rGADEM error retrieving sequences
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Entering edit mode
@christopherchaney-12541
Last seen 4.8 years ago

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 

 

 

rgadem • 1.2k views
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Entering edit mode
@martin-morgan-1513
Last seen 17 hours ago
United States

See A: Combining RangedData objects is broken (IRanges 2.8.1 with R version 3.3.3 RC) and reinstall your Bioconductor-based packages. I believe the problem comes from updating R over top of your existing libraries, rather installing new libraries with your new version of R.

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