[Bioc-devel] "forceAndCall" is not a SPECIAL function ERROR when using ShortRead readAligned function

[Dan Tenenbaum]

Try updating to R-alpha (3.2.0) instead of R-devel (3.3.0).
Dan


----- Original Message -----
> From: "Nicolas Delhomme" <nicolas.delhomme at umu.se>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Cc: "bioC-devel" <bioc-devel at 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 My R-devel is rather outdated, I'm updating it to see if that is the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.delhomme at umu.se
> SLU - Umeå universitet
> Umeå S-901 87 Sweden
> ---------------------------------------------------------------
> 
> > On 27 Mar 2015, at 19:09, Dan Tenenbaum <dtenenba at 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.delhomme at umu.se>
> >> To: "bioC-devel" <bioc-devel at 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.delhomme at umu.se
> >> SLU - Umeå universitet
> >> Umeå S-901 87 Sweden
> >> ---------------------------------------------------------------
> >> 
> >> _______________________________________________
> >> Bioc-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >> 
> 
>