Michael & Robert, If I load the graph package prior to rtracklayer, import.bed generates an error and fails. It otherwise succeeds if I don't load the graph package.
It happens both with rtracklayer from svn and production. Look: In a fresh session: > library(graph) > library(rtracklayer) Loading required package: RCurl Loading required package: bitops > b <- import.bed('my.bed') Error in function (classes, fdef, mtable) : unable to find an inherited method for function "import.ucsc", for signature "file" > sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.13.3 RCurl_1.5-0 bitops_1.0-4.1 graph_1.30.0 loaded via a namespace (and not attached): [1] BSgenome_1.20.0 Biostrings_2.20.1 GenomicRanges_1.4.6 [4] IRanges_1.10.4 XML_3.4-0 tools_2.13.0 > _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing