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

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