similar to: Problems with 'delay'/'delayedAssign' when installing data package

Neither biocLite nor the GUI menus can install packages on my system. Here is relevant output: > version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 11.1 year 2010 month 05 day 31 svn rev 52157 language R version.string R version 2.11.1 (2010-05-31) > source("http://bioconductor.org/biocLite.R") BioC_mirror =

Hi, I am trying to install Bioconductor onto R version 2.7.0 for Windows. I installed R, then followed the instructions on http://www.bioconductor.org/download, which state that you should type the following: source("http://bioconductor.org/biocLite.R") biocLite() When I do that, I get the following error: Running biocinstall version 2.2.9 with R version 2.7.0 Your version of R

I have developed a problem with the postscript output of plot on Windows. My code still works properly with R 2.3 but, with R 2.4, the white text on red background does not show up. It does, however, show up when output is sent to the screen. Below is my code and sessionInfo. R version 2.4.0 Under development (unstable) (2006-08-29 r39012) i386-pc-mingw32 locale: LC_COLLATE=English_United

I got this error when I tried to install the package in order to use the "logit"(logit transformation) function on linux. > install.packages(car) Error in install.packages(car) : object 'car' not found I was using the Terminal in my macbook accessing the server in the lab. I could successfully using library(car) to install this package use R.app GUI in my laptop, after

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

Hi again, I have been playing around with the order of loading packages, and as far as I can tell, there's nothing specific with affycoretools that's causing my Rgui to crash (i.e., shuts down and the Microsoft 'please send error report' box pops up). Instead, it has something to do with the order & type of packages that are loaded that add items to the menu bar by

Hallo, I just installed all needed packages for my project on my PC. But I cannot load all at one time. I now want to load limma. How can I realize the following plan: I want to install for example limma inclusive all needed other sub packages (add-on). Can anyone tell me the corresponding command? Thanks, Corinna Here is the result of the command library(): Pakete in Library

Hi, I have the following data frame: > print(mydatframe) __DATAFRAME__ V1 V2 V3 1 1007_s_at DDR1 discoidin domain receptor tyrosine kinase 1 2 1053_at RFC2 replication factor C (activator 1) 2, 40kDa 3 117_at HSPA6 heat shock 70kDa protein 6 (HSP70B') __END__ Is there a way to create a hash with V2 as Key and V3 as its value? - Gundala Viswanath Jakarta - Indonesia

Hi, I have been trying to find a solution to this issue, but have not been able to so ! I am trying to use sapply on the function getSYMBOL, an extract from the list is: > test.goP[13:14] $`GO:0000050` IEA IEA IEA IEA TAS TAS TAS IEA "5270753" "5720725" "1690128" "4850681" "110433" "2640544"

Hi I am running the following code: sym <- c(sym1,sym2,sym4) lifedxm <- c("O-BD","O-WELL","O-UNI") life <- c(lifedxm,lifedxm,lifedxm) tp <- c("TP-ANY","TP-ANY", "TP-ANY", "TP-SUB", "TP-SUB", "TP-SUB", "TP-CLIN" , "TP-CLIN", "TP-CLIN") data <-

Hello, ?delayedAssign presents substitute() as a way to look at the expression in the promise. However, msg <- "old" delayedAssign("x", msg) msg <- "new!" x #- new! substitute(x) #- x (was 'msg' ?) Here, we just got 'x'... shouldn't we got 'msg'? Same result when the promise is not evaluated yet: delayedAssign("x",

The help files for delayedAssign and substitute both say that substitute() can be used to see the expression associated with a promise. However, I can't see how to do that. When I try the example in help file for delayedAssign I don't see substitute() extracting the promise, e.g.: > msg <- "old" > delayedAssign("x", msg) > msg <-

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 All, maybe this is something obvious, I seem to be incapable of understanding how S4 works. So, in package 'A' I defined a "summary" method for my class: setMethod("summary", signature(object="ListHyperGResult"), function(object, pvalue=pvalueCutoff(object), categorySize=NULL) { "whatever" })

I'm not sure if this is a known peculiarity or a bug, but I stumbled across what I think is very odd behavior from delayedAssign. In the below example x switches values the first two times it is evaluated. > delayedAssign("x", {x <- 2; x+3}) > x==x [1] FALSE > delayedAssign("x", {x <- 2; x+3}) > x [1] 5 > x [1] 2 The ?delayedAssign documentation says

The last two lines of example(delayedAssign) give this: > e <- (function(x, y = 1, z) environment())(1+2, "y", {cat(" HO! "); pi+2}) > (le <- as.list(e)) # evaluates the promises $x <promise: 0x032b31f8> $y <promise: 0x032b3230> $z <promise: 0x032b3268> which contrary to the comment appears unevaluated. Is the comment wrong or is it supposed to

Dear all, I am a PhD student working with Affymetrix HGU133atag array for analyzing the Latin square experiment. I was trying to generate gene expression index for hgu133atag array for PDNN model. While extracting the chiptype specific data structure, I got the following error- > library(affypdnn) Loading required package: affy Loading required package: Biobase Welcome to Bioconductor

The Bioconductor build for a package DirichletMultinomial on R Under development (unstable) (2013-02-26 r62077) -- "Unsuffered Consequences" at http://bioconductor.org/checkResults/devel/bioc-LATEST/DirichletMultinomial/george2-buildsrc.html shows * creating vignettes ... ERROR ... Error: processing vignette ?DirichletMultinomial.Rnw? failed with diagnostics: chunk 21 (label

Hi, Trying to compile one of the latest snapshot tarballs of R-devel gives me the following error (64-bit openSUSE 10.3): ... make[2]: Entering directory `/loc/home/biocbuild/bbs-2.4-bioc/R/src/library/Recommended' make[2]: *** No rule to make target `VR.ts', needed by `stamp-recommended'. Stop. make[2]: Leaving directory

Hi, I'm running into a case where byte-compilation changes the semantic of a function. This is with R 3.4.0: foo <- function(x) { TRUE && x } foo(c(a=FALSE)) # [1] FALSE # OK foo(c(a=TRUE)) # [1] TRUE # OK foo(c(a=FALSE)) # a # ???? # FALSE The 3rd call returned a result that it different from the 1st call! After