[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My R-devel is rather outdated, I'm updating it to see if that is the reason (2015-02-11).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
Ume? Plant Science Center

Tel: +46 90 786 5478
Email: nicolas.delhomme at umu.se
SLU - Ume? universitet
Ume? 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
Ume? Plant Science Center

Tel: +46 90 786 5478
Email: nicolas.delhomme at umu.se
SLU - Ume? universitet
Ume? S-901 87 Sweden
---------------------------------------------------------------