Hej Hervé (I guess that ones for you :-)! In R dev / Bioc 3.3; calling as.table on an HitsList stopped working:
Browse[2]> ovl HitsList of length 6 names(6): chr2L chr2R chr3L chr3R chr4 chrX Browse[2]> as.table(ovl) Error during wrapup: cannot coerce to a table I suppose this may have to do with the refactoring of the IRanges/S4Vectors packages? Will the functionality be re-instated, or should I switch my code to using as.matrix instead? My session info: R Under development (unstable) (2015-12-15 r69777) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.2 (El Capitan) locale: [1] C/UTF-8/C/C/C/C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RnaSeqTutorial_0.9.0 easyRNASeq_2.7.2 loaded via a namespace (and not attached): [1] RColorBrewer_1.1-2 futile.logger_1.4.1 [3] GenomeInfoDb_1.7.3 XVector_0.11.1 [5] futile.options_1.0.0 bitops_1.0-6 [7] tools_3.3.0 zlibbioc_1.17.0 [9] biomaRt_2.27.2 annotate_1.49.0 [11] RSQLite_1.0.0 lattice_0.20-33 [13] DBI_0.3.1 parallel_3.3.0 [15] DESeq_1.23.0 genefilter_1.53.0 [17] hwriter_1.3.2 Biostrings_2.39.3 [19] S4Vectors_0.9.15 IRanges_2.5.18 [21] locfit_1.5-9.1 stats4_3.3.0 [23] grid_3.3.0 LSD_3.0 [25] Biobase_2.31.3 AnnotationDbi_1.33.3 [27] XML_3.98-1.3 survival_2.38-3 [29] BiocParallel_1.5.1 limma_3.27.6 [31] latticeExtra_0.6-26 geneplotter_1.49.0 [33] lambda.r_1.1.7 edgeR_3.13.4 [35] intervals_0.15.1 Rsamtools_1.23.1 [37] genomeIntervals_1.27.0 splines_3.3.0 [39] BiocGenerics_0.17.2 GenomicAlignments_1.7.3 [41] GenomicRanges_1.23.7 ShortRead_1.29.1 [43] SummarizedExperiment_1.1.11 xtable_1.8-0 [45] RCurl_1.95-4.7 Thanks! Nico PS Have a good Christmas time! --------------------------------------------------------------- Nicolas Delhomme, PhD Acting Manager UPSC bioinformatics core facility Umeå Plant Science Center, Swedish University for Agricultural Sciences (SLU) and Umeå University Tel: +46 90 786 5478 Email: nicolas.delho...@umu.se SLU - Umeå universitet Umeå S-901 87 Sweden --------------------------------------------------------------- _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
