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

[Nicolas Delhomme]

Hej Martin!

Thanks for the comment. I have not looked at that bit of the tutorial in a while and - if I recollect - correctly, it was used to demonstrate the advantage of using Rsamtools over ShortRead for reading BAM files; so exactly along your line. Anyway, that tutorial is definitely outdated and I'm preparing a dataset with much more recent and more comprehensive data.

Cheers,

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 30 Mar 2015, at 19:29, Martin Morgan <mtmorgan at fredhutch.org> wrote:
> 
> 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 My R-devel is rather outdated, I'm updating it to see if that is the reason (2015-02-11).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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