Hello, I want to draw a methylation heatmap by chromosome location using a package 'Gviz', but got an error w/ 'IdeogramTrack' function.
> library(Gviz) Loading required package: S4Vectors Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit Attaching package: 'S4Vectors' The following objects are masked from 'package:base': colMeans, colSums, expand.grid, rowMeans, rowSums Loading required package: IRanges Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: grid > itr=IdeogramTrack(genome="hg19",chromosome="chr1") Error: Expectation Failed
> sessionInfo() R version 3.3.0 (2016-05-03) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.9.5 (Mavericks) locale:  C attached base packages:  grid parallel stats4 stats graphics grDevices utils datasets methods base other attached packages:  Gviz_1.16.1 GenomicRanges_1.24.0 GenomeInfoDb_1.8.1 IRanges_2.6.0 S4Vectors_0.10.1  BiocGenerics_0.18.0 loaded via a namespace (and not attached):  SummarizedExperiment_1.2.2 VariantAnnotation_1.18.1 splines_3.3.0  lattice_0.20-33 colorspace_1.2-6 htmltools_0.3.5  rtracklayer_1.32.0 GenomicFeatures_1.24.2 chron_2.3-47  interactiveDisplayBase_1.10.3 survival_2.39-4 XML_3.98-1.4  foreign_0.8-66 DBI_0.4-1 ensembldb_1.4.5  BiocParallel_1.6.2 RColorBrewer_1.1-2 matrixStats_0.50.2  plyr_1.8.3 zlibbioc_1.18.0 Biostrings_2.40.1  munsell_0.4.3 gtable_0.2.0 latticeExtra_0.6-28  Biobase_2.32.0 biomaRt_2.28.0 BiocInstaller_1.22.2  httpuv_1.3.3 AnnotationDbi_1.34.3 Rcpp_0.12.5  acepack_1.3-3.3 xtable_1.8-2 BSgenome_1.40.0  scales_0.4.0 Hmisc_3.17-4 XVector_0.12.0  mime_0.4 Rsamtools_1.24.0 gridExtra_2.2.1  AnnotationHub_2.4.2 ggplot2_2.1.0 digest_0.6.9  biovizBase_1.20.0 shiny_0.13.2 tools_3.3.0  bitops_1.0-6 RCurl_1.95-4.8 RSQLite_1.0.0  dichromat_2.0-0 Formula_1.2-1 cluster_2.0.4  Matrix_1.2-6 data.table_1.9.6 httr_1.1.0  R6_2.1.2 rpart_4.1-10 GenomicAlignments_1.8.0  nnet_7.3-12
Although the error message "Expectation failed" would be given when connection to the server is troubled, I could access to UCSC (http://genome.ucsc.edu), which the function 'IdeogramTrack' requires access to.
Could anyone help me w/ possible solutions?
Bummer. Hate when we fail expectations :-)
I very much think that this was/is an issue with connectivity to UCSC. I can't reproduce the error on any of the machines that I have tried. Could have been a temporary timeout of the UCSC API. Being able to access the UCSC home page does not rule out problems in the REST API that Gviz/rtracklayer is using for the connection. You may also suffer from network access issues from within R. Are you behind a proxy? And can you access the web from within R at all. (e.g., can you do readLines("http://genome.ucsc.edu") )
Can you try again to check whether the problem still exists? And if so, please attach the output of traceback() after the error occurs in order to get a better idea of the call stack.
Thank you for your helping hands!
As you mentioned, I am behind a proxy using in-hospital LAN.
readLines("http://genome.ucsc.edu") generated a 485-line output w/o error, but the original codes still end up w error...
Attached please see the output of traceback().
I switched to mobile network and the codes passed!
I didn't realise the in hospital LAN was the cause.