Hej Bioc! I've got the following error and can't really track its origin.
Cheers, Nico > aln2 <- readAligned(getwd(),pattern="subset.bam$",type="BAM") Error: Input/Output 'readAligned' failed to parse files dirPath: '/Users/delhomme/Documents/Git/RnaSeqTutorial' pattern: 'subset.bam$' type: 'BAM' error: "forceAndCall" is not a SPECIAL function > sessionInfo() R Under development (unstable) (2015-02-11 r67792) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.2 (Yosemite) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] ShortRead_1.25.9 GenomicAlignments_1.3.32 Rsamtools_1.19.49 GenomicRanges_1.19.48 [5] GenomeInfoDb_1.3.16 Biostrings_2.35.12 XVector_0.7.4 IRanges_2.1.43 [9] S4Vectors_0.5.22 BiocParallel_1.1.21 BiocGenerics_0.13.10 RnaSeqTutorial_0.3.2 [13] easyRNASeq_2.3.4 locfit_1.5-9.1 loaded via a namespace (and not attached): [1] RColorBrewer_1.1-2 futile.logger_1.4 bitops_1.0-6 futile.options_1.0.0 tools_3.2.0 [6] zlibbioc_1.13.3 biomaRt_2.23.5 annotate_1.45.4 RSQLite_1.0.0 lattice_0.20-30 [11] DBI_0.3.1 DESeq_1.19.0 genefilter_1.49.2 hwriter_1.3.2 grid_3.2.0 [16] LSD_3.0 Biobase_2.27.3 AnnotationDbi_1.29.20 XML_3.98-1.1 survival_2.38-1 [21] limma_3.23.11 latticeExtra_0.6-26 geneplotter_1.45.0 lambda.r_1.1.7 edgeR_3.9.14 [26] intervals_0.15.0 genomeIntervals_1.23.2 splines_3.2.0 xtable_1.7-4 RCurl_1.95-4.5 --------------------------------------------------------------- Nicolas Delhomme The Street Lab Department of Plant Physiology Umeå Plant Science Center 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
