[R] Error: unexpected symbol in [with read.table]

[Jim Lemon]

Hi Kate,
I could well be wrong, but are you sure that your data file is TAB
delimited and not whitespace delimited?

Jim


On Sat, Jun 27, 2015 at 7:37 AM, MacQueen, Don <macqueen1 at llnl.gov> wrote:
> If
>
> a <- read.table(args[1],sep="\t",header=T, stringsAsFactors=F)
>
>
> fails but
>
> a <- read.table("/path/to/file/filename.txt", header=T,sep="\t",
> stringsAsFactors=F)
>
>
> succeeds, then since those two commands are otherwise identical, you had
> better put
>
>   print(args[1])
>
> before the call to read.table, to find out if it is actually what you
> think it is.
>
> Also, obviously, the argument(s) that you supply after
>   /path/to/R/R-3.0.2/bin/Rscript
> are relevant.
>
> -Don
>
> --
> Don MacQueen
>
> Lawrence Livermore National Laboratory
> 7000 East Ave., L-627
> Livermore, CA 94550
> 925-423-1062
>
>
>
>
>
> On 6/26/15, 12:48 PM, "R-help on behalf of Kate Ignatius"
> <r-help-bounces at r-project.org on behalf of kate.ignatius at gmail.com> wrote:
>
>>Oops - error on my part.  Sorry.
>>
>>On Fri, Jun 26, 2015 at 2:54 PM, Bert Gunter <bgunter.4567 at gmail.com>
>>wrote:
>>> ... and you should also know by now to cc the list and not respond just
>>>to me!
>>> Bert Gunter
>>>
>>> "Data is not information. Information is not knowledge. And knowledge
>>> is certainly not wisdom."
>>>    -- Clifford Stoll
>>>
>>>
>>> On Fri, Jun 26, 2015 at 10:58 AM, Kate Ignatius
>>><kate.ignatius at gmail.com> wrote:
>>>> "reading in a tab delimited file using args"
>>>>
>>>> What I mean by that is that I'm using a bash script to call in an R
>>>> script and using the command: args <- commandArgs(TRUE) in my R
>>>> script.
>>>>
>>>> In my shell script I'm calling the R program as follows:
>>>> /path/to/R/R-3.0.2/bin/Rscript
>>>>
>>>> I'm not sure if that will help - sure you will all know if it doesn't.
>>>>
>>>> K.
>>>>
>>>> On Fri, Jun 26, 2015 at 1:39 PM, Bert Gunter <bgunter.4567 at gmail.com>
>>>>wrote:
>>>>> ??
>>>>> Are you expecting us to guess what your code was from
>>>>>
>>>>> "reading in a tab delimited file using args" ?
>>>>>
>>>>> You've posted here before and should know by now that explicit code
>>>>> should be provided whenever possible.
>>>>>
>>>>>
>>>>> Cheers,
>>>>> Bert
>>>>> Bert Gunter
>>>>>
>>>>> "Data is not information. Information is not knowledge. And knowledge
>>>>> is certainly not wisdom."
>>>>>    -- Clifford Stoll
>>>>>
>>>>>
>>>>> On Fri, Jun 26, 2015 at 10:32 AM, Kate Ignatius
>>>>><kate.ignatius at gmail.com> wrote:
>>>>>> When reading in a tab delimited file using args I keep getting the
>>>>>>error:
>>>>>>
>>>>>> Error: unexpected symbol in "Name index"
>>>>>>
>>>>>> Execution halted
>>>>>>
>>>>>> The code is this:
>>>>>>
>>>>>> a <- read.table(args[1],sep="\t",header=T, stringsAsFactors=F)
>>>>>>
>>>>>> When inputting the file directly, as follows, this produces no
>>>>>>errors:
>>>>>>
>>>>>> a <- read.table("/path/to/file/filename.txt", header=T,sep="\t",
>>>>>> stringsAsFactors=F).
>>>>>>
>>>>>> The file is such:
>>>>>>
>>>>>> Name               index
>>>>>> Bob                  1
>>>>>> George             2
>>>>>> Dave                3
>>>>>> Eric                  4
>>>>>> .
>>>>>> .
>>>>>> .
>>>>>> .
>>>>>> Andrew            20
>>>>>>
>>>>>> Is there anything I should be looking out for that might be producing
>>>>>> this error.   Any help will be greatly appreciated.
>>>>>>
>>>>>> ______________________________________________
>>>>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>>> PLEASE do read the posting guide
>>>>>>http://www.R-project.org/posting-guide.html
>>>>>> and provide commented, minimal, self-contained, reproducible code.
>>
>>______________________________________________
>>R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>https://stat.ethz.ch/mailman/listinfo/r-help
>>PLEASE do read the posting guide
>>http://www.R-project.org/posting-guide.html
>>and provide commented, minimal, self-contained, reproducible code.
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.