Easy enough :-) I'm running the RnaSeqTutorial package vignette and the chunks 6, 7 and 8 fail with that forceAndCall error.
My R-devel is rather outdated, I'm updating it to see if that is the reason (2015-02-11). Nico --------------------------------------------------------------- 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 --------------------------------------------------------------- > On 27 Mar 2015, at 19:09, Dan Tenenbaum <dtene...@fredhutch.org> wrote: > > 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
