Hi I'm trying to use summarizeOverlaps but I keep running into errors. Here is what I'm doing.

#Generate transcriptdb from gtf for features

txdb <- makeTranscriptDbFromGFF(file="data/humangene.gtf",
+                                 format="gtf",
+                                 dataSource="UCSC",
+                                 species="Homo Sapiens")

> saveDb(txdb, file="./data/humangene.sqlite")
> txdb <- loadDb("./data/humangene.sqlite")

#Extract exons

> eByg <- exonsBy(txdb, by="gene")

#Open bamfile for reads

> bf2 = open(BamFile("data/wgEncodeSydhRnaSeqK562Ifna6hPolyaAln.bam", "data/wgEncodeSydhRnaSeqK562Ifna6hPolyaAln.bam.bai")) #generate BAM reference

#put in BamFile into BamFileList

bfl2<-BamFileList(bf2)

#try to use summarizeOverlaps

genehits <- summarizeOverlaps(eByg, bfl2, mode="Union")

and I get this error

Error in bplapply(X, FUN, ..., BPRESUME = BPRESUME, BPPARAM = BPPARAM) : 
  error in evaluating the argument 'BPPARAM' in selecting a method for function 'bplapply': Error in registered()[[bpparamClass]] : 
  attempt to select less than one element

whether I use a BamFile a BamFileList or a direct pathway

Sessioninfo()

R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] GenomicFeatures_1.18.3  AnnotationDbi_1.28.1    Biobase_2.26.0          ShortRead_1.24.0        GenomicAlignments_1.2.1
 [6] Rsamtools_1.18.2        GenomicRanges_1.18.4    GenomeInfoDb_1.2.4      Biostrings_2.34.1       XVector_0.6.0          
[11] IRanges_2.0.1           S4Vectors_0.4.0         BiocParallel_1.0.0      BiocGenerics_0.12.1    

loaded via a namespace (and not attached):
 [1] base64enc_0.1-2     BatchJobs_1.5       BBmisc_1.8          biomaRt_2.22.0      bitops_1.0-6        brew_1.0-6         
 [7] checkmate_1.5.1     codetools_0.2-9     DBI_0.3.1           digest_0.6.8        fail_1.2            foreach_1.4.2      
[13] grid_3.1.2          hwriter_1.3.2       iterators_1.0.7     lattice_0.20-29     latticeExtra_0.6-26 RColorBrewer_1.1-2 
[19] RCurl_1.95-4.5      RSQLite_1.0.0       rtracklayer_1.26.2  sendmailR_1.2-1     stringr_0.6.2       tools_3.1.2        
[25] XML_3.98-1.1        zlibbioc_1.12.0    

Hi,

Unfortunately I can't reproduce the problem. You're getting this error with a file path, BamFile and BamFileList. Is that also true with the examples on the man page? For example, can you run this?

library(pasillaBamSubset)
library(TxDb.Dmelanogaster.UCSC.dm3.ensGene)
exbygene <- exonsBy(TxDb.Dmelanogaster.UCSC.dm3.ensGene, "gene")
fl <- untreated1_chr4()
res <- summarizeOverlaps(exbygene, fl)
> res
class: SummarizedExperiment
dim: 15682 1
exptData(0):
assays(1): counts
rownames(15682): FBgn0000003 FBgn0000008 ... FBgn0264726 FBgn0264727
rowData metadata column names(0):
colnames(1): untreated1_chr4.bam
colData names(0):

The error you're seeing says bplapply() (from BiocParallel pkg) can't find a backend for parallel execution. A default backend is used if none is provided but you can specify your own with the 'BPPARAM' arg. Do you see an error with these calls?

summarizeOverlaps(eByg, bf2, BPPARAM=SerialParam())

or

summarizeOverlaps(eByg, bf2, BPPARAM=SnowParam(1))

A couple of things worth mentioning though likely unrelated to the problem. There is no need manually 'open' the BamFile, summarizeOverlaps() does that internally.  BamFileList is only needed when there is >1 Bam file, otherwise just use BamFile.

Valerie

I also sometimes get this error , then when I restart the computer and call the functions again in RStudio it works fine. I have no clue what might be the reason.