I think we'd need to see your files in order to try to reproduce this. Dan
----- Original Message ----- > From: "Nicolas Delhomme" <nicolas.delho...@umu.se> > To: "bioC-devel" <bioc-de...@stat.math.ethz.ch> > Sent: Friday, March 27, 2015 11:04:17 AM > Subject: [Bioc-devel] "forceAndCall" is not a SPECIAL function ERROR when > using ShortRead readAligned function > > 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 > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel