Try updating to R-alpha (3.2.0) instead of R-devel (3.3.0). Dan
----- Original Message ----- > From: "Nicolas Delhomme" <nicolas.delho...@umu.se> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "bioC-devel" <bioc-de...@stat.math.ethz.ch> > Sent: Friday, March 27, 2015 11:12:00 AM > Subject: Re: [Bioc-devel] "forceAndCall" is not a SPECIAL function ERROR when > using ShortRead readAligned function > > 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 My R-devel is rather outdated, I'm updating it to see if that is the 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
