When executing the example code below from the user's guide, the error below is returned after the last statement. I've noted posts regarding similar errors and so removed and reinstalled local libraries to no avail.
Any guidance would be greatly appreciated.
pwd<-"" #INPUT FILES- BedFiles, FASTA, etc.
path<- system.file("extdata/Test_100.bed",package="rGADEM")
BedFile<-paste(pwd,path,sep="")
BED<-read.table(BedFile,header=FALSE,sep="\t")
BED <-data.frame(chr=as.factor(BED[,1]),start=as.numeric(BED[,2]),end=as.numeric(BED[,3]))
rgBED <- IRanges(start=BED[,2],end=BED[,3])
Sequences <- RangedData(rgBED,space=BED[,1])
gadem<-GADEM(Sequences,verbose=1,genome=Hsapiens)
Retrieving sequences...
Error in .Primitive("c")(<S4 object of class "DNAStringSet">) :
could not find symbol "recursive" in environment of the generic function
traceback()
9: .Primitive("c")(<S4 object of class "DNAStringSet">)
8: do.call(c, unname(x))
7: do.call(c, unname(x))
6: unsplit_list_of_XVectorList("DNAStringSet", dnaset_list, as.factor(seqnames(names)))
5: .extractFromBSgenomeSingleSequences(x, sseq_args$names, sseq_args$start,
sseq_args$end, sseq_args$width, sseq_args$strand)
4: .local(x, ...)
3: getSeq(genome, spSeq, start = stSeq, end = edSeq, as.character = FALSE)
2: getSeq(genome, spSeq, start = stSeq, end = edSeq, as.character = FALSE)
1: GADEM(Sequences, verbose = 1, genome = Hsapiens)
R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X El Capitan 10.11.6
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] grid stats4 parallel stats graphics grDevices utils datasets
[9] methods base
other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome.Mmusculus.UCSC.mm10_1.4.0
[3] rGADEM_2.22.0 seqLogo_1.40.0
[5] BSgenome_1.42.0 rtracklayer_1.34.1
[7] GenomicRanges_1.26.2 GenomeInfoDb_1.10.2
[9] Biostrings_2.42.1 XVector_0.14.0
[11] IRanges_2.8.1 S4Vectors_0.12.1
[13] BiocGenerics_0.20.0 BiocInstaller_1.24.0
loaded via a namespace (and not attached):
[1] zlibbioc_1.20.0 GenomicAlignments_1.10.0 BiocParallel_1.8.1
[4] lattice_0.20-34 tools_3.3.3 SummarizedExperiment_1.4.0
[7] Biobase_2.34.0 Matrix_1.2-8 bitops_1.0-6
[10] RCurl_1.95-4.8 Rsamtools_1.26.1 XML_3.98-1.5
[13] locfit_1.5-9.1
