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

[Michael Lawrence]

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
>