similar to: package dependencies specification

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

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

Hi there, I got a problem when trying to read in a .cel file using ReadAffy(). R codes: require(affy) ReadAffy(filenames="CH1.CEL") It failed and I got the error, Error in read.celfile.header(as.character(filenames[[1]])) : Is CH1.CEL really a CEL file? tried reading as text, gzipped text, binary, gzipped binary, command console and gzipped command console formats Also, I tried

Hi, While trying to install hgu133acdf- windows package in R im getting the following error and unable to install the same. > source("http://bioconductor.org/biocLite.R") > biocLite("hgu133acdf") Using R version 2.10.0, biocinstall version 2.5.10. Installing Bioconductor version 2.5 packages: [1] "hgu133acdf" Please wait... trying URL '

Hi together, we received a question about the bioconductor package, maybe anybody could help the guy and I will deliver the message over our forum to him. If this way is allowed ... Regards Knut Here the question: Hello, I have installed R on a linux machine. I have then installed the biocLite.R package from bioconductor. I wanted to install a few other packages - hgu133plus2cdf, rma . I

Dear Madam/ Sir, I am using?R version 3.4.2.?I want to analyse microarray data. when I want to install "simpleaffy" package I get this error "package ?simpleaffy? is not available (for R version 3.4.2)". I have the same problem with?R version 3.3.2. Could you please help me to solve it? I am working with RStudio 0.99.903.exe. I also have problem in getting the new release of

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, I'm using a command in bioconductor that seems to require a package called hu6800cdf. I've installed this properly but I still get the same error: Could not find array definition file ' hu6800cdf.qcdef '. Simpleaffy does not know the QC parameters for this array type. See the package vignette for details about how to specify QC parameters manually. I've tried specifying

Hi, I have built R (current development version) and BioConductor 1.7 with portland group compiler on a AMD Opteron. When I ran qc assessment on Affymetrix latin square data set, I got the following output, Loading required package: affy Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view,

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Dear all, I am meeting some problems with memory allocation. I know it is an old issue, I'm sorry. I looked for a solution in the FAQs and manuals, mails, but without finding the working answer. I really hope you can help me. For instance, if I try to read micorarray data I get: > mab=ReadAffy(cdfname="hgu133plus2cdf") Error: cannot allocate vector of size 858.0 Mb > I

Hi, I decided to upgrade to 1.8 today... :-) Anyway, we are writing our own package that is dependent on a bioconductor library - 'affy'. I've checked and when I fire up R, library(affy) behaves as expected... so it all seems to be installed and OK... In the DESCRIPTION file in my package source I have the line: Depends: affy When I run R CMD check simpleaffy I get to: ... *

Hi everybody, I have a problem when trying to do the quality control with the packages simpleaffy and affyQCReport with the drosophila chip 2.0 At first I got the messeage, that the *.qcdef file is not there. I followed the instructions in tha manual and created the file like that: array drosophila2cdf alpha1 0.05 alpha2 0.065 spk bioB AFFX-r2-Ec-bioB-3_at spk bioC AFFX-r2-Ec-bioC-3_at spk bioD

Hi, Plotting a graphic into a postscript device using family="mono" returns the following error message: >> family 'mono' not included in PostScript device Looking at postscriptFonts() however lists the "Courier" font as availeable mono font. So where is the problem? Thanks guys for your help. Best regards Benjamin sessionInfo() R version 2.5.0

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>

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

Hello, I want to use expresso for preprocessing the hgu133a-spikein data from affycompII. But there is an error: > library(affy) > path <- "z:/Microarray/hgu133a-spikein/rawdata" > celFile <- list.celfiles(path=path,full.names=TRUE); > affyBatch <- ReadAffy(filenames=celFile[1:6]); > eset1 <-

Hi all , I have one query. i have list of some .cel files. in my program i have to mention the path of these .cel files part of my program is, rna.data<-exprs(justRMA(filenames=file.names, celfile.path=*datadir*, sampleNames=sample.names, phenoData=pheno.data, cdfname=cleancdfname(hg18_Affymetrix U133A))) in the place of "datadir" i have to mention the character string of the

Hello, I'm very new in working with tcl/tk in R and have a problem which will probably sound silly to most of you. Here is the code I have problems with: readcelfiles <- function() { require(tcltk) tt <- tktoplevel() tkgrid(tklabel(tt,text="Choose a directory!")) OnOK <- function() { fileDir<-tclvalue(tkchooseDirectory()) data.raw <-

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