Entering edit mode
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
