Question

Error: IdeogramTrack (Gviz)

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Tim Smith ★ 1.1k

@tim-smith-1532

Last seen 10.2 years ago

Hi, I believe I have the latest version of Gviz, but still get an error: > ideoTrack <- IdeogramTrack(genome="hg19", chromosome=3) Error in validObject(.Object) : Â invalid class âSeqinfoâ object: 'seqnames(x)' cannot contain zero-length or duplicated names Am I doing something wrong? My sessionInfo() is given below. thanks! =============================================== > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] gridÂ Â Â Â Â splinesÂ Â statsÂ Â Â Â graphicsÂ grDevices utilsÂ Â Â Â datasetsÂ methodsÂ Â baseÂ Â Â Â other attached packages: Â [1] xtable_1.7-1Â Â Â Â Â Â Â Â Â IRanges_1.14.4Â Â Â Â Â Â Â Gviz_1.0.1Â Â Â Â Â Â Â Â Â Â Â GenomeGraphs_1.16.0Â Â quantsmooth_1.22.2Â Â Â quantreg_4.97Â Â Â Â Â Â Â Â [7] SparseM_0.97Â Â Â Â Â Â Â Â Â seqLogo_1.22.0Â Â Â Â Â Â Â lsr_0.2.2Â Â Â Â Â Â Â Â Â Â Â Â KEGG.db_2.7.1Â Â Â Â Â Â Â Â multicore_0.1-7Â Â Â Â Â Â gplots_2.11.0Â Â Â Â Â Â Â [13] MASS_7.3-23Â Â Â Â Â Â Â Â Â Â KernSmooth_2.23-10Â Â Â caTools_1.14Â Â Â Â Â Â Â Â Â gdata_2.12.0Â Â Â Â Â Â Â Â Â heatmap.plus_1.3Â Â Â Â Â gridExtra_0.9.1Â Â Â Â Â [19] ggdendro_0.1-12Â Â Â Â Â Â ggplot2_0.9.3.1Â Â Â Â Â Â hgu133a.db_2.7.1Â Â Â Â Â affy_1.34.0Â Â Â Â Â Â Â Â Â Â genefilter_1.38.0Â Â Â Â biomaRt_2.12.0Â Â Â Â Â Â [25] org.Hs.eg.db_2.7.1Â Â Â GOstats_2.22.0Â Â Â Â Â Â Â graph_1.34.0Â Â Â Â Â Â Â Â Â Category_2.22.0Â Â Â Â Â Â GO.db_2.7.1Â Â Â Â Â Â Â Â Â Â RSQLite_0.11.2Â Â Â Â Â Â [31] DBI_0.2-5Â Â Â Â Â Â Â Â Â Â Â Â geneplotter_1.34.0Â Â Â annotate_1.34.1Â Â Â Â Â Â AnnotationDbi_1.18.4Â Biobase_2.16.0Â Â Â Â Â Â Â BiocGenerics_0.2.0Â Â [37] colorRamps_2.3Â Â Â Â Â Â Â RColorBrewer_1.0-5Â Â Â sparcl_1.0.3Â Â Â Â Â Â Â Â Â gap_1.1-9Â Â Â Â Â Â Â Â Â Â Â Â plotrix_3.4-6Â Â Â Â Â Â Â Â som_0.3-5Â Â Â Â Â Â Â Â Â Â Â [43] pvclust_1.2-2Â Â Â Â Â Â Â Â compute.es_0.2.1Â Â Â Â Â sm_2.2-4.1Â Â Â Â Â Â Â Â Â Â Â imputation_2.0.1Â Â Â Â Â locfit_1.5-9Â Â Â Â Â Â Â Â Â TimeProjection_0.2.0 [49] Matrix_1.0-12Â Â Â Â Â Â Â Â timeDate_2160.97Â Â Â Â Â lubridate_1.2.0Â Â Â Â Â Â gbm_2.0-8Â Â Â Â Â Â Â Â Â Â Â Â lattice_0.20-15Â Â Â Â Â Â survival_2.37-4Â Â Â Â Â [55] RobustRankAggreg_1.0Â impute_1.30.0Â Â Â Â Â Â Â Â reshape_0.8.4Â Â Â Â Â Â Â Â plyr_1.8Â Â Â Â Â Â Â Â Â Â Â Â Â zoo_1.7-9Â Â Â Â Â Â Â Â Â Â Â Â data.table_1.8.8Â Â Â Â [61] foreach_1.4.0Â Â Â Â Â Â Â Â foreign_0.8-53Â Â Â Â Â Â Â languageR_1.4Â Â Â Â Â Â Â Â preprocessCore_1.18.0 gtools_2.7.1Â Â Â Â Â Â Â Â Â BiocInstaller_1.4.9Â [67] hash_2.2.6Â Â Â Â Â Â Â Â Â Â loaded via a namespace (and not attached): Â [1] affyio_1.24.0Â Â Â Â Â Â Â Biostrings_2.24.1Â Â Â bitops_1.0-4.2Â Â Â Â Â Â BSgenome_1.24.0Â Â Â Â Â codetools_0.2-8Â Â Â Â Â colorspace_1.2-1Â Â Â Â dichromat_2.0-0Â Â Â Â Â [8] digest_0.6.3Â Â Â Â Â Â Â Â GenomicRanges_1.8.13 GSEABase_1.18.0Â Â Â Â Â gtable_0.1.2Â Â Â Â Â Â Â Â iterators_1.0.6Â Â Â Â Â labeling_0.1Â Â Â Â Â Â Â Â munsell_0.4Â Â Â Â Â Â Â Â [15] proto_0.3-10Â Â Â Â Â Â Â Â RBGL_1.32.1Â Â Â Â Â Â Â Â Â RCurl_1.95-4.1Â Â Â Â Â Â reshape2_1.2.2Â Â Â Â Â Â Rsamtools_1.8.6Â Â Â Â Â rtracklayer_1.16.3Â Â scales_0.2.3Â Â Â Â Â Â Â [22] stats4_2.15.2Â Â Â Â Â Â Â stringr_0.6.2Â Â Â Â Â Â Â tools_2.15.2Â Â Â Â Â Â Â Â tree_1.0-33Â Â Â Â Â Â Â Â Â XML_3.96-1.1Â Â Â Â Â Â Â Â zlibbioc_1.2.0Â [[alternative HTML version deleted]]

