On 13-11-20 10:45 PM, Earl Brown wrote:
R-helpers,
I'm using system() to run a shell script that uses a library written in C++ to
analyze natural language (FreeLing: http://nlp.lsi.upc.edu/freeling). When I
run the following code in RStudio (0.97.248) and R.app (1.62) on Max OSX
(10.7.5):
cmd <- "analyze -f /usr/local/share/freeling/config/es.cfg --lang es --outf tagged
</Users/earlbrown/temp_input.txt"
tagged.text <- do.call(system, args = list(command = cmd, intern = T))
I sometimes receive a "Segmentation fault" error:
/usr/local/bin/analyze: line 39: 2806 Segmentation fault: 11
$FREELING/bin/analyzer $param
Warning message:
running command 'analyze -f /usr/local/share/freeling/config/es.cfg --lang es
--outf tagged </Users/earlbrown/temp_input.txt' had status 139
That's clearly a bug in the library or in the program that calls it
(i.e. "analyze").
and sometimes I receive a "Trace/BPT trap: 5" error:
dyld: lazy symbol binding failed: Symbol not found: __ZN6icu_496LocaleD1Ev
Referenced from: /usr/local/lib/libfreeling-3.1-alfa1.dylib
Expected in: flat namespace
dyld: Symbol not found: __ZN6icu_496LocaleD1Ev
Referenced from: /usr/local/lib/libfreeling-3.1-alfa1.dylib
Expected in: flat namespace
/usr/local/bin/analyze: line 39: 2864 Trace/BPT trap: 5
$FREELING/bin/analyzer $param
Warning message:
running command 'analyze -f /usr/local/share/freeling/config/es.cfg --lang es
--outf tagged </Users/earlbrown/temp_input.txt' had status 133
However, when I open a Terminal window and start R there and then run the code
I don't get either error message and I get the output I expect. So, the obvious
work-around is to simply run my R scripts that use FreeLing (the C++ library)
in an R session within Terminal. But, I'm curious to know why RStudio and R.app
have problems with it, and if there is anything that I can do to be able to use
RStudio and/or R.app when I want to call this C++ library.
Presumably R.app and RStudio run the program in a different environment
than R does at the command line. One obvious guess is that the standard
file handles (stdin, stdout, stderr) would be handled quite differently.
Another is that the program may be loaded at a different address, or
with a different amount of memory available to it.
In any case, it's pretty clearly not a bug in R.app or RStudio.
Duncan Murdoch
Here's my info:
sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_3.0.2
Thanks in advance for your help and ideas. Earl Brown
-----
Earl K. Brown, PhD
Assistant Professor of Spanish (Linguistics)
Advisor, TEFL MA Program
Department of Modern Languages
Kansas State University
www-personal.ksu.edu/~ekbrown
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