'impute' package is published both on CRAN and Bioconductor; http://cran.r-project.org/web/packages/impute/ http://bioconductor.org/packages/2.3/bioc/html/impute.html The one on CRAN is v1.0-5, and the one on BioC is v1.14.0. The two

some time ago i communicated the same issue to sean, and i'm very glad he has improved the package -- thanks! i'm purposefully posting to r-devel rather than to bioconductor. i think that download.file could be improved to avoid this sort of spamming output seen previously with getGEO. currently, it prints dots (when it does) in 5 10-packs per line, line after line. instead, it could

On 03/27/2014 06:31 PM, Herv? Pag?s wrote: > On 03/27/2014 02:13 AM, Ulrich Bodenhofer wrote: >> [...] >> >> For the time being, it seems I have three options: >> >> 1) not supplying the sort() function yet (it is not yet in the release, >> but only in my internal devel version) >> 2) including a dependency to BiocGenerics >> 3) leaving the

This is (hopefully) a "once in ten years" event, happening today, from 17--19 CET (= 16--18 UTC = 11--13 US Eastern == 8--10 US Pacific Time) The main `vault' (security, air condition,..) where our mail server hypatia is located will undergo a major `network re-connection' event that will affect a considerable part of ETH -- including all the mailing lists

Dear All, There is a question I met when using Affy package in Bioconductor. I asked it in BioC and didn't get any responses. Sorry to post again: Could anyone tell me how to draw a deep-blue Affymetrix image through Image() function in Affy package? The default settings of image() draw me a black-white image and if I modify it to 256 colors, I get a somehow yellowish image. The reason

Thanks for the suggestions, one option i was thinking was to center the universal channel and sample channels by normalising the medians of each column of the matrix on each channel. But I don't know if it is appropriate to do a loess after this? Does the quantile option actually do this? Peter At 06:59 PM 7/28/2004, you wrote: >At 06:02 AM 29/07/2004, Peter Wilkinson wrote:

Thanks Sean! Your reply was very helpful. I already got almost what I wanted. I have some NA values but I will look if I can find them through bibliography or an external tool. Best Regards, Eleni On Mon, May 19, 2008 at 6:07 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > On Mon, May 19, 2008 at 10:47 AM, Eleni Christodoulou > <elenichri@gmail.com> wrote: > > Dear list,