Hej Martin! Thanks for the comment. I have not looked at that bit of the tutorial in a while and - if I recollect - correctly, it was used to demonstrate the advantage of using Rsamtools over ShortRead for reading BAM files; so exactly along your line. Anyway, that tutorial is definitely outdated and I'm preparing a dataset with much more recent and more comprehensive data.
Cheers, 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 30 Mar 2015, at 19:29, Martin Morgan <mtmor...@fredhutch.org> wrote: > > On 03/27/2015 11:12 AM, Nicolas Delhomme wrote: >> 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 My R-devel is rather outdated, I'm updating it to see if that is the reason 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$",type="BAM") >>>> >>>> Error: Input/Output >>>> 'readAligned' failed to parse files > > readAligned should not be sued to read BAM files, only 'legacy' formats (old > Bowtie, MAQ, Solexa export, ...). Use GenomicAlignments::readGAlignment* > instead, everyone will be much happier. Martin > >>>> dirPath: '/Users/delhomme/Documents/Git/RnaSeqTutorial' >>>> pattern: 'subset.bam$' >>>> 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 >> > > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
