Status 1 and Call executeables from R


#1

Hello,

I am new to R and command line softwares as well. I am using Win7 and R studio. Whenever I call hmmerScan.exe from R, it gives me this error. Kindly guide me about the problem and solution.

hmmerScan: Scanning D:/R-files/Micropan/prepped/NIH1_GID1.fasta ...
Failed to parse command line: Arg looks like option? Use --domtblout=--cpu if you really mean it.
Usage: hmmscan [-options] <hmm database> <query seqfile>

where most common options are:
  -h : show brief help on version and usage

To see more help on available options, do /Genomes/hmmscan -h

Warning messages:
1: running command 'hmmscan -o hmmer3.txt --cut_ga --noali --domtblout --cpu 0 D:/R-files/Micropan/pfam/GID1_vs_Pfam-A.hmm.txt D:/R-files/Micropan/Pfam-A.hmm D:/R-files/Micropan/prepped/NIH1_GID1.fasta' had status 1 

Thanks


#2

You have not shown us how you are calling the function (i.e. what R code are you using)? Also, without the hmmerScan.exe file, it will be difficult for us to reproduce your issue. It looks like your options are being misinterpreted. Ensure that you can execute the command you are building from the terminal, and maybe from the RStudio terminal. Then, if you want to execute from R code, you can look into the help pages to system2 or system.

For instance, it is important to note that only the first part (hmmscan) is necessary for the command for system2 - everything else is in an arg character vector.

EDIT: Simple examples:

system2("echo","test")
system2("ping",c("-c 2","8.8.8.8"))