Hi Holly, This list is intended for those that are developing packages. Your question should be asked on the support site (https://support.bioconductor.org). Please repost over there.
Best, Jim On Wed, Jul 20, 2016 at 2:04 PM, Holly <xya...@uchicago.edu> wrote: > 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 > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
