Oh man, one day at a time i guess. Thanks for the help. On Thu, May 2, 2013 at 3:42 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Sam, > > > On 5/2/2013 4:35 PM, Sam McInturf wrote: > >> Bioconductor users, >> I have been mapping my RNA seq reads using the GenomicRanges package, >> and was doing alright with it until I upgraded to R-3.0.0. At least I >> assume that the upgrade was the problem. After loading GenomicRanges the >> function BamFileList() is not longer a function. As below >> > > IIRC, the BamFileList function has never been in GenomicRanges, instead > being defined in Rsamtools. > > Best, > > Jim > > > >> library(GenomicRanges) >>> >> Loading required package: BiocGenerics >> Loading required package: parallel >> >> Attaching package: āBiocGenericsā >> >> The following objects are masked from āpackage:parallelā: >> >> >> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, >> clusterExport, clusterMap, parApply, parCapply, parLapply, >> parLapplyLB, parRapply, parSapply, parSapplyLB >> >> The following object is masked from āpackage:statsā: >> >> xtabs >> >> The following objects are masked from āpackage:baseā: >> >> >> anyDuplicated, as.data.frame, cbind, colnames, duplicated, eval, >> Filter, Find, get, intersect, lapply, Map, mapply, match, mget, >> order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, >> rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, >> tapply, union, unique, unlist >> >> Loading required package: IRanges >> >> BamFileList() >>> >> Error: could not find function "BamFileList" >> >> I work on two clusters, and both no longer work. What am I doing wrong, >> or >> what is an alternative to this method? I have been following the >> summerizeOverlaps vignette for mapping. >> >> thanks in advance! >> >> >> >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > -- Sam McInturf [[alternative HTML version deleted]]