CODEWITHSUNDEEP
rbashpipe
ILoveCoding
ILoveCoding

Reputation: 926

Piping two bash commands in R: broken pipe error

I'm trying to pipe two bash commands in R but I get a broken pipe error; any suggestion is appreciated. Here's where I am:

#Create a long file (2GB on your drive...)
write.csv(rep(1,1E8),file="long.txt", row.names=FALSE)

system("grep 1 tmp.txt")    #This works
system("grep 1 tmp.txt| head -n 10")    #This gives a broken pipe error

I get grep: writing output: broken pipe With a short file it works properly. How can I work arround that please?

Thanks.

Upvotes: 5

Views: 5526

Answers (2)

user1922406
user1922406

Reputation:

Alternatively, if your implementation of grep supports it, you could use

grep -m 10 PATTERN FILE

Partial description from: man grep on Ubuntu 12.04

-m NUM, --max-count=NUM
      Stop reading a file after NUM matching lines.

This option was also available on my Red Hat 5.8 box where I was having a similar issue.

Upvotes: 2

mrb
mrb

Reputation: 3330

grep is complaining because it has more output than 10 lines, and head is cutting it off before it finishes.

I suggest hiding grep's stderr output (this is where the broken pipe error is printed).

system("grep 1 tmp.txt 2>/dev/null | head -n 10")

This won't work if you need to see other errors from grep; in that case, you will need a more complicated solution.

Upvotes: 7

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