[Bioc-devel] as(vcf, "VRanges") is broken in devel, possibly caused by S4Vectors:::recycleVector()

[Robert Castelo]

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