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Question: Gviz error in IdeogramTrack command
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gravatar for Taiki Tsutsui
22 days ago by
Taiki Tsutsui0 wrote:

Dear all,

I am new in this field. I am trying to visualizing genomic element using Gviz following its tutorial linked below.

https://www.bioconductor.org/help/course-materials/2012/BiocEurope2012/GvizEuropeanBioc2012.pdf

When I try IdeogramTrack command, I got a error message like following.

Perhaps I do not understand the clearly how Gviz works. Help is greatly appreciated! 

> itr <- IdeogramTrack(genome="mm9", chromosome="chr1")
Error in UseMethod("xmlNamespaceDefinitions") : 
  no applicable method for 'xmlNamespaceDefinitions' applied to an object of class "NULL"

My condition 

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=Japanese_Japan.932  LC_CTYPE=Japanese_Japan.932   
[3] LC_MONETARY=Japanese_Japan.932 LC_NUMERIC=C                  
[5] LC_TIME=Japanese_Japan.932    

attached base packages:
 [1] grid      parallel  stats4    stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
[1] XML_3.98-1.9         AnnotationHub_2.8.2  Gviz_1.20.0         
[4] GenomicRanges_1.28.6 GenomeInfoDb_1.12.3  IRanges_2.10.4      
[7] S4Vectors_0.14.6     BiocGenerics_0.22.0 

 

ADD COMMENTlink modified 22 days ago • written 22 days ago by Taiki Tsutsui0
0
gravatar for Taiki Tsutsui
22 days ago by
Taiki Tsutsui0 wrote:

I solved this. This is simply due to network issue in my institute.

When I change another network, IdeogramTrack works fine!

Thanks,

Taiki

ADD COMMENTlink written 22 days ago by Taiki Tsutsui0
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