Rtracklayer not able to set session genome to mm9 using US server. hg19 and european server are working
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krijgerp • 0
@krijgerp-7726
Last seen 6.2 years ago
Netherlands

Dear all,

When I try to set the mm9 genome using rtracklayer  from the US UCSC server it does not work. 

session <- browserSession("UCSC")
genome(session)<-"mm9"  

 

Error in `genome<-`(`*tmp*`, value = "mm9") : 

  Failed to set session genome to 'mm9'

 

However, the hg19 genome is working when I use the US server. 

session <- browserSession("UCSC")
genome(session)<-"hg19"

Also when I use the european server, the mm9 genome is working.

session <- browserSession("UCSC",url="http://genome-euro.ucsc.edu/cgi-bin/")
genome(session)<-"mm9"
 

 

Any suggestions?

thanks,

Peter


> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=Dutch_Netherlands.1252  LC_CTYPE=Dutch_Netherlands.1252   
[3] LC_MONETARY=Dutch_Netherlands.1252 LC_NUMERIC=C                      
[5] LC_TIME=Dutch_Netherlands.1252    

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

other attached packages:
[1] rtracklayer_1.28.2   GenomicRanges_1.20.3 GenomeInfoDb_1.4.0   IRanges_2.2.1       
[5] S4Vectors_0.6.0      BiocGenerics_0.14.0 

loaded via a namespace (and not attached):
 [1] XML_3.98-1.1            Rsamtools_1.20.1        Biostrings_2.36.0      
 [4] bitops_1.0-6            GenomicAlignments_1.4.1 futile.options_1.0.0   
 [7] zlibbioc_1.14.0         XVector_0.8.0           futile.logger_1.4.1    
[10] lambda.r_1.1.7          BiocParallel_1.2.1      tools_3.2.0            
[13] RCurl_1.95-4.6         
 

rtracklayer mm9 ucsc • 2.1k views
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Likely related to what I describe here: Failed to set session genome to ...

Federico

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Yes, the same issue. Somehow related to the internet routing.

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thank you Michael. 

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oh,i have a similar problem, when i used IdeoViz::getIdeo to download table containing chromosomal extent and band locations from the UCSC genome browser.

> ideo <- getIdeo("hg19")   #Download table containing chromosomal extent and band locations from the UCSC genome browser; example "hg19"
Error in `genome<-`(`*tmp*`, value = "hg19") : 
  Failed to set session genome to 'hg19'


sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936 
[2] LC_CTYPE=Chinese (Simplified)_China.936   
[3] LC_MONETARY=Chinese (Simplified)_China.936
[4] LC_NUMERIC=C                              
[5] LC_TIME=Chinese (Simplified)_China.936    

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

other attached packages:
 [1] Gviz_1.14.7          IdeoViz_1.4.0        rtracklayer_1.30.4  
 [4] RColorBrewer_1.1-2   GenomicRanges_1.22.4 GenomeInfoDb_1.6.3  
 [7] IRanges_2.4.6        S4Vectors_0.8.11     Biobase_2.30.0      
[10] BiocGenerics_0.16.1  BiocInstaller_1.20.3

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.5                futile.logger_1.4.1       
 [3] plyr_1.8.3                 XVector_0.10.0            
 [5] GenomicFeatures_1.22.13    bitops_1.0-6              
 [7] futile.options_1.0.0       tools_3.2.3               
 [9] zlibbioc_1.16.0            rpart_4.1-10              
[11] biomaRt_2.26.1             digest_0.6.8              
[13] BSgenome_1.38.0            gtable_0.1.2              
[15] RSQLite_1.0.0              lattice_0.20-33           
[17] biovizBase_1.18.0          DBI_0.3.1                 
[19] gridExtra_2.0.0            cluster_2.0.3             
[21] Biostrings_2.38.3          nnet_7.3-11               
[23] AnnotationDbi_1.32.3       XML_3.98-1.3              
[25] survival_2.38-3            BiocParallel_1.4.3        
[27] foreign_0.8-66             Formula_1.2-1             
[29] latticeExtra_0.6-26        ggplot2_2.0.0             
[31] lambda.r_1.1.7             Rsamtools_1.22.0          
[33] scales_0.3.0               Hmisc_3.17-1              
[35] matrixStats_0.50.1         GenomicAlignments_1.6.3   
[37] splines_3.2.3              dichromat_2.0-0           
[39] SummarizedExperiment_1.0.2 colorspace_1.2-6          
[41] acepack_1.3-3.3            RCurl_1.95-4.7            
[43] munsell_0.4.2              VariantAnnotation_1.16.4  
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@martin-morgan-1513
Last seen 19 days ago
United States

A solution has been identified  on C: Gviz error 'Expectation Failed' and subsequent comments, and involves either using a mirror in the same region that you belong to or using rtracklayer from devel. It would be helpful to here whether this works.

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