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Full Discussion: [Solved] Running a R script with in a shell script
Top Forums Shell Programming and Scripting [Solved] Running a R script with in a shell script Post 302886310 by Kanja on Thursday 30th of January 2014 02:51:39 PM
Old 01-30-2014
[Solved] Running a R script with in a shell script
Hi,

I do have an R script named KO.R. Basically reads thousands of files, whose name has a pattern that differs at a portion of the file name, List.txt.

Row_file1_mile.txt
Row_file2_mile.txt
Row_file3_mile.txt
...
...
Row_file1000_mile.txt

Below is a portion of my Rscript that reads the file.
Code:
vi KO.R

Sample =
  read.delim("/Users/dropBox/Row_$file_mile.txt")
...
...
...

If I provide the list of the variable portion of the file name like

Code:
file1
file2
file3
...
..
file1000

how could I run this script one by one by reading each of the files and execute the script.

This is what I tried by making a .sh file
Code:
while read file
do

R CMD BATCH KO.R 

done < /Users/dropBox/List.txt

where List.txt contains the list of the variable portion of the file.

Could you please let me know the best way to excecute this R script with in the .sh executable shell script?
 

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LEARN ABOUT REDHAT

mac2unix

dos2unix(1)						      General Commands Manual						       dos2unix(1)

NAME

       dos2unix - DOS/MAC to UNIX text file format converter

SYNOPSYS

       dos2unix [options] [-c convmode] [-o file ...] [-n infile outfile ...]

       Options:

       [-hkqV] [--help] [--keepdate] [--quiet] [--version]

DESCRIPTION

       This manual page documents dos2unix, the program that converts plain text files in DOS/MAC format to UNIX format.

OPTIONS

       The following options are available:

       -h --help
	      Print online help.

       -k --keepdate
	      Keep the date stamp of output file same as input file.

       -q --quiet
	      Quiet mode. Suppress all warning and messages.

       -V --version
	      Prints version information.

       -c --convmode convmode
	      Sets conversion mode. Simulates dos2unix under SunOS.

       -o --oldfile file ...
	      Old file mode. Convert the file and write output to it. The program default to run in this mode. Wildcard names may be used.

       -n --newfile infile outfile ...
	      New  file  mode.	Convert the infile and write output to outfile. File names must be given in pairs and wildcard names should NOT be
	      used or you WILL lost your files.

EXAMPLES

       Get input from stdin and write output to stdout.

	      dos2unix

       Convert and replace a.txt. Convert and replace b.txt.

	      dos2unix a.txt b.txt

	      dos2unix -o a.txt b.txt

       Convert and replace a.txt in ASCII conversion mode.  Convert and replace b.txt in ISO conversion mode.  Convert	c.txt  from  Mac  to  Unix
       ascii format.

	      dos2unix a.txt -c iso b.txt

	      dos2unix -c ascii a.txt -c iso b.txt

	      dos2unix -c mac a.txt b.txt

       Convert and replace a.txt while keeping original date stamp.

	      dos2unix -k a.txt

	      dos2unix -k -o a.txt

       Convert a.txt and write to e.txt.

	      dos2unix -n a.txt e.txt

       Convert a.txt and write to e.txt, keep date stamp of e.txt same as a.txt.

	      dos2unix -k -n a.txt e.txt

       Convert and replace a.txt. Convert b.txt and write to e.txt.

	      dos2unix a.txt -n b.txt e.txt

	      dos2unix -o a.txt -n b.txt e.txt

       Convert c.txt and write to e.txt. Convert and replace a.txt.  Convert and replace b.txt. Convert d.txt and write to f.txt.

	      dos2unix -n c.txt e.txt -o a.txt b.txt -n d.txt f.txt

DIAGNOSTICS

BUGS

       The program does not work properly under MSDOS in stdio processing mode.  If you know why is that so, please tell me.

AUTHORS

       Benjamin Lin - <blin@socs.uts.edu.au>

       Bernd Johannes Wuebben (mac2unix mode) <wuebben@kde.org>

MISCELLANY

       Tested environment:

	      Linux 1.2.0 with GNU C 2.5.8

	      SunOS 4.1.3 with GNU C 2.6.3

	      MS-DOS 6.20 with Borland C++ 4.02

       Suggestions and bug reports are welcome.

SEE ALSO

       unix2dos(1) mac2unix(1)

1995.03.31							   dos2unix v3.0						       dos2unix(1)
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