Was there a new version of TxDb.Hsapiens.UCSC.hg19.knownGene in the last day or two (v 2.9.2)? It looks like there are some issues with seqlevels replacing isActiveSeq() in the new version: > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > txdb=TxDb.Hsapiens.UCSC.hg19.knownGene For example, I never call isActiveSeq(), so I'm not sure where the warning is coming in: > seqlevels(txdb,force=TRUE) = paste0("chr",c(1:22,"X","Y","M")) Warning message: 'isActiveSeq' is deprecated. Use 'seqinfo' instead. See help("Deprecated") and help("GenomicFeatures-deprecated"). Other calls now throw warning flags for this: > introns = intronsByTranscript(txdb) Warning messages: 1: 'isActiveSeq' is deprecated. Use 'seqinfo' instead. See help("Deprecated") and help("GenomicFeatures-deprecated"). 2: 'isActiveSeq' is deprecated. Use 'seqinfo' instead. See help("Deprecated") and help("GenomicFeatures-deprecated"). 3: 'isActiveSeq' is deprecated. Use 'seqinfo' instead. See help("Deprecated") and help("GenomicFeatures-deprecated"). 4: 'isActiveSeq' is deprecated. Use 'seqinfo' instead. See help("Deprecated") and help("GenomicFeatures-deprecated"). 5: 'isActiveSeq' is deprecated. Use 'seqinfo' instead. See help("Deprecated") and help("GenomicFeatures-deprecated"). 6: 'isActiveSeq' is deprecated. Use 'seqinfo' instead. See help("Deprecated") and help("GenomicFeatures-deprecated"). Lastly, some calls work at all, and are met with an error > utr5 = fiveUTRsByTranscript(txdb) Error in validObject(.Object) : invalid class "GRanges" object: 'seqnames' contains missing values In addition: Warning messages: 1: 'isActiveSeq' is deprecated. Use 'seqinfo' instead. See help("Deprecated") and help("GenomicFeatures-deprecated"). 2: 'isActiveSeq' is deprecated. Use 'seqinfo' instead. See help("Deprecated") and help("GenomicFeatures-deprecated"). 3: 'isActiveSeq' is deprecated. Use 'seqinfo' instead. See help("Deprecated") and help("GenomicFeatures-deprecated"). Any help would be appreciated. Below is sessionInfo() results -Andrew > sessionInfo() R Under development (unstable) (2013-08-22 r63646) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915 [7] LC_PAPER=en_US.iso885915 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices datasets utils methods [8] base other attached packages: [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.9.2 [2] GenomicFeatures_1.13.32 [3] AnnotationDbi_1.23.18 [4] Biobase_2.21.6 [5] GenomicRanges_1.13.36 [6] XVector_0.1.0 [7] IRanges_1.19.24 [8] BiocGenerics_0.7.4 loaded via a namespace (and not attached): [1] biomaRt_2.17.2 Biostrings_2.29.15 bitops_1.0-6 BSgenome_1.29.1 [5] DBI_0.2-7 RCurl_1.95-4.1 Rsamtools_1.13.29 RSQLite_0.11.4 [9] rtracklayer_1.21.9 stats4_3.1.0 tools_3.1.0 XML_3.98-1.1 [13] zlibbioc_1.7.0 [[alternative HTML version deleted]]

Hi Andrew, This post probably belonged on bioc-devel since you are talking only about the development branch. But thanks for mentioning this. To answer your question: there was not in fact any new version of the annotation package. The code for this is actually in GenomicFeatures where I have been deprecating isActiveSeq (as it is now largely redundant with seqinfo and the related functions). Also, I fixed this yesterday. So pretty soon you should not get any more mysterious warnings in devel. Marc On 08/22/2013 10:26 AM, Andrew Jaffe wrote: > Was there a new version of TxDb.Hsapiens.UCSC.hg19.knownGene in the last > day or two (v 2.9.2)? It looks like there are some issues with seqlevels > replacing isActiveSeq() in the new version: > >> library(TxDb.Hsapiens.UCSC.hg19.knownGene) >> txdb=TxDb.Hsapiens.UCSC.hg19.knownGene > For example, I never call isActiveSeq(), so I'm not sure where the warning > is coming in: > >> seqlevels(txdb,force=TRUE) = paste0("chr",c(1:22,"X","Y","M")) > Warning message: > 'isActiveSeq' is deprecated. > Use 'seqinfo' instead. > See help("Deprecated") and help("GenomicFeatures-deprecated"). > > Other calls now throw warning flags for this: >> introns = intronsByTranscript(txdb) > Warning messages: > 1: 'isActiveSeq' is deprecated. > Use 'seqinfo' instead. > See help("Deprecated") and help("GenomicFeatures-deprecated"). > 2: 'isActiveSeq' is deprecated. > Use 'seqinfo' instead. > See help("Deprecated") and help("GenomicFeatures-deprecated"). > 3: 'isActiveSeq' is deprecated. > Use 'seqinfo' instead. > See help("Deprecated") and help("GenomicFeatures-deprecated"). > 4: 'isActiveSeq' is deprecated. > Use 'seqinfo' instead. > See help("Deprecated") and help("GenomicFeatures-deprecated"). > 5: 'isActiveSeq' is deprecated. > Use 'seqinfo' instead. > See help("Deprecated") and help("GenomicFeatures-deprecated"). > 6: 'isActiveSeq' is deprecated. > Use 'seqinfo' instead. > See help("Deprecated") and help("GenomicFeatures-deprecated"). > > Lastly, some calls work at all, and are met with an error > >> utr5 = fiveUTRsByTranscript(txdb) > Error in validObject(.Object) : > invalid class "GRanges" object: 'seqnames' contains missing values > In addition: Warning messages: > 1: 'isActiveSeq' is deprecated. > Use 'seqinfo' instead. > See help("Deprecated") and help("GenomicFeatures-deprecated"). > 2: 'isActiveSeq' is deprecated. > Use 'seqinfo' instead. > See help("Deprecated") and help("GenomicFeatures-deprecated"). > 3: 'isActiveSeq' is deprecated. > Use 'seqinfo' instead. > See help("Deprecated") and help("GenomicFeatures-deprecated"). > > Any help would be appreciated. Below is sessionInfo() results > > -Andrew > > >> sessionInfo() > R Under development (unstable) (2013-08-22 r63646) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C > [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 > [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915 > [7] LC_PAPER=en_US.iso885915 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices datasets utils methods > [8] base > > other attached packages: > [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.9.2 > [2] GenomicFeatures_1.13.32 > [3] AnnotationDbi_1.23.18 > [4] Biobase_2.21.6 > [5] GenomicRanges_1.13.36 > [6] XVector_0.1.0 > [7] IRanges_1.19.24 > [8] BiocGenerics_0.7.4 > > loaded via a namespace (and not attached): > [1] biomaRt_2.17.2 Biostrings_2.29.15 bitops_1.0-6 > BSgenome_1.29.1 > [5] DBI_0.2-7 RCurl_1.95-4.1 Rsamtools_1.13.29 RSQLite_0.11.4 > [9] rtracklayer_1.21.9 stats4_3.1.0 tools_3.1.0 XML_3.98-1.1 > [13] zlibbioc_1.7.0 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor