In the RNA-Seq workflow: gene-level exploratory analysis and differential expression

source('http://www.bioconductor.org/help/workflows/rnaseqGene/rnaseqGene.R')

in this step, the error appear,
se <- summarizeOverlaps(features=genes, reads=bamfiles,
                        mode="Union",
                        singleEnd=FALSE,
                        ignore.strand=TRUE,
                        fragments=TRUE )

Error: 8 errors; first error:
  Error in findOverlaps(query, grglist(unlist(subject, use.names = FALSE)), : error in evaluating the argument 'subject' in selecting a method for function 'findOverlaps': Error in .Call2("cigar_ranges", cigar, flag, space, pos, f, ops, drop.empty.ranges,  : 
  function '_new_RangeAE' not provided by package 'S4Vectors'

For more information, use bplasterror(). To resume calculation, re-call the function and
  set the argument 'BPRESUME' to TRUE or wrap the previous call in bpresume().

First traceback:
  42: source("http://www.bioconductor.org/help/workflows/rnaseqGene/rnaseqGene.R")
  41: withVisible(eval(ei, envir))
  40: eval(ei, envir)
  39: eval(expr, envir, enclos)
  38: summarizeOverlaps(features = genes, reads = bamfiles, mode = "Union", 
          singleEnd = FALSE, ignore.strand = TRUE, fragments = TRUE)
  37: summarizeOverlaps(features = genes, reads = bamfiles, mode = "Union", 
          singleEnd = FALSE, ignore.strand = TRUE, fragments = TR
In addition: Warning messages:
1: 'makeTranscriptDbFromGFF' is deprecated.
Use 'makeTxDbFromGFF' instead.
See help("Deprecated") 
2: In matchCircularity(seqlevels(gr), circ_seqs) :
  None of the strings in your circ_seqs argument match your seqnames.

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.3 (Yosemite)

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] stats4    parallel  graphics  grDevices utils     datasets  stats     methods   base     

other attached packages:
 [1] BiocInstaller_1.18.3    knitr_1.10.5            BiocStyle_1.6.0         GenomicAlignments_1.4.1
 [5] GenomicFeatures_1.20.1  AnnotationDbi_1.30.1    Biobase_2.28.0          Rsamtools_1.20.4       
 [9] Biostrings_2.36.1       XVector_0.8.0           airway_0.102.0          GenomicRanges_1.20.5   
[13] GenomeInfoDb_1.4.0      IRanges_2.2.4           S4Vectors_0.6.0         BiocGenerics_0.14.0    
[17] readr_0.1.1             sqldf_0.4-10            RSQLite_1.0.0           DBI_0.3.1              
[21] gsubfn_0.6-6            proto_0.3-10            dplyr_0.4.1             plyr_1.8.3             

loaded via a namespace (and not attached):
 [1] Rcpp_0.11.6        bitops_1.0-6       base64enc_0.1-2    iterators_1.0.7    BatchJobs_1.6     
 [6] tools_3.2.0        zlibbioc_1.14.0    biomaRt_2.24.0     digest_0.6.8       checkmate_1.5.3   
[11] foreach_1.4.2      rtracklayer_1.28.4 stringr_1.0.0.9000 tcltk_3.2.0        XML_3.98-1.2      
[16] fail_1.2           BiocParallel_1.2.3 sendmailR_1.2-1    magrittr_1.5       BBmisc_1.9        
[21] codetools_0.2-11   assertthat_0.1     brew_1.0-6         stringi_0.4-1      RCurl_1.95-4.6    
[26] chron_2.3-45 

how to solve the proble???

I'm not sure the cause of this error, because the major package version numbers match the sessionInfo() from the workflow.

Just a guess: can you try adding this line above the summarizeOverlaps() call:

library(BiocParallel)
register(SerialParam())

Hi,

I've got the same error. This error is due to version of "S4Vectors" package. In my computer i can run this code with the version 0.4.0 (instead of 0.6.0) without error.

This is very embarrassing because I need S4Vectors >= 0.5.0 for another packages ("ShortRead"). It is possible to have 2 versions for one package ?

Hope this help !