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

Not reproducing for me. This is with S4Vectors, VariantAnnotation,
etc, from svn.

R Under development (unstable) (2016-12-13 r71785)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] VariantAnnotation_1.21.19  Rsamtools_1.27.16
 [3] Biostrings_2.43.5          XVector_0.15.2
 [5] SummarizedExperiment_1.5.9 DelayedArray_0.1.11
 [7] matrixStats_0.51.0         Biobase_2.34.0
 [9] GenomicRanges_1.27.22      GenomeInfoDb_1.11.9
[11] IRanges_2.9.19             S4Vectors_0.13.15
[13] BiocGenerics_0.21.3

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.8              AnnotationDbi_1.36.0     GenomicAlignments_1.10.0
 [4] zlibbioc_1.20.0          BiocParallel_1.8.1       BSgenome_1.42.0
 [7] lattice_0.20-34          tools_3.4.0              grid_3.4.0
[10] DBI_0.5-1                digest_0.6.10            Matrix_1.2-7.1
[13] GenomeInfoDbData_0.99.0  rtracklayer_1.35.9       bitops_1.0-6
[16] biomaRt_2.30.0           RCurl_1.95-4.8           memoise_1.0.0
[19] RSQLite_1.1-1            compiler_3.4.0           BiocInstaller_1.25.3
[22] GenomicFeatures_1.27.14  XML_3.98-1.5



On Wed, Apr 19, 2017 at 7:06 AM, Robert Castelo <robert.castelo at upf.edu> wrote:

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