[BioC] DESeq2 stuck running

[Mingfeng [guest]]

It is the exciting news of the coming of DESeq2.
There are many updates and incorporation with other software, e.g., Wald test and cqn.
My question is the nbinomWaldTest may stuck running for long time when using multiple factors, e.g., running several days but no results or messages coming out. It works well when I remove the "type" factor.
I paste the meta data in the following:
           condition type
S103         W  U
S149         W Y
S114         W Y
S98          K  U
S92          K  U
S159         K Y






Thanks.




 -- output of sessionInfo(): 

> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] splines   parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] cqn_1.10.0              quantreg_5.05           SparseM_1.03           
 [4] preprocessCore_1.26.0   nor1mix_1.1-4           mclust_4.3             
 [7] DESeq2_1.4.1            RcppArmadillo_0.4.300.0 Rcpp_0.11.1            
[10] GenomicRanges_1.16.2    GenomeInfoDb_1.0.2      IRanges_1.22.4         
[13] BiocGenerics_0.10.0    

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.26.0 Biobase_2.24.0       DBI_0.2-7           
 [4] RColorBrewer_1.0-5   RSQLite_0.11.4       XML_3.98-1.1        
 [7] XVector_0.4.0        annotate_1.42.0      genefilter_1.46.0   
[10] geneplotter_1.42.0   grid_3.1.0           lattice_0.20-29     
[13] locfit_1.5-9.1       stats4_3.1.0         survival_2.37-7     
[16] xtable_1.7-3  

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