Question: RIPSeeker package import error
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gravatar for Endre Sebestyen
6.3 years ago by
Endre Sebestyen10 wrote:
Hi! I have some issues with the RIPSeeker package at the start, when trying to import BED files. > bedfile1 <- getAlignGal(bedfiles[1],flagMultiHits=TRUE,genomeBuild=" hg19",format="bed") Processing /home/razor/work/prbb- cpeb4/data/pipeline/run2//sample_9-2_sorted_head.bed ... Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ?import? for signature ?"function", "missing", "missing"? > traceback() 4: stop(gettextf("unable to find an inherited method for function %s for signature %s", sQuote(fdef at generic), sQuote(cnames)), domain = NA) 3: (function (classes, fdef, mtable) { methods <- .findInheritedMethods(classes, fdef, mtable) if (length(methods) == 1L) return(methods[[1L]]) else if (length(methods) == 0L) { cnames <- paste0("\"", sapply(classes, as.character), "\"", collapse = ", ") stop(gettextf("unable to find an inherited method for function %s for signature %s", sQuote(fdef at generic), sQuote(cnames)), domain = NA) } else stop("Internal error in finding inherited methods; didn't return a unique method", domain = NA) })(list("function", "missing", "missing"), function (con, format, text, ...) standardGeneric("import"), <environment>) 2: import(file, asRangedData = FALSE) 1: getAlignGal(bedfiles[1], flagMultiHits = TRUE, genomeBuild = "hg19", format = "bed") > sessionInfo() R version 3.0.0 (2013-04-03) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] RIPSeeker_1.0.0 Rsamtools_1.12.0 Biostrings_2.28.0 rtracklayer_1.20.0 GenomicRanges_1.12.1 [6] IRanges_1.18.0 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] bitops_1.0-5 BSgenome_1.28.0 RCurl_1.95-4.1 stats4_3.0.0 tools_3.0.0 XML_3.96-1.1 zlibbioc_1.6.0 Thanks for any help. Endre
ripseeker • 869 views
ADD COMMENTlink written 6.3 years ago by Endre Sebestyen10
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