similar to: Install bioconductor

Hi, I am unable to build a package I maintain using a relatively current build of R-2.4.0 alpha, whereas the package builds just fine on R-2.3.1. Both versions of R were built from source. I'm hoping a guRu might be able to give some help. Some snippets from the build process: R-2.3.1 making DLL ... gcc -Ic:/R-2.3.1/src/extra/zlib -DHAVE_ZLIB -Ic:/R-2.3.1/include -Wall -O2 -c

Hi List, I'm trying to install aroma.affymetrix, which depend on many packages, affyio is one of them. The task is done on 32-bit Linux without problem. The same task was done on Solaris 9 with R-2.5.1 without problem. Following is the error message when installation affyio. I did try to put a file stdint.h I got from the web in the path, but got more error messages. Jun root@biostatsun1

My machine has 8GB memory. I had quit all other programs that might take a lot of memory when I try the script (before I post the first message in this thread). The cdf file is of only 741 MB. It is strange to me to see the error. On Mon, Dec 28, 2009 at 2:38 AM, Wolfgang Huber <whuber at embl.de> wrote: > Dear Peng Yu > > how big is the RAM of your computer? You could try with

Hi all, I figured out some things about an earlier question I posted today; this is a new question: I have a for-loop in which I have the following lines for (i in list.files(pattern = "*.dmp")) { currentfile <- read.table(i) vecrawrts <- as.vector(currentfile$V3) ... } Now, vecrawrts is numeric, but if I run the script on all the files with extension .dmp, I get the

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 all, Am new to R. I am having problems installing Bioconductor package in R on fedora core 4 running on AMD64 bit machine. this is the error message I get : gcc -shared -L/usr/local/lib -o affyPLM.so avg_log.o biweight.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o LESN.o lm.o lm_threestep.o log_avg.o matrix_functions.o

Hi all, All the files related to the question below are in http://ling.ohio-state.edu/~vasishth/TempRdir/ I've been using a script (called newresiduals.R, the code is in the above directory; I wanted to avoid cluttering up this message) that is run in the following manner at the command prompt: R --vanilla "wordlen-2-01-g1" < newresiduals.R What it does is: it goes through a

Hello, After running R CMD check on my package I received the following error on package dependencies: * using log directory 'C:/z-zBackup/Nuvera Bio on Iatros01/Development/RPackages/nvNormalize/nvNormalize.Rcheck' * using R version 2.9.1 (2009-06-26) * using session charset: ISO8859-1 * checking for file 'nvNormalize/DESCRIPTION' ... OK * checking extension type ... Package *

Hi everybody, I want to use macro in my R code. But defmacro was not in my libraries. So I installed it : > install.packages("gtools") Installing package(s) into ?C:/Program Files/R/R-2.13.2/library? (as ?lib? is unspecified) essai de l'URL 'http://cran.cict.fr/bin/windows/contrib/2.13/gtools_2.6.2.zip' Content type 'application/zip' length 102500 bytes (100 Kb)

Hello, I have problems running the R.matlab package. I work with R 2.3.1, under windows (using the Rgui). It seems that, even after loading the package, the "simple" functions such as writeMat() or readMat() are not recognized. For example, the following script leads to an error: > install.packages("R.matlab") --- Please select a CRAN mirror for use in this session ---

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, I follow the Bioconductor instruction (http://www.bioconductor.org/download <http://www.bioconductor.org/download> ) to install Biocoductor, there have some errors: /usr/lib/R/bin/SHLIB: line 115: make: command not found chmod: cannot access `/usr/local/lib/R/site-library/affyio/libs/*': No such file or directory ERROR: compilation failed for package 'affyio' **

Hi, when I try to import a microarray CEL batch, I get this error message: > myAB <- ReadAffy () Error in .Call("read_abatch", filenames, rm.mask, rm.outliers, rm.extra, : cannot allocate vector of length 1287151200 which, assuming the value is in bites, is below my RAM values (3 Gb recognized by Windows). The isse is, when I try to do memory.limit (size = 3000 ) the

I am developing a package that imports some functions from another package. The imported package (qcc) does not have a namespace and this is causing problems with loading of my package, which has a namespace. Is there a workaround to allow loading the namespace-less package? I searched the archives and found a suggestion that the package should be included in the Depends list, but this has not

Running R2.4.0 on Apple Mac OS X 10.4.8, in Emacs ESS mode, and also R.app. In an attempt to learn a bit more about a particular method (geneNames in package affy) I invoked getMethods("geneNames") which produced geneNames methods, but not the one in affy (output below). I had to know the signature (AffyBatch) in order to find the method > getMethod("geneNames",

Dear Help, After loading the pd.Citrus library and checking the DataFrame, I ran > the R code for: > > 1) 'oligo' > > > > {> library(pd.citrus) > Loading required package: RSQLite > Loading required package: DBI > > data(pmSequence) > > > show(pmSequence) > DataFrame with 341730 rows and 2 columns > fid sequence > <integer>

Hello, I am a new user of R and Linux (debian squeeze), and I am trying to install the ncdf library. First I don't know wich is the best to use (ncdf or ncdf4), But not matter the one I tried to install, it always failled. I try to find a solution to this common problem on the web, but I never find the good way to solve it. I hope you could help me I try many things during two days and now I

Steffen, When the new biomaRt tries to load it errors out because I do not have RMySQL installed. There is not a Windows binary for RMySQL and it does contain C code that I do not know how to build. I do not use the MySQL option in biomaRt. Does RMySQL need to be a required dependency? Below is my screen output and sessionINfo. require(biomaRt) Loading required package: biomaRt Loading required

Hi all, I tried to do normalization of affymetrix data with bioconductor on a Linux server. When I read in the cel files all seemed ok. But the next step caused an error. With Win XP all works fine. Did anyone experience similar problems? Thanks, Thomas > PI <- ReadAffy() > PI AffyBatch object size of arrays=712x712 features (14 kb) cdf=ATH1-121501 (??? affyids) number of

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