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

[Nicolas Delhomme]

That did it, sorry for whining too early :-\

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 19:13, Dan Tenenbaum <dtenenba at fredhutch.org> wrote:
> 
> Try updating to R-alpha (3.2.0) instead of R-devel (3.3.0).
> Dan
> 
> 
> ----- Original Message -----
>> From: "Nicolas Delhomme" <nicolas.delhomme at umu.se>
>> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
>> Cc: "bioC-devel" <bioc-devel at stat.math.ethz.ch>
>> Sent: Friday, March 27, 2015 11:12:00 AM
>> Subject: Re: [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 My R-devel is rather outdated, I'm updating it to see if that is the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
>> 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
>>>> 
>> 
>>