[BioC] VariantTools: callVariants error

[Hervé Pagès]

and also you are mixing release and devel packages, which is only going
to give you headaches. Make sure you stick either to BioC release (2.13)
or to BioC devel (2.14) by doing:

   library(BiocInstaller)
   biocValid()

Cheers,
H.


On 11/13/2013 09:18 AM, Michael Lawrence wrote:
> Please update your VariantAnnotation package.
>
>
> On Wed, Nov 13, 2013 at 8:08 AM, heyi xiao <xiaoheyiyh at 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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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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