[BioC] cosmo vignette example error

[Simon [guest]]

Hi, 

I tried using the cosmo bioconductor package but it produced errors, when I executed the samples from the Vignette. 

### R code from vignette source 'cosmo.Rnw'

###################################################
### code chunk number 1: load
###################################################
library(cosmo) 

.... according to the R script ...

###################################################
### code chunk number 17: example1
###################################################
seqFile <- system.file("Exfiles/seq.fasta", package="cosmo")
res <- cosmo(seqs=seqFile, constraints=list(conSet1, conSet2) , minW=7, maxW=8, models=c("OOPS", "TCM")) 

Executing this command produces the error: 
maxNumSites cannot be less than minNumSites. Exiting ...
After specifying the parameters minSite, maxSite the hmm order has to be specified too...
and then I get the error: sampleMalloc: Don't allocate n = 0 objects! 
(with whatever parameters I choose for example: minSite=2, maxSite=50, order=1 )

What am I doing wrong?

bw,
Simon




 -- output of sessionInfo(): 


R version 2.15.1 (2012-06-22)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=de_AT.UTF-8          LC_NUMERIC=C                 
 [3] LC_TIME=de_AT.UTF-8           LC_COLLATE=de_AT.UTF-8       
 [5] LC_MONETARY=de_AT.UTF-8       LC_MESSAGES=de_AT.UTF-8      
 [7] LC_PAPER=de_AT.UTF-8          LC_NAME=de_AT.UTF-8          
 [9] LC_ADDRESS=de_AT.UTF-8        LC_TELEPHONE=de_AT.UTF-8     
[11] LC_MEASUREMENT=de_AT.UTF-8    LC_IDENTIFICATION=de_AT.UTF-8

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

other attached packages:
[1] cosmo_1.22.0   seqLogo_1.22.0 rj_1.1.0-4    

loaded via a namespace (and not attached):
[1] rj.gd_1.1.0-1 tools_2.15.1 


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