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

[Nicolas Delhomme]

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My R-devel is rather outdated, I'm updating it to see if that is the reason (2015-02-11).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$",type="BAM")
>> 
>> Error: Input/Output
>>  'readAligned' failed to parse files
>>  dirPath: '/Users/delhomme/Documents/Git/RnaSeqTutorial'
>>  pattern: 'subset.bam$'
>>  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
>>