[BioC] VariantTools: callVariants error

[heyi xiao]

I tried the Basic usage example in VariantTools. I got error at the callVariants step. The error message shows that the indirect call to BiocParallel::bpmapply had some problem, but not sure what that is. Note that my VariantTools and depends are up-to-date. Below is the error and sessionInfo(). Thanks for any help in advance.

> called.variants <- callVariants(bam, tally.param)
Error in LastError$store(results = results, is.error = is.error, throw.error = TRUE) : 
  Errors occurred during execution. First error message:
Error in nrow(softFilterMatrix): error in evaluating the argument 'x' in selecting a method for function 'nrow': Error in FilterMatrix(nrow = length(gr), ncol = 0L, filterRules = FilterRules()) : 
  unused arguments (nrow = length(gr), ncol = 0)


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

First traceback:
28: callVariants(bam, tally.param)
27: callVariants(bam, tally.param)
26: .local(x, ...)
25: tallyVariants(x, tally.param)
24: tallyVariants(x, tally.param)
23: .local(x, ...)
22: bplapply(ind, tally_region, x = x, param = param, BPPARAM = BPPARAM)
21: bplapply(ind, tally_region, x = x, param = param, BPPARAM = BPPARAM)
20: bpmapply(FUN, X, MoreArgs = list(...), SIMPLIFY = FALSE, USE.NAMES = FALSE, 
        resume = resume, BPPARAM = BPPARAM)
19: bpmapply(FUN, X, MoreArgs = list(...), SIMPLIFY = FALS
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

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

other attached packages:
 [1] RSQLite_0.11.4           DBI_0.2-7                GenomicFeatures_1.13.19 
 [4] AnnotationDbi_1.23.18    Biobase_2.21.6           VariantTools_1.4.4      
 [7] VariantAnnotation_1.7.36 Rsamtools_1.13.25        Biostrings_2.29.14      
[10] GenomicRanges_1.14.3     XVector_0.2.0            IRanges_1.20.5          
[13] BiocGenerics_0.8.0      

loaded via a namespace (and not attached):
 [1] BBmisc_1.4                             
 [2] BSgenome_1.29.0                        
 [3] BatchJobs_1.1-1135                     
 [4] BiocParallel_0.4.1                     
 [5] LungCancerLines_0.0.9                  
 [6] Matrix_1.0-12                          
 [7] RCurl_1.95-4.1                         
 [8] TxDb.Hsapiens.UCSC.hg19.knownGene_2.9.2
 [9] XML_3.98-1.1                           
[10] biomaRt_2.17.2                         
[11] bitops_1.0-6                           
[12] brew_1.0-6                             
[13] codetools_0.2-8                        
[14] digest_0.6.3                           
[15] fail_1.2                               
[16] foreach_1.4.1                          
[17] gmapR_1.4.2                            
[18] grid_3.0.1                             
[19] iterators_1.0.6                        
[20] lattice_0.20-15                        
[21] org.Hs.eg.db_2.9.0                     
[22] plyr_1.8                               
[23] rtracklayer_1.21.9                     
[24] sendmailR_1.1-2                        
[25] stats4_3.0.1                           
[26] tools_3.0.1                            
[27] zlibbioc_1.7.0