[BioC] RIPSeeker package import error

[Endre Sebestyen]

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