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.
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.
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:  en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages:  grid stats4 parallel stats graphics grDevices utils datasets  methods base other attached packages:  Gviz_1.12.0 rtracklayer_1.28.1 GenomicRanges_1.20.2  GenomeInfoDb_1.4.0 IRanges_2.2.1 S4Vectors_0.6.0  BiocGenerics_0.14.0 loaded via a namespace (and not attached):  Rcpp_0.11.5 RColorBrewer_1.1-2 futile.logger_1.4.1  plyr_1.8.2 XVector_0.8.0 GenomicFeatures_1.20.0  bitops_1.0-6 futile.options_1.0.0 tools_3.2.0  zlibbioc_1.14.0 rpart_4.1-9 biomaRt_2.24.0  digest_0.6.8 BSgenome_1.36.0 RSQLite_1.0.0  gtable_0.1.2 lattice_0.20-31 biovizBase_1.16.0  DBI_0.3.1 proto_0.3-10 cluster_2.0.1  stringr_0.6.2 Biostrings_2.36.0 nnet_7.3-9  Biobase_2.28.0 AnnotationDbi_1.30.0 XML_3.98-1.1  survival_2.38-1 BiocParallel_1.2.0 foreign_0.8-63  latticeExtra_0.6-26 Formula_1.2-1 reshape2_1.4.1  ggplot2_1.0.1 lambda.r_1.1.7 MASS_7.3-40  Rsamtools_1.20.1 scales_0.2.4 Hmisc_3.15-0  matrixStats_0.14.0 GenomicAlignments_1.4.0 splines_3.2.0  dichromat_2.0-0 colorspace_1.2-6 acepack_1.3-3.3  RCurl_1.95-4.5 munsell_0.4.2 VariantAnnotation_1.14.0