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Question: Gviz: BiomartGeneRegionTrack error
0
gravatar for Chao-Jen Wong
2.9 years ago by
USA/Seattle/Fred Hutchinson Cancer Research Center
Chao-Jen Wong30 wrote:

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         

ADD COMMENTlink modified 2.9 years ago by Thomas Maurel730 • written 2.9 years ago by Chao-Jen Wong30
0
gravatar for florian.hahne@novartis.com
2.9 years ago by
Switzerland

Looks like Biomart is currently down. Here is part of the content of the XML file that R tries to parse:

The Ensembl web service you requested is temporarily unavailable.\n  We are working to restore the service as soon as possible. We\napologise for any inconvenience caused.\n\n\n   

\n      More information about this downtime may be available on the http://www.ensembl.info/\">Ensembl Blog or the http://wtsi-status.blogspot.com\">Sanger status blog.\n   

\n   

 

Probably just a temporary outage.

Florian

ADD COMMENTlink written 2.9 years ago by florian.hahne@novartis.com1.5k
0
gravatar for Chao-Jen Wong
2.9 years ago by
USA/Seattle/Fred Hutchinson Cancer Research Center
Chao-Jen Wong30 wrote:

Thanks, Florian.

ADD COMMENTlink written 2.9 years ago by Chao-Jen Wong30
0
gravatar for Thomas Maurel
2.9 years ago by
Thomas Maurel730
United Kingdom
Thomas Maurel730 wrote:

Dear all,

I am afraid we experienced a power failure affecting many of our servers yesterday and some of our archive websites were down all night.

Most of the archive websites are now back online.

Apologies for any inconvenienced caused.

Regards,

Thomas

ADD COMMENTlink written 2.9 years ago by Thomas Maurel730
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