cosmo vignette example error
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Last seen 9.6 years ago
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 -- Sent via the guest posting facility at bioconductor.org.
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