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
Likely related to what I describe here: Failed to set session genome to ...
Federico
Yes, the same issue. Somehow related to the internet routing.
thank you Michael.
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