Question: Error when using Gviz
0
gravatar for Asma rabe
3.5 years ago by
Asma rabe290
Japan
Asma rabe290 wrote:

Hi,

when i tried

itrack <- IdeogramTrack(genome ="hg19", chromosome = "chr3")

I got

Error in `genome<-`(`*tmp*`, value = "hg19") : 
  Failed to set session genome to 'hg19'​

Any idea?

sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS release 6.7 (Final)

locale:
[1] C

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

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg19_1.4.0      
 [2] BSgenome_1.38.0                        
 [3] rtracklayer_1.30.4                     
 [4] minfi_1.16.1                           
 [5] bumphunter_1.10.0                      
 [6] locfit_1.5-9.1                         
 [7] iterators_1.0.8                        
 [8] foreach_1.4.3                          
 [9] Biostrings_2.38.4                      
[10] XVector_0.10.0                         
[11] SummarizedExperiment_1.0.2             
[12] lattice_0.20-33                        
[13] Homo.sapiens_1.3.1                     
[14] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[15] org.Hs.eg.db_3.2.3                     
[16] GO.db_3.2.2                            
[17] RSQLite_1.0.0                          
[18] DBI_0.4-1                              
[19] OrganismDbi_1.12.1                     
[20] GenomicFeatures_1.22.13                
[21] AnnotationDbi_1.32.3                   
[22] Biobase_2.30.0                         
[23] Gviz_1.14.7                            
[24] GenomicRanges_1.22.4                   
[25] GenomeInfoDb_1.6.3                     
[26] IRanges_2.4.8                          
[27] S4Vectors_0.8.11                       
[28] BiocGenerics_0.16.1                    
[29] BiocInstaller_1.20.3                   

loaded via a namespace (and not attached):
 [1] nlme_3.1-128             bitops_1.0-6             matrixStats_0.50.2      
 [4] RColorBrewer_1.1-2       tools_3.2.3              doRNG_1.6               
 [7] nor1mix_1.2-1            R6_2.1.2                 rpart_4.1-10            
[10] Hmisc_3.17-4             colorspace_1.2-6         nnet_7.3-12             
[13] gridExtra_2.2.1          base64_2.0               preprocessCore_1.32.0   
[16] chron_2.3-47             graph_1.48.0             pkgmaker_0.22           
[19] scales_0.4.0             genefilter_1.52.1        quadprog_1.5-5          
[22] RBGL_1.46.0              stringr_1.0.0            digest_0.6.9            
[25] Rsamtools_1.22.0         foreign_0.8-66           illuminaio_0.12.0       
[28] siggenes_1.44.0          GEOquery_2.36.0          dichromat_2.0-0         
[31] limma_3.26.9             mclust_5.2               BiocParallel_1.4.3      
[34] dplyr_0.4.3              acepack_1.3-3.3          VariantAnnotation_1.16.4
[37] RCurl_1.95-4.8           magrittr_1.5             Formula_1.2-1           
[40] futile.logger_1.4.1      Matrix_1.2-6             Rcpp_0.12.5             
[43] munsell_0.4.3            stringi_1.1.1            MASS_7.3-45             
[46] zlibbioc_1.16.0          plyr_1.8.4               splines_3.2.3           
[49] multtest_2.26.0          annotate_1.48.0          beanplot_1.2            
[52] igraph_1.0.1             rngtools_1.2.4           corpcor_1.6.8           
[55] reshape2_1.4.1           codetools_0.2-14         biomaRt_2.26.1          
[58] mixOmics_6.0.0           futile.options_1.0.0     XML_3.98-1.4            
[61] biovizBase_1.18.0        latticeExtra_0.6-28      lambda.r_1.1.7          
[64] data.table_1.9.6         tidyr_0.5.1              gtable_0.2.0            
[67] openssl_0.9.4            assertthat_0.1           reshape_0.8.5           
[70] ggplot2_2.1.0            xtable_1.8-2             survival_2.39-4         
[73] tibble_1.0               ellipse_0.3-8            GenomicAlignments_1.6.3 
[76] registry_0.3             cluster_2.0.4           

 

Thank you very much in advance 

 

 

gviz • 460 views
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Asma rabe290
Answer: Error when using Gviz
0
gravatar for florian.hahne@novartis.com
3.5 years ago by
Switzerland

Could be related to this:

C: Gviz error 'Expectation Failed'

You are not running the current Bioconductor/R release versions. Can you upgrade your R and Bioc installation and try again.

Florian

ADD COMMENTlink written 3.5 years ago by florian.hahne@novartis.com1.6k
Answer: Error when using Gviz
0
gravatar for Asma rabe
3.5 years ago by
Asma rabe290
Japan
Asma rabe290 wrote:

Thank you  Folrian !

The problem i have seems to be related to networking. I could not access http://genome-euro.ucsc.edu/cgi-bin/  from internet browser (not sure why) but I can access (http://genome-euro.ucsc.edu/cgi-bin/hgTables)

When i tried the code below, it works fine but i got the latest genome (hg38 genome. Is there a way to specify hg19 instead of hg38?

 session <- browserSession("UCSC")

 genome(session)
[1] "hg38"

iTrack <- IdeogramTrack(genome ="hg38", chromosome ="chr3") #works fine

 

ADD COMMENTlink written 3.5 years ago by Asma rabe290
1

genome(session) <- "hg19"

But that is exactly what happens in Gviz under the hood. If that command fails, but if you can get the latest human genome than this must be an issue in the rtrackkayer package or with the UCSC web service API

 

ADD REPLYlink written 3.5 years ago by florian.hahne@novartis.com1.6k

Thanks Folrian !

Yeah, it fails with hg19 but not with hg38. Any suggestions?

genome(session) <- "hg38" #works fine
genome(session) <- "hg19"
Error in `genome<-`(`*tmp*`, value = "hg19") : 
  Failed to set session genome to 'hg19'

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by Asma rabe290
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