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.
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.
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.