Closed lcolladotor closed 9 years ago
Hi,
Running the following code generates invalid if statements:
library('GenomicRanges') library('bumphunter') library('TxDb.Hsapiens.UCSC.hg19.knownGene') txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene query <- GRanges('chr21', IRanges(22115534, 22115894), strand = "*") genes <- annotateTranscripts(txdb = txdb) res <- matchGenes(x = query, subject = genes) traceback() devtools::session_info()
> library('GenomicRanges') Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from ‘package:stats’: xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist, unsplit Loading required package: S4Vectors Loading required package: stats4 Loading required package: IRanges Loading required package: GenomeInfoDb > library('bumphunter') Loading required package: foreach foreach: simple, scalable parallel programming from Revolution Analytics Use Revolution R for scalability, fault tolerance and more. http://www.revolutionanalytics.com Loading required package: iterators Loading required package: locfit locfit 1.5-9.1 2013-03-22 Warning message: multiple methods tables found for ‘score’ > 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; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: ‘AnnotationDbi’ The following object is masked from ‘package:GenomeInfoDb’: species > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > > query <- GRanges('chr21', IRanges(22115534, 22115894), strand = "*") > genes <- annotateTranscripts(txdb = txdb) No annotationPackage supplied. Trying org.Hs.eg.db. Loading required package: org.Hs.eg.db Loading required package: DBI Getting TSS and TSE. Getting CSS and CSE. Getting exons. Annotating genes. > > > res <- matchGenes(x = query, subject = genes) Error in if (S < CS & E < CS) { : missing value where TRUE/FALSE needed > traceback() 1: matchGenes(x = query, subject = genes) > > devtools::session_info() Session info------------------------------------------------------------------------------------------ setting value version R Under development (unstable) (2014-11-01 r66923) system x86_64, darwin10.8.0 ui AQUA language (EN) collate en_US.UTF-8 tz America/New_York Packages---------------------------------------------------------------------------------------------- package * version date source AnnotationDbi * 1.29.17 2015-01-21 Bioconductor base64enc 0.1.2 2014-06-26 CRAN (R 3.2.0) BatchJobs 1.4 2014-09-24 CRAN (R 3.2.0) BBmisc 1.7 2014-06-21 CRAN (R 3.2.0) Biobase * 2.27.2 2015-02-28 Bioconductor BiocGenerics * 0.13.6 2015-03-01 Bioconductor BiocParallel 1.1.13 2015-01-27 Bioconductor biomaRt 2.23.5 2014-11-22 Bioconductor Biostrings 2.35.11 2015-02-22 Bioconductor bitops 1.0.6 2013-08-17 CRAN (R 3.2.0) brew 1.0.6 2011-04-13 CRAN (R 3.2.0) bumphunter * 1.7.5 2015-03-13 Github (lcolladotor/bumphunter@cbf10cd) checkmate 1.5.0 2014-10-19 CRAN (R 3.2.0) codetools 0.2.9 2014-08-21 CRAN (R 3.2.0) DBI * 0.3.1 2014-09-24 CRAN (R 3.2.0) devtools 1.6.1 2014-10-07 CRAN (R 3.2.0) digest 0.6.4 2013-12-03 CRAN (R 3.2.0) doRNG 1.6 2014-03-07 CRAN (R 3.2.0) fail 1.2 2013-09-19 CRAN (R 3.2.0) foreach * 1.4.2 2014-04-11 CRAN (R 3.2.0) GenomeInfoDb * 1.3.13 2015-02-13 Bioconductor GenomicAlignments 1.3.29 2015-02-27 Bioconductor GenomicFeatures * 1.19.20 2015-03-02 Bioconductor GenomicRanges * 1.19.42 2015-03-01 Bioconductor IRanges * 2.1.41 2015-03-01 Bioconductor iterators * 1.0.7 2014-04-11 CRAN (R 3.2.0) lattice 0.20.29 2014-04-04 CRAN (R 3.2.0) locfit * 1.5.9.1 2013-04-20 CRAN (R 3.2.0) matrixStats 0.10.3 2014-10-15 CRAN (R 3.2.0) org.Hs.eg.db * 3.0.0 2014-09-26 Bioconductor pkgmaker 0.22 2014-05-14 CRAN (R 3.2.0) R.methodsS3 1.6.1 2014-01-05 CRAN (R 3.2.0) RCurl 1.95.4.3 2014-07-29 CRAN (R 3.2.0) registry 0.2 2012-01-24 CRAN (R 3.2.0) rngtools 1.2.4 2014-03-06 CRAN (R 3.2.0) Rsamtools 1.19.38 2015-02-28 Bioconductor RSQLite * 1.0.0 2014-10-25 CRAN (R 3.2.0) rstudioapi 0.1 2014-03-27 CRAN (R 3.2.0) rtracklayer 1.27.8 2015-03-02 Bioconductor S4Vectors * 0.5.21 2015-02-22 Bioconductor sendmailR 1.2.1 2014-09-21 CRAN (R 3.2.0) stringr 0.6.2 2012-12-06 CRAN (R 3.2.0) TxDb.Hsapiens.UCSC.hg19.knownGene * 3.0.0 2014-09-26 Bioconductor XML 3.98.1.1 2013-06-20 CRAN (R 3.2.0) xtable 1.7.4 2014-09-12 CRAN (R 3.2.0) XVector * 0.7.4 2015-02-08 Bioconductor zlibbioc 1.13.1 2015-02-11 Bioconductor >
Hi,
Running the following code generates invalid if statements:
Output