Gviz::BiomartGeneRegionTrack works perfectly fine until today. It starts to return error messages. Below is what I did:
library(Gviz)
biomTrack <- BiomartGeneRegionTrack(genome="hg19", chromosome="chr5",
start=140769048, end=140811151)
The return message is:
Extra content at the end of the document
Error: 1: Extra content at the end of the document
Any ideas what is going on?
> sessionInfo()
R version 3.1.3 (2015-03-09)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8
[9] LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8
attached base packages:
[1] grid parallel stats4 stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] RColorBrewer_1.1-2 XLConnect_0.2-10
[3] XLConnectJars_0.2-9 biovizBase_1.14.1
[5] lattice_0.20-31 dichromat_2.0-0
[7] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.34.1
[9] rtracklayer_1.26.3 Biostrings_2.34.1
[11] XVector_0.6.0 GenomicFeatures_1.18.7
[13] AnnotationDbi_1.28.2 Biobase_2.26.0
[15] Gviz_1.12.0 GenomicRanges_1.18.4
[17] GenomeInfoDb_1.2.5 IRanges_2.0.1
[19] S4Vectors_0.4.0 BiocGenerics_0.12.1
[21] BiocInstaller_1.16.4
loaded via a namespace (and not attached):
[1] acepack_1.3-3.3 base64enc_0.1-2 BatchJobs_1.6
[4] BBmisc_1.9 BiocParallel_1.0.3 biomaRt_2.22.0
[7] bitops_1.0-6 brew_1.0-6 checkmate_1.5.2
[10] cluster_2.0.1 codetools_0.2-11 colorspace_1.2-6
[13] DBI_0.3.1 digest_0.6.8 fail_1.2
[16] foreach_1.4.2 foreign_0.8-63 Formula_1.2-1
[19] GenomicAlignments_1.2.2 ggplot2_1.0.1 gridExtra_0.9.1
[22] gtable_0.1.2 Hmisc_3.16-0 iterators_1.0.7
[25] latticeExtra_0.6-26 magrittr_1.5 MASS_7.3-40
[28] matrixStats_0.13.1 munsell_0.4.2 nnet_7.3-9
[31] plyr_1.8.2 proto_0.3-10 R.methodsS3_1.7.0
[34] Rcpp_0.11.6 RCurl_1.95-4.6 reshape2_1.4.1
[37] rJava_0.9-6 rpart_4.1-9 Rsamtools_1.18.3
[40] RSQLite_1.0.0 scales_0.2.4 sendmailR_1.2-1
[43] splines_3.1.3 stringi_0.4-1 stringr_1.0.0
[46] survival_2.38-1 tools_3.1.3 VariantAnnotation_1.12.8
[49] XML_3.98-1.1 zlibbioc_1.12.0
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