hi,
it seems that recent changes to S4Vectors are breaking the coercion from
the '*VCF' class to the 'VRanges' class. the traceback points to the
private function 'recycleVector() from the 'S4Vectors' package, please
find below the minimal example that reproduces the problem with the
session information.
cheers,
robert.
library(VariantAnnotation)
example(VRanges)
as(vcf, "VRanges")
Error in ans[] <- x : replacement has length zero
traceback()
4: S4Vectors:::recycleVector(ref, maxLen)
3: VRanges(seqnames, ranges, ref, alt, totalDepth, refDepth, altDepth,
hardFilters = FilterRules(), sampleNames = sampleNames,
softFilterMatrix = filter,
meta)
2: asMethod(object)
1: as(vcf, "VRanges")
sessionInfo()
R Under development (unstable) (2017-03-23 r72385)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /opt/R/R-devel/lib64/R/lib/libRblas.so
LAPACK: /opt/R/R-devel/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF8 LC_COLLATE=en_US.UTF8
[5] LC_MONETARY=en_US.UTF8 LC_MESSAGES=en_US.UTF8
[7] LC_PAPER=en_US.UTF8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices
[6] utils datasets methods base
other attached packages:
[1] VariantAnnotation_1.21.18 Rsamtools_1.27.16
[3] Biostrings_2.43.8 XVector_0.15.2
[5] SummarizedExperiment_1.5.9 DelayedArray_0.1.11
[7] matrixStats_0.52.2 Biobase_2.35.1
[9] GenomicRanges_1.27.23 GenomeInfoDb_1.11.10
[11] IRanges_2.9.19 S4Vectors_0.13.15
[13] BiocGenerics_0.21.3 BiocInstaller_1.25.3
[15] setwidth_1.0-4 colorout_1.1-2
loaded via a namespace (and not attached):
[1] Rcpp_0.12.10 AnnotationDbi_1.37.4
[3] GenomicAlignments_1.11.12 zlibbioc_1.21.0
[5] BiocParallel_1.9.6 BSgenome_1.43.7
[7] lattice_0.20-35 tools_3.4.0
[9] grid_3.4.0 DBI_0.6-1
[11] digest_0.6.12 Matrix_1.2-9
[13] GenomeInfoDbData_0.99.0 rtracklayer_1.35.12
[15] bitops_1.0-6 biomaRt_2.31.10
[17] RCurl_1.95-4.8 memoise_1.0.0
[19] RSQLite_1.1-2 compiler_3.4.0
[21] GenomicFeatures_1.27.14 XML_3.98-1.6
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