Dear all, I've come up against an error I can't explain trying to extract transcript/gene IDs for a given set of genomic coordinates. I checked the coordinates against the UCSC genome browser so I know that this region does actually contain some genes. The curious thing is that this worked yesterday and doesn't work today. I did upgrade several bioconductor packages overnight and I think it may be down to a change in the version of GenomicRanges but I'm not certain. The code below shows a minimal case that reproduces the error message. library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene library(GenomicRanges) #absolute minimal GRanges object gr <- GRanges(seqnames='chr1', ranges=IRanges(start=40221856, end=40502499), strand='*') #attempt to get transcript IDs and gene IDs out of TxDb.Hsapiens.UCSC.hg19.knownGene result <- transcriptsByOverlaps(txdb, gr, columns=c('tx_id', 'tx_name', 'gene_id')) If I try to display the contents of the object 'result' then I ge t the following: > result GRanges with 0 ranges and 3 metadata columns: Error: identical(colnames(classinfo), colnames(out)) is not TRUE Output of traceback() > traceback() 5: stop(paste0(ch, " is not ", if (length(r) > 1L) "all ", "TRUE"), call. = FALSE) 4: stopifnot(identical(colnames(classinfo), colnames(out))) 3: showGenomicRanges(object, margin = " ", with.classinfo = TRUE, print.seqlengths = TRUE) 2: function (object) standardGeneric("show")(<s4 object="" of="" class="" "granges"="">) 1: function (object) standardGeneric("show")(<s4 object="" of="" class="" "granges"="">) I did do some searching before posting this and found this in the archives https://stat.ethz.ch/pipermail/bioc- devel/2012-April/003344.html which seems related. I had a look into the GenomicRanges source code and the error seems to occur in the function showGenomicRanges around lines 729-731: classinfo <- makeClassinfoRowForCompactPrinting(x, .COL2CLASS) ## A sanity check, but this should never happen! stopifnot(identical(colnames(classinfo), colnames(out))) out <- rbind(classinfo, out) That's as far as I've been able to get. So, two related questions 1)Am I doing something wrong and if so what can I do to get around this error? 2)Is it possible to install older versions of bioconductor packages and if so how? I'd like to see if I can reprodce this with the previous version of GenomicRanges Any help appreciated, Richard -- output of sessionInfo(): > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] org.Hs.eg.db_2.8.0 RSQLite_0.11.2 DBI_0.2-5 TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0 [5] GenomicFeatures_1.10.2 AnnotationDbi_1.20.6 Biobase_2.18.0 biomaRt_2.14.0 [9] ggbio_1.6.6 gridExtra_0.9.1 scales_0.2.3 ggplot2_0.9.3.1 [13] GenomicRanges_1.10.7 IRanges_1.16.6 BiocGenerics_0.4.0 knitr_1.1 loaded via a namespace (and not attached): [1] Biostrings_2.26.3 biovizBase_1.6.2 bitops_1.0-5 BSgenome_1.26.1 cluster_1.14.3 colorspace_1.2-1 [7] dichromat_2.0-0 digest_0.6.3 evaluate_0.4.3 formatR_0.7 gtable_0.1.2 Hmisc_3.10-1 [13] labeling_0.1 lattice_0.20-13 MASS_7.3-23 munsell_0.4 parallel_2.15.2 plyr_1.8 [19] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 reshape2_1.2.2 Rsamtools_1.10.2 rtracklayer_1.18.2 [25] stats4_2.15.2 stringr_0.6.2 tools_2.15.2 VariantAnnotation_1.4.12 XML_3.95-0.2 zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org.