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ADD COMMENT • link updated 11.4 years ago by Steve Lianoglou ★ 13k • written 11.4 years ago by Tim Smith ★ 1.1k

score 0 · Answer 1 · 2013-06-22

Hi, On Saturday, June 22, 2013, Tim Smith wrote: > Hi, > > I believe I have the latest version of Gviz, but still get an error: You do not have the latest version. In order to get it, you'll need to upgrade your version of R to the latest (3.0.1) then reinstall via biocLite -Steve > > > ideoTrack <- IdeogramTrack(genome="hg19", chromosome=3) > Error in validObject(.Object) : > invalid class Seqinfo object: 'seqnames(x)' cannot contain zero- length > or duplicated names > > Am I doing something wrong? > > My sessionInfo() is given below. > > thanks! > > =============================================== > > > > sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] grid splines stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] xtable_1.7-1 IRanges_1.14.4 Gviz_1.0.1 > GenomeGraphs_1.16.0 quantsmooth_1.22.2 quantreg_4.97 > [7] SparseM_0.97 seqLogo_1.22.0 lsr_0.2.2 > KEGG.db_2.7.1 multicore_0.1-7 gplots_2.11.0 > [13] MASS_7.3-23 KernSmooth_2.23-10 caTools_1.14 > gdata_2.12.0 heatmap.plus_1.3 gridExtra_0.9.1 > [19] ggdendro_0.1-12 ggplot2_0.9.3.1 hgu133a.db_2.7.1 > affy_1.34.0 genefilter_1.38.0 biomaRt_2.12.0 > [25] org.Hs.eg.db_2.7.1 GOstats_2.22.0 graph_1.34.0 > Category_2.22.0 GO.db_2.7.1 RSQLite_0.11.2 > [31] DBI_0.2-5 geneplotter_1.34.0 annotate_1.34.1 > AnnotationDbi_1.18.4 Biobase_2.16.0 BiocGenerics_0.2.0 > [37] colorRamps_2.3 RColorBrewer_1.0-5 sparcl_1.0.3 > gap_1.1-9 plotrix_3.4-6 som_0.3-5 > [43] pvclust_1.2-2 compute.es_0.2.1 sm_2.2-4.1 > imputation_2.0.1 locfit_1.5-9 TimeProjection_0.2.0 > [49] Matrix_1.0-12 timeDate_2160.97 lubridate_1.2.0 > gbm_2.0-8 lattice_0.20-15 survival_2.37-4 > [55] RobustRankAggreg_1.0 impute_1.30.0 reshape_0.8.4 > plyr_1.8 zoo_1.7-9 data.table_1.8.8 > [61] foreach_1.4.0 foreign_0.8-53 languageR_1.4 > preprocessCore_1.18.0 gtools_2.7.1 BiocInstaller_1.4.9 > [67] hash_2.2.6 > > loaded via a namespace (and not attached): > [1] affyio_1.24.0 Biostrings_2.24.1 bitops_1.0-4.2 > BSgenome_1.24.0 codetools_0.2-8 colorspace_1.2-1 > dichromat_2.0-0 > [8] digest_0.6.3 GenomicRanges_1.8.13 GSEABase_1.18.0 > gtable_0.1.2 iterators_1.0.6 labeling_0.1 > munsell_0.4 > [15] proto_0.3-10 RBGL_1.32.1 RCurl_1.95-4.1 > reshape2_1.2.2 Rsamtools_1.8.6 rtracklayer_1.16.3 > scales_0.2.3 > [22] stats4_2.15.2 stringr_0.6.2 tools_2.15.2 > tree_1.0-33 XML_3.96-1.1 zlibbioc_1.2.0 > > [[alternative HTML version deleted]] > > -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech [[alternative HTML version deleted]]