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Question: Error: Failed to set session genome to...
2
gravatar for liz.ingsimmons
3.2 years ago by
United Kingdom
liz.ingsimmons120 wrote:

Hi,

I'm having the same "Failed to set session genome to..." error as Failed to set session genome to ... and Rtracklayer not able to set session genome to mm9 using US server. hg19 and european server are working.

Example:

library(rtracklayer)
session <- browserSession()
genome(session) <- "hg19" #this works
genome(session) <- "mm9" #this doesn't work, neither does hg18, mm10, dm6, dr7, etc
#Error in `genome<-`(`*tmp*`, value = "mm9") :
# Failed to set session genome to 'mm9'

session <- browserSession(url = 'http://genome-euro.ucsc.edu/cgi-bin/')
genome(session) <- "mm9" #this now works

This is okay as a workaround but my actual use case is for getting an ideogram track from Gviz:

library(Gviz)
itrack <- IdeogramTrack(genome = "mm9", chromosome = "chr6") #fails with same error as above

There's no option to specify which url to use with Gviz.

I realise that the previous people with this problem have been told it's likely a local network issue that needs to be debugged on their end, but I don't know where to begin to try to debug it. Does anyone have any suggestions? The same error occurs using both my home and work internet connections, and using different computers.

If it's not possible to fix this issue, it'd be great to get an option to specify which url to use for getting the ideogram track for Gviz, or another workaround.

Thanks for any help.

Liz

sessionInfo:

R version 3.2.0 (2015-04-16)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.2 (Yosemite)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
[1] Gviz_1.12.0          rtracklayer_1.28.1   GenomicRanges_1.20.2
[4] GenomeInfoDb_1.4.0   IRanges_2.2.1        S4Vectors_0.6.0     
[7] BiocGenerics_0.14.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.11.5              RColorBrewer_1.1-2       futile.logger_1.4.1     
 [4] plyr_1.8.2               XVector_0.8.0            GenomicFeatures_1.20.0  
 [7] bitops_1.0-6             futile.options_1.0.0     tools_3.2.0             
[10] zlibbioc_1.14.0          rpart_4.1-9              biomaRt_2.24.0          
[13] digest_0.6.8             BSgenome_1.36.0          RSQLite_1.0.0           
[16] gtable_0.1.2             lattice_0.20-31          biovizBase_1.16.0       
[19] DBI_0.3.1                proto_0.3-10             cluster_2.0.1           
[22] stringr_0.6.2            Biostrings_2.36.0        nnet_7.3-9              
[25] Biobase_2.28.0           AnnotationDbi_1.30.0     XML_3.98-1.1            
[28] survival_2.38-1          BiocParallel_1.2.0       foreign_0.8-63          
[31] latticeExtra_0.6-26      Formula_1.2-1            reshape2_1.4.1          
[34] ggplot2_1.0.1            lambda.r_1.1.7           MASS_7.3-40             
[37] Rsamtools_1.20.1         scales_0.2.4             Hmisc_3.15-0            
[40] matrixStats_0.14.0       GenomicAlignments_1.4.0  splines_3.2.0           
[43] dichromat_2.0-0          colorspace_1.2-6         acepack_1.3-3.3         
[46] RCurl_1.95-4.5           munsell_0.4.2            VariantAnnotation_1.14.0

 

ADD COMMENTlink modified 2.9 years ago by florian.hahne@novartis.com1.6k • written 3.2 years ago by liz.ingsimmons120

Hi Liz,

I also do still experience the same issue and I didn't succeed in solving it, besides using the workaround you reported. 

ADD REPLYlink written 3.2 years ago by federico.comoglio100
3
gravatar for florian.hahne@novartis.com
3.2 years ago by
Switzerland

I will make some changes to Gviz to allow passing in a non-default URL to UCSC. Since we are using these connections in a bunch of places, the natural route to make changes is probably through a package option. Something like

options(GvizUCSCPath="someURl")

In a way this actually belongs to the rtracklayer package, but for a quick fox I don't mind having this within Gviz. Will get back with details soon.

ADD COMMENTlink written 3.2 years ago by florian.hahne@novartis.com1.6k

That would be very helpful. Having it as a package option makes sense. Thank you!

ADD REPLYlink written 3.2 years ago by liz.ingsimmons120
1
gravatar for florian.hahne@novartis.com
2.9 years ago by
Switzerland

Your R and Bioc are quite outdated. Please upgrade the the latest version, which should fix these issues. You want R 3.2.1 and Gviz >=1.12.1

 

Florian

ADD COMMENTlink written 2.9 years ago by florian.hahne@novartis.com1.6k
0
gravatar for Senthil
2.9 years ago by
Senthil0
Germany
Senthil0 wrote:

Any success with this issue? I am getting the same problem....

Error in `genome<-`(`*tmp*`, value = "mm9") :
  Failed to set session genome to 'mm9'

 

 

 

 

ADD COMMENTlink written 2.9 years ago by Senthil0
0
gravatar for florian.hahne@novartis.com
2.9 years ago by
Switzerland

This should be fixed now. Please send your sessionInfo() output.

ADD COMMENTlink written 2.9 years ago by florian.hahne@novartis.com1.6k
0
gravatar for Senthil
2.9 years ago by
Senthil0
Germany
Senthil0 wrote:

R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

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=C              LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] GenomicRanges_1.16.4 GenomeInfoDb_1.0.2   IRanges_1.22.10     
[4] Gviz_1.8.4           BiocGenerics_0.10.0

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3          AnnotationDbi_1.26.1     base64enc_0.1-3         
 [4] BatchJobs_1.6            BBmisc_1.9               Biobase_2.24.0          
 [7] BiocParallel_0.6.1       biomaRt_2.20.0           Biostrings_2.32.1       
[10] biovizBase_1.12.3        bitops_1.0-6             brew_1.0-6              
[13] BSgenome_1.32.0          checkmate_1.6.2          cluster_2.0.3           
[16] codetools_0.2-14         colorspace_1.2-6         DBI_0.3.1               
[19] dichromat_2.0-0          digest_0.6.8             fail_1.2                
[22] foreach_1.4.2            foreign_0.8-66           Formula_1.2-1           
[25] GenomicAlignments_1.0.6  GenomicFeatures_1.16.3   ggplot2_1.0.1           
[28] gridExtra_2.0.0          gtable_0.1.2             Hmisc_3.16-0            
[31] iterators_1.0.7          lattice_0.20-33          latticeExtra_0.6-26     
[34] magrittr_1.5             MASS_7.3-44              matrixStats_0.14.2      
[37] munsell_0.4.2            nnet_7.3-8               plyr_1.8.3              
[40] proto_0.3-10             RColorBrewer_1.1-2       Rcpp_0.12.1             
[43] RCurl_1.95-4.7           reshape2_1.4.1           rpart_4.1-10            
[46] Rsamtools_1.16.1         RSQLite_1.0.0            rtracklayer_1.24.2      
[49] scales_0.3.0             sendmailR_1.2-1          splines_3.1.0           
[52] stats4_3.1.0             stringi_0.5-5            stringr_1.0.0           
[55] survival_2.38-3          tools_3.1.0              VariantAnnotation_1.10.5
[58] XML_3.98-1.3             XVector_0.4.0            zlibbioc_1.10.0         
>

 

ADD COMMENTlink written 2.9 years ago by Senthil0
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