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Question: Error: IdeogramTrack (Gviz)
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gravatar for Tim Smith
4.4 years ago by
Tim Smith1.0k
Tim Smith1.0k wrote:
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) :   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]]
ADD COMMENTlink modified 4.4 years ago by Steve Lianoglou12k • written 4.4 years ago by Tim Smith1.0k
0
gravatar for Steve Lianoglou
4.4 years ago by
Genentech
Steve Lianoglou12k wrote:
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]]
ADD COMMENTlink written 4.4 years ago by Steve Lianoglou12k
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