importFrom("utils", "close.socket", "make.socket", "read.socket", "write.socket")

importFrom("stats", "cor", "qnorm", "runif", "sd")

# Wildcard exports causes check to complain about undocumented (C++) functions to need to
# manually specify exported functions (including those used in tests)
# (Trying to use roxygen2 to autogenerate this file just causes massive problems - not resolving the C++ synbols at all)

importFrom(stats, family, pnorm, pt, qnorm, rchisq, rnorm, runif, median, cor, sd)
importFrom(reader, cat.path, reader, shift.rownames )
importFrom(graphics, abline, lines, points, rect, text, plot)
importFrom(methods, as, callNextMethod, is, new, prototype, representation, setAs, setClass, setGeneric, setMethod, setValidity)
importMethodsFrom(GenomicRanges, "names<-", length, names, start, end)
importMethodsFrom(GenomicRanges, width, strand, show, findOverlaps)
importMethodsFrom("GenomicRanges", "length", "names", "names<-", "[", "[<-", "[[<-", "$", "$<-")
importMethodsFrom(GenomeInfoDb, "seqlevels", "seqlevels<-", "genome<-", "genome", seqinfo, "seqinfo<-", seqnames, "seqnames<-", "seqlengths")
importFrom(IRanges, "%over%", IRanges, RangedData, showAsCell, PartitioningByEnd)
importMethodsFrom(IRanges, "colnames<-", "rownames<-", "universe<-", showAsCell)
importMethodsFrom(IRanges, as.data.frame, as.list, as.matrix, cbind, rbind, colnames)
importMethodsFrom(IRanges, end, findOverlaps, subsetByOverlaps, gsub, intersect, lapply)
importMethodsFrom(IRanges, mean, nrow, ncol, order, as.list)
importMethodsFrom(IRanges, ranges, rownames, runLength, space, flank, reduce, resize)
importMethodsFrom(IRanges, start, universe, unlist, width, "start<-", "width<-", "end<-", ranges, "ranges<-")
importFrom(S4Vectors, subjectHits, queryHits, mcols, "mcols<-", head, tail, DataFrame, Rle, runValue)
importFrom(utils, capture.output, download.file, read.table, write.table, read.delim)
importFrom("genoset", chrIndices, chrInfo, chrNames, "chrNames<-")

importFrom("stats", "formula", "glm", "poisson", "update")