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

[Dan Tenenbaum]

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
> ---------------------------------------------------------------
> 
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