Excellent! Thank you very much, Leonardo On Thu, Dec 8, 2011 at 9:35 AM, Michael Lawrence <lawrence.michael@gene.com>wrote: > This was caused by a bug in IRanges. The fix (in release) will come with > IRanges 1.12.5. > > Michael > > On Mon, Dec 5, 2011 at 2:52 PM, Leonardo Collado Torres < > lcollado@jhsph.edu> wrote: > >> Hello BioC-list, >> >> I've been organizing some code for a local package, and was doing so in R >> 2.13.1. I just installed R 2.14.0 today and I found out that the liftOver >> function from the rtracklayer package no longer works. The example for >> that >> function is defined as: >> >> > example(liftOver) >> >> lftOvr> ## Not run: >> lftOvr> ##D chain <- import.chain("hg19ToHg18.over.chain") >> lftOvr> ##D library(TxDb.Hsapiens.UCSC.hg19.knownGene) >> lftOvr> ##D tx_hg19 <- transcripts(TxDb.Hsapiens.UCSC.hg19.knownGene) >> lftOvr> ##D tx_hg18 <- liftOver(tx_hg19, chain) >> lftOvr> ## End(Not run) >> lftOvr> >> lftOvr> >> lftOvr> >> > >> >> So, I simply tried re-running the example. Note that I had the chain file >> from before on our local package bumphunter. >> >> > library(GenomicRanges); library(rtracklayer) >> Loading required package: IRanges >> >> Attaching package: ‘IRanges’ >> >> The following object(s) are masked from ‘package:base’: >> >> cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, >> pmin, pmin.int, rbind, rep.int, setdiff, table, union >> >> Loading required package: RCurl >> Loading required package: bitops >> > chain <- import.chain(system.file("extdata", "hg19ToHg18.over.chain", >> package="bumphunter")) >> > chain >> Chain of length 25 >> names(25): chr22 chr21 chr19 chr20 chr18 chrY ... chr6 chr5 chr4 chr3 chr2 >> chr1 >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene) >> Loading required package: GenomicFeatures >> Loading required package: AnnotationDbi >> Loading required package: Biobase >> >> Welcome to Bioconductor >> >> Vignettes contain introductory material. To view, type >> 'browseVignettes()'. To cite Bioconductor, see >> 'citation("Biobase")' and for packages 'citation("pkgname")'. >> >> >> Attaching package: ‘Biobase’ >> >> The following object(s) are masked from ‘package:IRanges’: >> >> updateObject >> >> > tx_hg19 <- transcripts(TxDb.Hsapiens.UCSC.hg19.knownGene) >> > tx_hg18 <- liftOver(tx_hg19, chain) >> Discarding unchained sequences: chr6_ssto_hap7, chr6_mcf_hap5, >> chr6_cox_hap2, chr6_mann_hap4, chr6_apd_hap1, chr6_qbl_hap6, >> chr6_dbb_hap3, >> chr17_ctg5_hap1, chr4_ctg9_hap1, chr1_gl000192_random, chrUn_gl000225, >> chr4_gl000194_random, chr4_gl000193_random, chr9_gl000200_random, >> chrUn_gl000222, chrUn_gl000212, chr7_gl000195_random, chrUn_gl000223, >> chrUn_gl000224, chrUn_gl000219, chr17_gl000205_random, chrUn_gl000215, >> chrUn_gl000216, chrUn_gl000217, chr9_gl000199_random, chrUn_gl000211, >> chrUn_gl000213, chrUn_gl000220, chrUn_gl000218, chr19_gl000209_random, >> chrUn_gl000221, chrUn_gl000214, chrUn_gl000228, chrUn_gl000227, >> chr1_gl000191_random, chr19_gl000208_random, chr9_gl000198_random, >> chr17_gl000204_random, chrUn_gl000233, chrUn_gl000237, chrUn_gl000230, >> chrUn_gl000242, chrUn_gl000243, chrUn_gl000241, chrUn_gl000236, >> chrUn_gl000240, chr17_gl000206_random, chrUn_gl000232, chrUn_gl000234, >> chr11_gl000202_random, chrUn_gl000238, chrUn_gl000244, chrUn_gl000248, >> chr8_gl000196_random, chrUn_gl000249, chrUn_gl000246, >> chr17_gl000203_random, chr8_gl000197_random, chrUn_gl000245, >> chrUn_gl000247, chr9_gl000201_random, chrUn_gl000235, chrUn_gl000239, >> chr21_gl000210_random, chrUn_gl000231, chrUn_gl000229, chrUn_gl000226, >> chr18_gl000207_random >> Error in unlist(mseqapply(liftOverSpace, rl[sharedNames], >> chain[sharedNames], : >> error in evaluating the argument 'x' in selecting a method for function >> 'unlist': Error in `[.default`(strandRevCodes, as.vector(flipped)) : >> only 0's may be mixed with negative subscripts >> >> >> >> I guess that the error wasn't noticed before since the example is set as >> notrun. I guess that's simply because of the process of getting the chain >> file. >> >> Thank you for your help. >> >> Cheers, >> Leonardo >> >> >> Here is my session information: >> >> > sessionInfo() >> R version 2.14.0 (2011-10-31) >> Platform: x86_64-apple-darwin9.8.0/x86_64 (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] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.6.2 >> [2] GenomicFeatures_1.6.4 >> [3] AnnotationDbi_1.16.8 >> [4] Biobase_2.14.0 >> [5] rtracklayer_1.14.4 >> [6] RCurl_1.7-0 >> [7] bitops_1.0-4.1 >> [8] GenomicRanges_1.6.4 >> [9] IRanges_1.12.4 >> >> loaded via a namespace (and not attached): >> [1] biomaRt_2.10.0 Biostrings_2.22.0 BSgenome_1.22.0 DBI_0.2-5 >> [5] RSQLite_0.10.0 tools_2.14.0 XML_3.4-3 zlibbioc_1.0.0 >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]