[BioC] matchPdict error

[Hervé Pagès]

Hi Burak,

Thanks for reporting this. A fix is in the way. I'll announce here when
it's ready.

Cheers,
H.


burak kutlu wrote:
> Hi
> I am trying to use matchPDict() and below's the error I get.
> This happens with my objects as well, but I am showing the vignette example. 
> thanks in advance
> -burak
> 
> # I've made sure that ce2dict0 was corectly created
>> ce2dict0cw15 <- DNAStringSet(ce2dict0, end=15)
>> runAnalysis2(ce2dict0cw15, outfile="ce2dict0cw15_ana2.txt")
> 
> Target: strand + of ce2 chromosomes chrI, chrII, chrIII, chrIV, chrV, chrX, chrM
>>>> Finding all hits in strand + of chromosome chrI ...
> Error in initialize(value, ...) :
>   invalid names for slots of class "ByName_MIndex": length
> 
> 
>> sessionInfo()
> R version 2.8.1 (2008-12-22)
> x86_64-unknown-linux-gnu
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] grDevices datasets  splines  graphics  stats    utils    tools
> [8] methods  base
> 
> other attached packages:
> [1] BSgenome.Celegans.UCSC.ce2_1.3.11 BSgenome_1.10.3
> [3] Biostrings_2.10.16                IRanges_1.0.12
> [5] simpleaffy_2.18.0                gcrma_2.14.1
> [7] matchprobes_1.14.1                genefilter_1.22.0
> [9] survival_2.34-1                  affy_1.20.0
> [11] Biobase_2.2.1
> 
> loaded via a namespace (and not attached):
> [1] affyio_1.10.1        annotate_1.20.1      AnnotationDbi_1.4.2
> [4] DBI_0.2-4            grid_2.8.1          lattice_0.17-17
> [7] Matrix_0.999375-17  preprocessCore_1.4.0 RSQLite_0.7-1
> 
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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