search for: makecdfenv

...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 read_cdffile.c -o read_cdffile.o read_cdffile.c: In function `readQC': read_cdffile.c:565: warning: unused variable `param_unit' windres --include-dir c:/R-2.3.1/include -i makecdfenv_res.rc -o makecdfenv_res.o gcc -shared -s -o makecdfenv.dll makecdfenv.def read_cdffile.o makecdfenv_res.o -Lc:/R-2.3.1/bin -lR ... DLL made R-2.4.0 beta making DLL ... gcc -Ic:/rw2040dev/src/extra/zlib -DHAVE_ZLIB -Ic:/rw2040dev/include -Wall -O2 -std=gnu99 -c read_cdffile.c -o rea...

Hello useRs, I'm trying to install bioconductor on ubuntu edgy eft and R 2.4.0. I have some error messages during installation, in particular for the package "affy" : "Error: package 'affy' required by 'makecdfenv' could not be found" I have tryed to install 'makecdfenv' with the command : getBioC("makecdfenv") But I have this message : Running getBioC version 0.1.8 with R version 2.4.0 Running biocinstall version 1.9.9 with R version 2.4.0 Your version of R requires version 1....

...the >> following link. I'm wondering what the problem is with >> make.cdf.package. >> >> >> http://www.affymetrix.com/Auth/support/downloads/library_files/MoEx-1_0-st-v1.text.cdf.zip >> >> $ Rscript MoEx-1_0-st-v1.cdf.R >>> >>> library(makecdfenv) >> >> Loading required package: Biobase >> >> Welcome to Bioconductor >> >> ?Vignettes contain introductory material. To view, type >> ?'openVignette()'. To cite Bioconductor, see >> ?'citation("Biobase")' and for packages &...

...stom 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 <- tempdir() >make.cdf.package("file.cdf", cdf.path=getwd(), compress=FALSE, species = "Homo_sapiens", package.path = pkgpath, verbose=TRUE) dir(pkgpath) Method 2 #Set the...

I would like to build a package for the HT HG-U133+ PM arrays from affy, but I can't find any good documentation on how to go about it. Naively using makecdfenv's make.cdf.package() causes R to seg-fault. I'm unfamiliar with the CDF format as such, but I'm guessing that it's changed somewhat because the PM arrays no longer have P/A and mismatches. I'm looking to build cdf and probe packages, if possible, but have yet to find any doc...

Hi How do I install "gregmisc" packages? I did- % sudo R > install.packages("gregmisc") . . > barplot2() but, Error: couldn't find function "barplot2" -- atuya Mac OSX 10.2.6 R 1.7.1

I have encountered an issue while preparing some of the Bioconductor packages for our upcoming release, and Duncan Murdoch suggested that I bring one of the related points up here. The background is that we are building our packages under Windows with "Rcmd install --build" which will flag the zip options. When the total size of files in <pkg>\data are over a certain threshold of

Hi, I am using R 2.1.0 on Windows XP and when I type data() to list the datasets in R, there is a helpful hint to type 'data(package = .packages(all.available = TRUE))' to see the datasets in all of the packages -- not just the active ones. However, when I do this, I get the following message: > data(package = .packages(all.available = TRUE)) Error in rbind(...) : number of columns

...excel friendly file from the expression component of an exprSet. * DynDoc: A new package that provides a set of functions to create and interact with dynamic documents and vignettes * limma: A new package that provides functionality to handle linear models for microarray data. * makecdfenv: A package to create hash table environments from CDF files, as well as functionality to create data packages out of these environments. * RBGL: A new package that provides an interface to the Boost libraries for graph manipulation. * Rgraphviz: A new package that provides an interf...

...for KEGG keggorth graph support for KO, KEGG Orthology KernSmooth Functions for kernel smoothing for Wand & Jones (1995) lattice Lattice Graphics limma Linear Models for Microarray Data makecdfenv CDF Environment Maker MAQCsubset Experimental Data Package: MAQCsubset marray Exploratory analysis for two-color spotted microarray data MASS Main Package of Venables and Ripley's MASS matchprobes...

...ory improvement of ReadAffy, read.affybatch, justRMA. A mas5calls method was added to get Affymetrix's P/M/A calls. Cel and Cdf classes are no longer supported. Function, read.celfile and other Cel related methods and functions removed. Most Cdf related functions have moved to the makecdfenv package. Function read.probematrix added. It reads CEL files and returns a matrix of PM, MM, or both. This function is more memory efficient than read.affybatch. Also, affy no longer depends on the affydata package. For this reason some examples have been moved from affy vignettes...

...ory improvement of ReadAffy, read.affybatch, justRMA. A mas5calls method was added to get Affymetrix's P/M/A calls. Cel and Cdf classes are no longer supported. Function, read.celfile and other Cel related methods and functions removed. Most Cdf related functions have moved to the makecdfenv package. Function read.probematrix added. It reads CEL files and returns a matrix of PM, MM, or both. This function is more memory efficient than read.affybatch. Also, affy no longer depends on the affydata package. For this reason some examples have been moved from affy vignettes...

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