[BioC] matchPdict error

[Hervé Pagès]

Hi Burak,

This problem is now fixed in release (Biostrings 2.10.21 and BSgenome 1.10.5)
and devel (Biostrings 2.11.40 and BSgenome 1.11.13).
The updated packages will be available in the next 12 hours for release and
are already available for devel. See http://bioconductor.org/docs/install/
for how to update your installation.

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
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319