[Bioc-devel] as(vcf, "VRanges") is broken in devel, possibly caused by S4Vectors:::recycleVector()
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.UTF8LC_COLLATE=en_US.UTF8 [5] LC_MONETARY=en_US.UTF8LC_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] stats4parallel 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_0.21.3BiocInstaller_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_1.9.6BSgenome_1.43.7 [7] lattice_0.20-35 tools_3.4.0 [9] grid_3.4.0DBI_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_1.95-4.8memoise_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
Re: [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-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_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] stats4parallel 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_0.5-1digest_0.6.10Matrix_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_1.1-1compiler_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 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.UTF8LC_COLLATE=en_US.UTF8 > [5] LC_MONETARY=en_US.UTF8LC_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] stats4parallel 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_0.21.3BiocInstaller_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_1.9.6BSgenome_1.43.7 > [7] lattice_0.20-35 tools_3.4.0 > [9] grid_3.4.0DBI_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_1.95-4.8memoise_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
Re: [Bioc-devel] as(vcf, "VRanges") is broken in devel, possibly caused by S4Vectors:::recycleVector()
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-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_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] stats4parallel 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_0.5-1digest_0.6.10Matrix_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_1.1-1compiler_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 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.UTF8LC_COLLATE=en_US.UTF8 [5] LC_MONETARY=en_US.UTF8LC_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] stats4parallel 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_0.21.3BiocInstaller_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_1.9.6BSgenome_1.43.7 [7] lattice_0.20-35 tools_3.4.0 [9] grid_3.4.0DBI_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_1.95-4.8memoise_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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
