{"action":"closed","issue":{"url":"https://api.github.com/repos/tengfei/ggbio/issues/70","repository_url":"https://api.github.com/repos/tengfei/ggbio","labels_url":"https://api.github.com/repos/tengfei/ggbio/issues/70/labels{/name}","comments_url":"https://api.github.com/repos/tengfei/ggbio/issues/70/comments","events_url":"https://api.github.com/repos/tengfei/ggbio/issues/70/events","html_url":"https://github.com/tengfei/ggbio/issues/70","id":141695542,"number":70,"title":"Issue with Rle objects","user":{"login":"cramanuj","id":3697274,"avatar_url":"https://avatars.githubusercontent.com/u/3697274?v=3","gravatar_id":"","url":"https://api.github.com/users/cramanuj","html_url":"https://github.com/cramanuj","followers_url":"https://api.github.com/users/cramanuj/followers","following_url":"https://api.github.com/users/cramanuj/following{/other_user}","gists_url":"https://api.github.com/users/cramanuj/gists{/gist_id}","starred_url":"https://api.github.com/users/cramanuj/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cramanuj/subscriptions","organizations_url":"https://api.github.com/users/cramanuj/orgs","repos_url":"https://api.github.com/users/cramanuj/repos","events_url":"https://api.github.com/users/cramanuj/events{/privacy}","received_events_url":"https://api.github.com/users/cramanuj/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-03-17T20:16:34Z","updated_at":"2016-03-17T20:40:00Z","closed_at":"2016-03-17T20:40:00Z","body":"Hi,\r\n\r\nI just started using the ggbio package and going over the documentation. I receive the following error message when trying to plot a karyogram -\r\n\r\n> autoplot(seqinfo(ideoCyto$hg19), layout = \"karyogram\")\r\nError in (function (classes, fdef, mtable)  : \r\n  unable to find an inherited method for function ‘Rle’ for signature ‘\"factor\", \"integer\"’\r\n\r\n> showMethods(\"Rle\")\r\nFunction: Rle (package S4Vectors)\r\nvalues=\"character\", lengths=\"integer\"\r\n    (inherited from: values=\"vectorORfactor\", lengths=\"integer\")\r\nvalues=\"character\", lengths=\"missing\"\r\n    (inherited from: values=\"vectorORfactor\", lengths=\"missing\")\r\nvalues=\"missing\", lengths=\"missing\"\r\nvalues=\"Rle\", lengths=\"missing\"\r\nvalues=\"vectorORfactor\", lengths=\"integer\"\r\nvalues=\"vectorORfactor\", lengths=\"missing\"\r\nvalues=\"vectorORfactor\", lengths=\"numeric\"\r\n\r\nHere's the session info-\r\n> sessionInfo()\r\nR version 3.2.4 (2016-03-10)\r\nPlatform: x86_64-apple-darwin13.4.0 (64-bit)\r\nRunning under: OS X 10.11.3 (El Capitan)\r\n\r\nlocale:\r\n[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8\r\n\r\nattached base packages:\r\n[1] stats4    parallel  stats     graphics  grDevices utils     datasets \r\n[8] methods   base     \r\n\r\nother attached packages:\r\n[1] GenomicRanges_1.22.4 GenomeInfoDb_1.6.3   IRanges_2.4.8       \r\n[4] S4Vectors_0.8.11     ggbio_1.18.5         ggplot2_2.1.0       \r\n[7] BiocGenerics_0.16.1 \r\n\r\nloaded via a namespace (and not attached):\r\n [1] SummarizedExperiment_1.0.2 VariantAnnotation_1.16.4  \r\n [3] reshape2_1.4.1             splines_3.2.4             \r\n [5] lattice_0.20-33            colorspace_1.2-6          \r\n [7] rtracklayer_1.30.3         GenomicFeatures_1.22.13   \r\n [9] RBGL_1.46.0                survival_2.38-3           \r\n[11] XML_3.98-1.4               foreign_0.8-66            \r\n[13] DBI_0.3.1                  BiocParallel_1.4.3        \r\n[15] RColorBrewer_1.1-2         lambda.r_1.1.7            \r\n[17] plyr_1.8.3                 stringr_1.0.0             \r\n[19] zlibbioc_1.16.0            Biostrings_2.38.4         \r\n[21] munsell_0.4.3              gtable_0.2.0              \r\n[23] futile.logger_1.4.1        OrganismDbi_1.12.1        \r\n[25] codetools_0.2-14           latticeExtra_0.6-28       \r\n[27] Biobase_2.30.0             GGally_1.0.1              \r\n[29] biomaRt_2.26.1             BiocInstaller_1.20.1      \r\n[31] AnnotationDbi_1.32.3       Rcpp_0.12.3               \r\n[33] acepack_1.3-3.3            scales_0.4.0              \r\n[35] BSgenome_1.38.0            graph_1.48.0              \r\n[37] Hmisc_3.17-2               XVector_0.10.0            \r\n[39] Rsamtools_1.22.0           gridExtra_2.2.1           \r\n[41] stringi_1.0-1              biovizBase_1.18.0         \r\n[43] grid_3.2.4                 tools_3.2.4               \r\n[45] bitops_1.0-6               magrittr_1.5              \r\n[47] RCurl_1.95-4.8             RSQLite_1.0.0             \r\n[49] dichromat_2.0-0            Formula_1.2-1             \r\n[51] cluster_2.0.3              futile.options_1.0.0      \r\n[53] reshape_0.8.5              rpart_4.1-10              \r\n[55] GenomicAlignments_1.6.3    nnet_7.3-12               \r\n\r\nThanks for your help!"}}