[BioC] VariantTools: callVariants error

heyi xiao xiaoheyiyh at yahoo.com
Wed Nov 13 22:16:49 CET 2013


Okay, I reinstalled/updated VariantAnnotation and BiocParallel using biocLite(). Only after restart a new R session, callVariants works now.
I appreciate Hervé’s suggestion too, I will update all other packages when I get time. 

--------------------------------------------
On Wed, 11/13/13, Hervé Pagès <hpages at fhcrc.org> wrote:

 Subject: Re: [BioC] VariantTools: callVariants error
 To: "Michael Lawrence" <lawrence.michael at gene.com>, "heyi xiao" <xiaoheyiy
 Cc: "bioconductor at r-project.org" <bioconductor at r-project.org>
 Date: Wednesday, November 13, 2013, 2:02 PM

 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.
 >
 >

 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
 >>
 >> _______________________________________________
 >> Bioconductor mailing list
 >> Bioconductor at r-project.org
 >> https://stat.ethz.ch/mailman/listinfo/bioconductor
 >> Search the archives:
 >> http://news.gmane.org/gmane.science.biology.informatics.conductor
 >>
 >
 >     [[alternative HTML version
 deleted]]
 >
 > _______________________________________________
 > Bioconductor mailing list
 > Bioconductor at r-project.org
 > https://stat.ethz.ch/mailman/listinfo/bioconductor
 > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
 >

 -- 
 Hervé Pagès

 Program in Computational Biology
 Division of Public Health Sciences
 Fred Hutchinson Cancer Research Center
 1100 Fairview Ave. N, M1-B514
 P.O. Box 19024
 Seattle, WA 98109-1024

 E-mail: hpages at fhcrc.org
 Phone:  (206) 667-5791
 Fax:    (206) 667-1319



More information about the Bioconductor mailing list