btw, based on the error, let me try to debug it. On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin wrote: > Hi Leonardo, > > Frankly speaking, the vignette is still in progress, and there are some > known bugs in ggbio I need to fix (still trying to find a time to do that > ... ), I am recently trying to install R 3.1 and Bioc 2.14 on my new MBP > with OSX 10.9, but fails, probably binary build is not ready for maverick > yet, maybe available by the end of April? > > Thanks for reporting the bug, I will keep you posted on this when I > successfully get it on my laptop and start fixing the problems. > > cheers > > Tengfei > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado Torres < > lcollado@jhsph.edu> wrote: > >> Hello Tengfei + bioc list, >> >> From >> http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/inst/doc/ggbio.pdf >> page 4 (complied on april 11 2014), the following example loads to an >> error as shown below. I wasn't seeing this error before (aka, last >> week). The only guess that comes to mind is the recent update to >> GenomicRanges (1.16.2) although that doesn't seem to be related from >> the traceback() output, well... maybe it's related to the >> ignore.strand = TRUE part as described in the error. >> >> I'll create a GitHub issue just for completeness. >> >> Thank you, >> Leonardo >> >> > library(ggbio) >> ## Removed the output, nothing out of ordinary >> >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene) >> ## Removed the output >> >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene >> > data(genesymbol, package = "biovizBase") >> > p.txdb <- autoplot(txdb, which = genesymbol["BRCA1"]) >> Aggregating TranscriptDb... >> Parsing transcripts... >> Parsing exons... >> Parsing cds... >> Parsing utrs... >> ------exons... >> ------cdss... >> ------introns... >> ------utr... >> aggregating... >> Done >> Constructing graphics... >> Error in sapply(listData, function(Xi) extends(class(Xi), elementTypeX)) : >> error in evaluating the argument 'X' in selecting a method for >> function 'sapply': Error in unlist(range(ranges(x.n, ignore.strand = >> TRUE))) : >> error in evaluating the argument 'x' in selecting a method for >> function 'unlist': Error in .local(x, ...) : unused argument >> (ignore.strand = TRUE) >> >> > traceback() >> 15: sapply(listData, function(Xi) extends(class(Xi), elementTypeX)) >> 14: .updateCompressedList(X, lapply_CompressedList(X, FUN, ...)) >> 13: endoapply(obj.lst, function(x) { >> if (!is.null(group.name)) { >> if (!group.selfish) { >> x.n <- split(x, values(x)[, group.name]) >> irs <- unlist(range(ranges(x.n, ignore.strand = TRUE))) >> irs.new <- resize(irs, fix = fix, width = width(irs) + >> extend.size) >> irs.new <- sort(irs.new) >> .lvs <- disjointBins(irs.new) >> values(x)$stepping <- .lvs[as.character(values(x)[, >> group.name])] >> x >> } >> else { >> values(x)$stepping <- as.numeric(as.factor(values(x)[, >> group.name])) >> x >> } >> } >> else { >> irs <- ranges(x) >> values(x)$stepping <- as.numeric(disjointBins(resize(irs, >> fix = "center", width = width(irs) + extend.size))) >> x >> } >> }) >> 12: endoapply(obj.lst, function(x) { >> if (!is.null(group.name)) { >> if (!group.selfish) { >> x.n <- split(x, values(x)[, group.name]) >> irs <- unlist(range(ranges(x.n, ignore.strand = TRUE))) >> irs.new <- resize(irs, fix = fix, width = width(irs) + >> extend.size) >> irs.new <- sort(irs.new) >> .lvs <- disjointBins(irs.new) >> values(x)$stepping <- .lvs[as.character(values(x)[, >> group.name])] >> x >> } >> else { >> values(x)$stepping <- as.numeric(as.factor(values(x)[, >> group.name])) >> x >> } >> } >> else { >> irs <- ranges(x) >> values(x)$stepping <- as.numeric(disjointBins(resize(irs, >> fix = "center", width = width(irs) + extend.size))) >> x >> } >> }) >> 11: .local(obj, ...) >> 10: addStepping(gr, group.name = "tx_id", group.selfish = FALSE, >> fix = "start", extend.size = es) >> 9: addStepping(gr, group.name = "tx_id", group.selfish = FALSE, >> fix = "start", extend.size = es) >> 8: .local(data, ...) >> 7: (function (data, ...) >> standardGeneric("geom_alignment"))(data = > "TranscriptDb">, >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", >> stat = "identity", names.expr = "tx_name", label = TRUE, >> which = , list()) >> 6: (function (data, ...) >> standardGeneric("geom_alignment"))(data = > "TranscriptDb">, >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", >> stat = "identity", names.expr = "tx_name", label = TRUE, >> which = , list()) >> 5: do.call(geom_alignment, args.res) >> 4: do.call(geom_alignment, args.res) >> 3: .local(object, ...) >> 2: autoplot(txdb, which = genesymbol["BRCA1"]) >> 1: autoplot(txdb, which = genesymbol["BRCA1"]) >> >> >> > sessionInfo() >> R version 3.1.0 (2014-04-10) >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets >> methods base >> >> other attached packages: >> [1] XVector_0.4.0 >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 GenomicFeatures_1.16.0 >> [4] AnnotationDbi_1.26.0 Biobase_2.24.0 >> GenomicRanges_1.16.2 >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 >> ggbio_1.12.0 >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 >> >> loaded via a namespace (and not attached): >> [1] BatchJobs_1.2 BBmisc_1.5 >> BiocParallel_0.6.0 biomaRt_2.20.0 Biostrings_2.32.0 >> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 >> BSgenome_1.32.0 cluster_1.15.2 >> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 >> dichromat_2.0-0 digest_0.6.4 >> [16] fail_1.2 foreach_1.4.2 Formula_1.1-1 >> GenomicAlignments_1.0.0 grid_3.1.0 >> [21] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.14-4 >> iterators_1.0.7 labeling_0.2 >> [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-31 >> munsell_0.4.2 plyr_1.8.1 >> [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 >> RCurl_1.95-4.1 reshape2_1.2.2 >> [36] Rsamtools_1.16.0 RSQLite_0.11.4 >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 >> [41] splines_3.1.0 stats4_3.1.0 stringr_0.6.2 >> survival_2.37-7 tools_3.1.0 >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 zlibbioc_1.10.0 >> > >> > > > > -- > Tengfei Yin, PhD > Seven Bridges Genomics > sbgenomics.com > 625 Mt. Auburn St. Suite #208 > Cambridge, MA 02138 > (617) 866-0446 > -- Tengfei Yin, PhD Seven Bridges Genomics sbgenomics.com 625 Mt. Auburn St. Suite #208 Cambridge, MA 02138 (617) 866-0446 [[alternative HTML version deleted]]