[R] reading in results from system(). There must be an easier way...

[Michael A. Gilchrist]

Sorry, I misunderstood what I was doing and misspoke.  I don't think there's 
a bug.  I had called COMMAND w/in read.delim.

Thanks for all of your help and sorry for the misinformation.

Sincerely,

Mike

-----------------------------------------------------
Department of Ecology & Evolutionary Biology
569 Dabney Hall
University of Tennessee
Knoxville, TN 37996-1610

phone:(865) 974-6453
fax:  (865) 974-6042

web: http://eeb.bio.utk.edu/gilchrist.asp
-----------------------------------------------------


On Thu, 18 Sep 2008, Henrik Bengtsson wrote:

> On Thu, Sep 18, 2008 at 1:39 PM, Michael A. Gilchrist <mikeg at utk.edu> wrote:
>> Wow, that's elegant and simple.  It's also faster than my approach.
>>
>> NB, you don't need to use close(), read.delim() closes the pipe when its
>> done reading.
>
> If read.delim() close the connection in this case, it's a bug.  It
> should only close the connection if it opens it.
>
> /Henrik
>
>>
>> Thank you all for your suggestions, they really helped me with this problem
>> and understand R just a bit better.
>>
>> Sincerely,
>>
>> Mike
>> -----------------------------------------------------
>> Department of Ecology & Evolutionary Biology
>> 569 Dabney Hall
>> University of Tennessee
>> Knoxville, TN 37996-1610
>>
>> phone:(865) 974-6453
>> fax:  (865) 974-6042
>>
>> web: http://eeb.bio.utk.edu/gilchrist.asp
>> -----------------------------------------------------
>>
>>
>> On Fri, 12 Sep 2008, Prof Brian Ripley wrote:
>>
>>> Why not use
>>>
>>> con <- pipe(COMMAND)
>>> foo <- read.delim(con, colClasses="numeric")
>>> close(con)
>>>
>>> ?  See the 'R Data Input/Output Manual'.
>>>
>>> On Fri, 12 Sep 2008, Michael A. Gilchrist wrote:
>>>
>>>> Hello,
>>>>
>>>> I am currently using R to run an external program and then read the
>>>> results the external program sends to the stdout which are tsv data.
>>>>
>>>> When R reads the results in it converts it to to a list of strings which
>>>> I then have to maniuplate with a whole slew of commands (which, figuring out
>>>> how to do was a reall challenge for a newbie like myself)--see below.
>>>>
>>>> Here's the code I'm using.  COMMAND runs the external program.
>>>>
>>>>   rawInput= system(COMMAND,intern=TRUE);##read in tsv values
>>>>   rawInput = strsplit(rawInput, split="\t");##split elements w/in the
>>>> list
>>>>                                              ##of character strings by
>>>> "\t"
>>>>   rawInput = unlist(rawInput); ##unlist, making it one long vector
>>>>   mode(rawInput)="double"; ##convert from strings to double
>>>>   finalInput = data.frame(t(matrix(rawInput, nrow=6))); ##convert
>>>>
>>>> Because I will be doing this 100,000 of times as part of an optimization
>>>> problem, I am interested in learning a more efficient way of doing this
>>>> conversion.
>>>>
>>>> Any suggestions would be appreciated.
>>>>
>>>>
>>>> Thanks in advance.
>>>>
>>>> Mike
>>>>
>>>>
>>>> -----------------------------------------------------
>>>> Department of Ecology & Evolutionary Biology
>>>> 569 Dabney Hall
>>>> University of Tennessee
>>>> Knoxville, TN 37996-1610
>>>>
>>>> phone:(865) 974-6453
>>>> fax:  (865) 974-6042
>>>>
>>>> web: http://eeb.bio.utk.edu/gilchrist.asp
>>>>
>>>
>>> --
>>> Brian D. Ripley,                  ripley at stats.ox.ac.uk
>>> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
>>> University of Oxford,             Tel:  +44 1865 272861 (self)
>>> 1 South Parks Road,                     +44 1865 272866 (PA)
>>> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>>>
>>
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>>
>