This took some discussion, but it's finally resolved in devel and release. Michael On Thu, May 2, 2013 at 12:26 AM, Hahne, Florian <florian.hahne@novartis.com>wrote: > Hi Michael(s), > this looks like a problem in the rtracklayer package. I can reproduce it > independently of any of the code in Gviz: > > session <- browserSession() > genome(session) <- "mm9" > gr <- GRanges(seqnames="chr12", ranges=IRanges(start=57589600, > end=57639895)) > ucscTableQuery(session, "cons30way", gr) > Error in makeNewSeqnames(x, new2old = new2old, seqlevels(value)) : > when 'new2old' is NULL, the first elements in the > supplied 'seqlevels' must be identical to 'seqlevels(x)' > > Would be great if you could take a look, Michael (Lawrence) > > Florian > > > > > > -- > > > > > > > On 5/1/13 6:13 PM, "Michael Morley [guest]" <guest@bioconductor.org> > wrote: > > > > >I recently upgraded to R 3.0 and BioC 2.12. I upgraded all my BioC > >packages and having an error with Gviz > > > >If I try: > > > >chr="chr12" > >start=57591600 > >end=57637895 > >conservation <- UcscTrack(genome = 'mm9', chromosome = chr, > > track = "Conservation", table = > >"phyloP30wayPlacental", > > from = start-2000, to = end+2000, trackType = > >"DataTrack", > > start = "start", end = "end", data = "score", > > type = "hist", window = "auto", col.histogram = > >"darkblue", > > fill.histogram = "darkblue", ylim = c(-.5, 4), > > name = "Conservation") > > > > > >I receive the following error: > > > >Error in makeNewSeqnames(x, new2old = new2old, seqlevels(value)) : > > when 'new2old' is NULL, the first elements in the > > supplied 'seqlevels' must be identical to 'seqlevels(x)' > > > >> traceback() > >9: stop("when 'new2old' is NULL, the first elements in the\n", " > >supplied 'seqlevels' must be identical to 'seqlevels(x)'") > >8: makeNewSeqnames(x, new2old = new2old, seqlevels(value)) > >7: `seqinfo<-`(`*tmp*`, value = <s4 object="" of="" class="" "seqinfo"="">) > >6: `seqinfo<-`(`*tmp*`, value = <s4 object="" of="" class="" "seqinfo"="">) > >5: normGenomeRange(range, x, single = FALSE) > >4: .local(x, ...) > >3: ucscTableQuery(sessionInfo$session, sessionInfo$track, gr) > >2: ucscTableQuery(sessionInfo$session, sessionInfo$track, gr) > >1: UcscTrack(genome = "mm9", chromosome = chr, track = "Conservation", > > table = "phyloP30wayPlacental", from = start - 2000, to = end + > > 2000, trackType = "DataTrack", start = "start", end = "end", > > data = "score", type = "hist", window = "auto", col.histogram = > >"darkblue", > > fill.histogram = "darkblue", ylim = c(-0.5, 4), name = > >"Conservation") > > > > > >Any suggestions? > > > >Thank you, > > > >Mike > > > > > > > > -- output of sessionInfo(): > > > >R version 3.0.0 (2013-04-03) > >Platform: x86_64-pc-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] grid stats graphics grDevices utils datasets methods > >[8] base > > > >other attached packages: > >[1] Gviz_1.4.1 > > > >loaded via a namespace (and not attached): > > [1] AnnotationDbi_1.22.3 Biobase_2.20.0 BiocGenerics_0.6.0 > > [4] biomaRt_2.16.0 Biostrings_2.28.0 biovizBase_1.8.0 > > [7] bitops_1.0-5 BSgenome_1.28.0 cluster_1.14.4 > >[10] colorspace_1.2-2 DBI_0.2-6 dichromat_2.0-0 > >[13] GenomicFeatures_1.12.1 GenomicRanges_1.12.2 Hmisc_3.10-1 > >[16] IRanges_1.18.0 labeling_0.1 lattice_0.20-15 > >[19] munsell_0.4 parallel_3.0.0 plyr_1.8 > >[22] RColorBrewer_1.0-5 RCurl_1.95-4.1 Rsamtools_1.12.2 > >[25] RSQLite_0.11.3 rtracklayer_1.20.1 scales_0.2.3 > >[28] stats4_3.0.0 stringr_0.6.2 tools_3.0.0 > >[31] XML_3.96-1.1 zlibbioc_1.6.0 > > > > > >-- > >Sent via the guest posting facility at bioconductor.org. > > [[alternative HTML version deleted]]