I have been perplexed by this and can't seem to get any traction debugging it. A quick Google search didn't turn up anything useful. I've had liftOver() work properly in the past, but not this time... # example > CpH.fwd = with(CpH, GRanges(chr, IRanges(end=site,width=50), strand=CpH.strand, names=rownames(CpH))) > CpH.fwd GRanges with 3091 ranges and 1 elementMetadata value: seqnames ranges strand | names <rle> <iranges> <rle> | <character> [1] chrX [ 7556494, 7556543] - | ch.X.7566543R [2] chrX [10104084, 10104133] - | ch.X.147603R [3] chrX [12813493, 12813542] - | ch.X.188238R # ... > hg18hg19 = import.chain('hg18ToHg19.over.chain') > liftOver(CpH.fwd, hg18hg19) Error in unique.default(x) : unique() applies only to vectors Anyone seen this before? Is it a sign that something is amiss or is it perhaps a bug? > sessionInfo() R Under development (unstable) (2011-10-13 r57229) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] rtracklayer_1.13.19 [2] RCurl_1.6-10 [3] bitops_1.0-4.1 [4] BSgenome.Hsapiens.UCSC.hg19_1.3.17 [5] BSgenome_1.21.7 [6] Biostrings_2.21.11 [7] GenomicRanges_1.5.51 [8] IRanges_1.11.31 [9] IlluminaHumanMethylation450kprobe_1.9.12 [10] AnnotationDbi_1.15.38 [11] Biobase_2.13.11 [12] BiocInstaller_1.1.28 [13] gtools_2.6.2 loaded via a namespace (and not attached): [1] DBI_0.2-5 RSQLite_0.10.0 tools_2.15.0 XML_3.4-3 zlibbioc_0.1.8 -- If people do not believe that mathematics is simple, it is only because they do not realize how complicated life is.John von Neumann<http: www-groups.dcs.st-="" and.ac.uk="" ~history="" biographies="" von_neumann.html=""> [[alternative HTML version deleted]]