[R] call to system returns warning : status 2 (Ubuntu)

[Eric Elguero]

Hi everybody,

I have to run under Ubuntu a programs repeatedly
with different arguments and I am using R just to 
generate the data files and call the external program.

basically, in my script I have inside a loop these two lines:

command <- paste(<some constant or variable strings>,sep="")
system(command,intern=T,wait=T)

when I run this script, I get a number of warnings,
like this one:

16: running command '~/LDhat22/ldconvert -seq ld/serca/serca-Trs.fas
-freqcut 0.0 -missfreqcut 100.0 -sites 1 3687 -nous 6 >
ld/serca/serca-Trs.out' had status 2


however, when I run the very same command at the bash prompt,
everything seems fine (no complaint).

in either cases, the output is the same and looks correct.

So, may I just ignore these warnings or is there something
I should fix?

thank you in advance,

Eric Elguero
MIVEGEC
IRD -CNRS - UM1
Montpellier - France