[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
>>
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--
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
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