Hi David and users of the BSgenome data packages, I've pushed a new roster of BSgenome data packages (v 1.3.13) to the current BioC release (2.4). This fixes the mask problem that David reported here. As usual, please update with (from R-2.9.0): source("http://bioconductor.org/biocLite.R") update.packages(rep=biocinstallRepos()) Only the source packages of this new roster are available for now. The binaries for Windows and Mac will follow soon. In the meantime the binaries for the old roster (< 1.3.13) are still available. Also I've added hg19 (released in Feb. 2009) to this new roster: > library(BSgenome.Hsapiens.UCSC.hg19) > Hsapiens Human genome | | organism: Homo sapiens (Human) | provider: UCSC | provider version: hg19 | release date: Feb. 2009 | release name: Genome Reference Consortium GRCh37 ... Note that BioC devel is still using the old roster and will be updated at some point too. Please let me know if you find any issue. Cheers, H. Hervé Pagès wrote: > Hi David, > > Thanks for the report! > The error is indeed occurring in the "show" method for IRanges objects. > It is occurring because the content of the NAMES slots of the IRanges > objects that are stored in the serialized MaskCollection objects found > in the BSgenome.* data packages is not valid anymore (because of changes > in the IRanges container). > > I will fix this. Thanks again. > > Cheers, > H. > > > David Rossell wrote: >> I just installed BSgenome.Dmelanogaster.UCSC.dm3, where there appears >> to be >> some bug in the masks. For instance, >> >>> masks(Dmelanogaster$chr2L)$RM >> NormalIRanges object: >> Error in width(x) : NAs in 'x' are not supported >> >> Same happens with other masks (TR etc.). Curiously, there are no NAs >> in the >> width slot >> >>> tableis.na(width(masks(Dmelanogaster$chr2L)$RM))) >> >> FALSE >> 12044 >> >> This seems to be an issue of the show method, as I can save the object >> and >> work normally with it >> >>> aa <- masks(Dmelanogaster$chr2L)$RM >>> head(start(aa)) >> [1] 2 313 457 771 915 1229 >>> head(width(aa)) >> [1] 153 96 156 96 156 96 >>> head(end(aa)) >> [1] 154 408 612 866 1070 1324 >> >> My session info is below. Best, >> >> David >> >>> sessionInfo() >> R version 2.9.0 (2009-04-17) >> i386-apple-darwin8.11.1 >> >> locale: >> C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] BSgenome.Dmelanogaster.UCSC.dm3_1.3.11 >> [2] ACME_1.10.0 >> [3] MDA_1.0.1 >> [4] multicore_0.1-3 >> [5] ShortRead_1.2.0 >> [6] lattice_0.17-22 >> [7] BSgenome_1.12.0 >> [8] Biostrings_2.12.3 >> [9] IRanges_1.2.2 >> [10] gdata_2.4.2 >> [11] GEOquery_2.8.0 >> [12] RCurl_0.94-1 >> [13] Biobase_2.4.1 >> >> loaded via a namespace (and not attached): >> [1] grid_2.9.0 gtools_2.6.1 hwriter_1.1 tools_2.9.0 >> > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319