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Question: GeneGA Error Message
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gravatar for chulmelowe
7 weeks ago by
chulmelowe0
chulmelowe0 wrote:

I've been attempting to run the examples from the GeneGA vignette but am getting an error message when I attempt to run the second block of code. The block of code in question is:

library(GeneGA)

seqfile = system.file("sequence","EGFP.fasta",package="GeneGA")
seq = unlist(getSequence(read.fasta(seqfile),as.string=TRUE))
GeneGA.result = GeneGA(sequence=seq,popSize=40,iters=150,crossoverRate=0.3,mutationChance=0.05,region=c(1,60),organism="ec",showGeneration=FALSE)

The error message, produced by the last line of code, is:

Error in system(paste("echo ", x, "|RNAfold", sep = ""), intern = T) : 
  'echo' not found

Has anyone else encountered this, and does anyone know how to fix it? Thanks.

Session Info:

R version 3.3.3 (2017-03-06)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
 [1] BiocInstaller_1.24.0 GeneGA_1.24.0        hash_2.2.6           seqinr_3.4-5         timeDate_3012.100    gtools_3.5.0        
 [7] RODM_1.1             sendmailR_1.2-1      R2wd_1.5             qcc_2.7              WriteXLS_4.0.0       xlsx_0.5.7          
[13] xlsxjars_0.6.1       rJava_0.9-8          RODBC_1.3-15        

loaded via a namespace (and not attached):
[1] MASS_7.3-47     tools_3.3.3     ade4_1.7-8      base64enc_0.1-3
ADD COMMENTlink written 7 weeks ago by chulmelowe0
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