Dear Bioconductor helpers, I am trying to plot a region of interest using the Gviz package. I met error when running the following example code: > library(Gviz) > library(GenomicRanges) > bmTrack <- BiomartGeneRegionTrack(start=26682683, end=26711643, + chromosome=7, genome="mm9") Entity 'nbsp' not defined Entity 'hellip' not defined Entity 'hellip' not defined Entity 'nbsp' not defined Entity 'raquo' not defined Entity 'hellip' not defined Entity 'hellip' not defined Entity 'hellip' not defined Entity 'hellip' not defined Entity 'hellip' not defined Opening and ending tag mismatch: img line 68 and li Opening and ending tag mismatch: li line 68 and ul Opening and ending tag mismatch: ul line 67 and div Entity 'copy' not defined Opening and ending tag mismatch: div line 19 and body Opening and ending tag mismatch: body line 17 and html Premature end of data in tag html line 2 Error: 1: Entity 'nbsp' not defined 2: Entity 'hellip' not defined 3: Entity 'hellip' not defined 4: Entity 'nbsp' not defined 5: Entity 'raquo' not defined 6: Entity 'hellip' not defined 7: Entity 'hellip' not defined 8: Entity 'hellip' not defined 9: Entity 'hellip' not defined 10: Entity 'hellip' not defined 11: Opening and ending tag mismatch: img line 68 and li 12: Opening and ending tag mismatch: li line 68 and ul 13: Opening and ending tag mismatch: ul line 67 and div 14: Entity 'copy' not defined 15: Opening and ending tag mismatch: div line 19 and body 16: Opening and ending tag mismatch: body line 17 and html 17: Premature end of data in tag html line 2 > sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1
locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] grid parallel stats4 stats graphics grDevices utils [8] datasets methods base other attached packages: [1] Gviz_1.16.1 GenomicRanges_1.24.2 GenomeInfoDb_1.8.2 [4] IRanges_2.6.1 S4Vectors_0.10.2 BiocGenerics_0.18.0 loaded via a namespace (and not attached): [1] SummarizedExperiment_1.2.3 VariantAnnotation_1.18.3 [3] splines_3.3.1 lattice_0.20-33 [5] colorspace_1.2-6 htmltools_0.3.5 [7] rtracklayer_1.32.1 GenomicFeatures_1.24.4 [9] chron_2.3-47 interactiveDisplayBase_1.10.3 [11] survival_2.39-5 XML_3.98-1.4 [13] foreign_0.8-66 DBI_0.4-1 [15] ensembldb_1.4.7 BiocParallel_1.6.2 [17] RColorBrewer_1.1-2 matrixStats_0.50.2 [19] plyr_1.8.4 zlibbioc_1.18.0 [21] Biostrings_2.40.2 munsell_0.4.3 [23] gtable_0.2.0 latticeExtra_0.6-28 [25] Biobase_2.32.0 biomaRt_2.28.0 [27] BiocInstaller_1.22.3 httpuv_1.3.3 [29] AnnotationDbi_1.34.4 Rcpp_0.12.5 [31] acepack_1.3-3.3 xtable_1.8-2 [33] BSgenome_1.40.1 scales_0.4.0 [35] Hmisc_3.17-4 XVector_0.12.0 [37] mime_0.5 Rsamtools_1.24.0 [39] gridExtra_2.2.1 AnnotationHub_2.4.2 [41] ggplot2_2.1.0 digest_0.6.9 [43] biovizBase_1.20.0 shiny_0.13.2 [45] tools_3.3.1 bitops_1.0-6 [47] RCurl_1.95-4.8 RSQLite_1.0.0 [49] dichromat_2.0-0 Formula_1.2-1 [51] cluster_2.0.4 Matrix_1.2-6 [53] data.table_1.9.6 httr_1.2.1 [55] R6_2.1.2 rpart_4.1-10 [57] GenomicAlignments_1.8.4 nnet_7.3-12 > Thank you for help, Holly _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
