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:
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.cast...@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
--
Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550
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