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

Nicolas Delhomme nicolas.delhomme at umu.se
Fri Mar 27 19:04:17 CET 2015

Hej Bioc!

I've got the following error and can't really track its origin.



> 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)

[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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