[Bioc-devel] BiomartGeneRegionTrack question

[James W. MacDonald]

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 <xyang2 at 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")
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> 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
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> 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
>
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>



-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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