GeneGA Error Message
1
0
Entering edit mode
chulmelowe • 0
@chulmelowe-14092
Last seen 6.6 years ago

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
software error • 741 views
ADD COMMENT
0
Entering edit mode
lynnamon • 0
@lynnamon-21211
Last seen 4.9 years ago

You need to install ViennaRNA. https://www.tbi.univie.ac.at/RNA/

ADD COMMENT

Login before adding your answer.

Traffic: 703 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6