R help - Oct 2007 - Problems with scan() in a tab-sep .txt file with cells that have '///' (three frontslashes)

Hello all,

I'm using the following scan() parameters on a tab-separated text file that
was generated by R.

temp_file <- scan(file = outfile, sep="\t", what = character(),
skip = 1, nlines = 1)

The problem is that within some cells, there are cases where there are three
frontslashes ( /// ). However, the file itself is tab-separated, and the exact
problem is that even if I specify sep="\t" in the argument to scan(),
whenever it encounters a /// it overrides the tab separation, and uses the ///
as the separator. Then within that column, I see a bunch of /t in the output,
and no ///. There are also some cells with two frontslashes ( // ), but scan
handles them just fine.

I've tried many, many other combinations of parameters, but have not found
the right one.

I know this shouldn't be a problem, b/c read.csv() and read.table() call
scan(), and when calling them, such as:

abc <- read.table(outfile, sep="\t", header=T)

...I don't have the problem. The /// show up in the output verbatim, and the
/t are used as proper delimiters.

If anyone can tell me which parameter I am missing in scan(), I would be very
grateful. I'd prefer not to have to use make.names() to handle the slashes.

Thanks in advance for any help,
-Ken
 
_________________________________________________________________
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ilnews
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On Fri, 26 Oct 2007, Ken Termiso wrote:
> Hello all,
>
> I'm using the following scan() parameters on a tab-separated text file
that was generated by R.
>
> temp_file <- scan(file = outfile, sep="\t", what =
character(), skip = 1, nlines = 1)
>
> The problem is that within some cells, there are cases where there are 
> three frontslashes ( /// ). However, the file itself is tab-separated, 
> and the exact problem is that even if I specify sep="\t" in the
argument
> to scan(), whenever it encounters a /// it overrides the tab separation, 
> and uses the /// as the separator. Then within that column, I see a 
> bunch of /t in the output, and no ///. There are also some cells with 
> two frontslashes ( // ), but scan handles them just fine.
>
I do not see that.
> ### 10 lines of "//\t///"
> cat(file="tmp.dat",
rep(paste(c("//","///"),collapse='\t'),10),sep='\n')
> scan('tmp.dat',sep='\t',what='a')
Read 20 items
  [1] "//"  "///" "//"  "///"
"//"  "///" "//"  "///" "//"
[10] "///" "//"  "///" "//" 
"///" "//"  "///" "//"  "///"
[19] "//"  "///"
>
> version
                _
platform       i386-pc-mingw32
arch           i386
os             mingw32
system         i386, mingw32
status
major          2
minor          6.0
year           2007
month          10
day            03
svn rev        43063
language       R
version.string R version 2.6.0 (2007-10-03)
>
As it says: "PLEASE do ... provide commented, minimal, self-contained, 
reproducible code."

Chuck
> I've tried many, many other combinations of parameters, but have not
found the right one.
>
> I know this shouldn't be a problem, b/c read.csv() and read.table()
call scan(), and when calling them, such as:
>
> abc <- read.table(outfile, sep="\t", header=T)
>
> ...I don't have the problem. The /// show up in the output verbatim,
and the /t are used as proper delimiters.
>
> If anyone can tell me which parameter I am missing in scan(), I would be
very grateful. I'd prefer not to have to use make.names() to handle the
slashes.
>
> Thanks in advance for any help,
> -Ken
>
> _________________________________________________________________
> [[replacing trailing spam]]
>
> ilnews
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> 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.
>
Charles C. Berry                            (858) 534-2098
                                             Dept of Family/Preventive Medicine
E mailto:cberry at tajo.ucsd.edu	            UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901