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

[Martin Morgan]

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 My R-devel is rather outdated, I'm updating it to see if that is the reason (2015-02-11).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

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.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
>>>
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


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