Hej! I'm getting this error when using summarizrOverlaps:
Error in findOverlaps(features, reads, algorithm = match.arg(algorithm), : could not find symbol "algorithm" in environment of the generic function Here is the stack: 16: summarizeOverlaps(features, chunk, ignore.strand = !stranded, inter.feature 17: .local(features, reads, mode, algorithm, ignore.strand, ...) 18: .dispatchOverlaps(features, reads, mode, match.arg(algorithm), ignore.stran 19: mode(features, reads, algorithm = algorithm, ignore.strand = ignore.strand, 20: findOverlaps(features, reads, algorithm = match.arg(algorithm), ignore.stra As it looks, it seems that summarizeOverlaps through its dispatch provide the argument algorithm to the findOverlaps function, which now does not support that argument anymore. Here's my sessionInfo: 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] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] GenomicAlignments_1.7.3 Rsamtools_1.23.1 [3] Biostrings_2.39.3 XVector_0.11.1 [5] SummarizedExperiment_1.1.11 Biobase_2.31.3 [7] GenomicRanges_1.23.7 GenomeInfoDb_1.7.3 [9] IRanges_2.5.18 S4Vectors_0.9.15 [11] BiocGenerics_0.17.2 BiocInstaller_1.21.2 [13] RnaSeqTutorial_0.9.0 RUnit_0.4.31 [15] easyRNASeq_2.7.1 loaded via a namespace (and not attached): [1] RColorBrewer_1.1-2 futile.logger_1.4.1 tools_3.3.0 [4] futile.options_1.0.0 bitops_1.0-6 zlibbioc_1.17.0 [7] biomaRt_2.27.2 annotate_1.49.0 RSQLite_1.0.0 [10] lattice_0.20-33 DBI_0.3.1 DESeq_1.23.0 [13] genefilter_1.53.0 hwriter_1.3.2 locfit_1.5-9.1 [16] grid_3.3.0 LSD_3.0 AnnotationDbi_1.33.3 [19] XML_3.98-1.3 survival_2.38-3 BiocParallel_1.5.1 [22] limma_3.27.6 latticeExtra_0.6-26 geneplotter_1.49.0 [25] lambda.r_1.1.7 edgeR_3.13.4 intervals_0.15.1 [28] genomeIntervals_1.27.0 splines_3.3.0 ShortRead_1.29.1 [31] xtable_1.8-0 RCurl_1.95-4.7 Am I overlooking something or is it just that I got slightly out of sync packages? Cheers, Nico --------------------------------------------------------------- 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