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 > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
