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

3 messages · Robert Castelo, Michael Lawrence

Original
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
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:
Robert Castelo
# 
hi,

got it, the current version on svn of VariantAnnotation (1.21.19) is 
ahead of what's available via biocLite(). i've checked out 
VariantAnnotation 1.21.19, installed it and the bug has dissapeared. 
problem solved.

thanks!

robert.
On 04/19/2017 05:39 PM, Michael Lawrence wrote: