search for: bufferedmatrix

I'm in the process of converting some S3 methods to S4 methods. I have this function : setGeneric("enrichmentCalc", function(rs, organism, seqLen, ...){standardGeneric("enrichmentCalc")}) setMethod("enrichmentCalc", c("GenomeDataList", "BSgenome"), function(rs, organism, seqLen, ...) { ... ... ... })

Hi all, Since I was having several problems trying to work with a large matrix I started to use the package R.huge but I'm having the following problem > x<-FileByteMatrix("covtype.data",nrow=581012,ncol=55) Error: cannot allocate vector of size 770.8 Mb In addition: Warning messages: 1: Reached total allocation of 447Mb: see help(memory.size) in: readChar(con = con, nchar =

...section Warning: BioSeqClass_1.7.0.tar.gz:3: All text must be in a section Warning: BioSeqClass_1.7.0.tar.gz:4: All text must be in a section Error : BioSeqClass_1.7.0.tar.gz: Sections \title, and \name must exist and be unique in Rd files >>> On 64-bit Windows: R\bin\R.exe CMD build BufferedMatrix --> produces no output at all and returns code 0. >>> On 32-bit Windows: R\bin\R.exe CMD check --no-vignettes --timings daMA_1.21.0.tar.gz * using log directory 'E:/biocbld/bbs-2.7-bioc/meat/daMA.Rcheck' * using R version 2.12.0 Under development (unstable) (2010-08-26 r5281...

...-argon2 * R-ascii * R-askpass * R-assertthat * R-AUC * R-backports * R-base64enc * R-Bessel * R-BH * R-biglm * R-bindr * R-bindrcpp * R-Biobase * R-BiocGenerics * R-BiocParallel * R-biomaRt * R-Biostrings * R-bit * R-bit64 * R-bitops * R-blob * R-brew * R-BSgenome * R-BSgenome.Celegans.UCSC.ce2 * R-BufferedMatrix * R-BufferedMatrixMethods * R-Cairo * R-callr * R-car * R-caTools * R-cellranger * R-chron * R-cli * R-cliapp * R-clipr * R-clisymbols * R-coda * R-colorspace * R-combinat * R-commonmark * R-corpus * R-crayon * R-curl * R-data.table * R-date * R-DBI * R-dbplyr * R-debugme * R-DelayedArray * R-deldi...

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