Please update your VariantAnnotation package.


On Wed, Nov 13, 2013 at 8:08 AM, heyi xiao <xiaoheyiyh@yahoo.com> wrote:

> 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
>
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