R Language Reading and writing strings Capture output of operating system command
Example
Functions which return a character vector
Base R has two functions for invoking a system command. Both require an additional parameter to capture the output of the system command.
system("top -a -b -n 1", intern = TRUE)
system2("top", "-a -b -n 1", stdout = TRUE)
Both return a character vector.
[1] "top - 08:52:03 up 70 days, 15:09, 0 users, load average: 0.00, 0.00, 0.00"
[2] "Tasks: 125 total, 1 running, 124 sleeping, 0 stopped, 0 zombie"
[3] "Cpu(s): 0.9%us, 0.3%sy, 0.0%ni, 98.7%id, 0.1%wa, 0.0%hi, 0.0%si, 0.0%st"
[4] "Mem: 12194312k total, 3613292k used, 8581020k free, 216940k buffers"
[5] "Swap: 12582908k total, 2334156k used, 10248752k free, 1682340k cached"
[6] ""
[7] " PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND "
[8] "11300 root 20 0 1278m 375m 3696 S 0.0 3.2 124:40.92 trala "
[9] " 6093 user1 20 0 1817m 269m 1888 S 0.0 2.3 12:17.96 R "
[10] " 4949 user2 20 0 1917m 214m 1888 S 0.0 1.8 11:16.73 R "
For illustration, the UNIX command
top -a -b -n 1is used. This is OS specific and may need to be amended to run the examples on your computer.
Package devtools has a function to run a system command and capture the output without an additional parameter. It also returns a character vector.
devtools::system_output("top", "-a -b -n 1")
Functions which return a data frame
The fread function in package data.table allows to execute a shell command and to read the output like read.table. It returns a data.table or a data.frame.
fread("top -a -b -n 1", check.names = TRUE)
PID USER PR NI VIRT RES SHR S X.CPU X.MEM TIME. COMMAND
1: 11300 root 20 0 1278m 375m 3696 S 0 3.2 124:40.92 trala
2: 6093 user1 20 0 1817m 269m 1888 S 0 2.3 12:18.56 R
3: 4949 user2 20 0 1917m 214m 1888 S 0 1.8 11:17.33 R
4: 7922 user3 20 0 3094m 131m 1892 S 0 1.1 21:04.95 R
Note, that fread automatically has skipped the top 6 header lines.
Here the parameter
check.names = TRUEwas added to convert%CPU,%MEN, andTIME+to syntactically valid column names.
