I would like to execute this DOS command under R:
iconv -f ISO-8859-1 -t UTF-8 FileName.md > FileNameNew.md
The above command creates new file after transforming from ISO to UTF.
I have tried execute this command however unsuccessfully with:
system(paste("iconv -f ISO-8859-1 -t UTF-8 FileName.md > FileNameNew.md", sep=""))
This gives me two types of errors:
Invalid argument
No such file or directory
I don't think the issue is the second since when I run the command under R it in fact executes the command as it re-reads the FileName.md, which means he found the file. I think it is just a issue with the > and hence formulation of the command in the system(paste("")) command.
When I rund this command directly under console it works.
The problem is (most likely) simply with where the R session is located. Check this by running getwd() in R and see if it is in the same place as the file. The paste part shouldn't be needed, as it is not really pasting anything (paste combines 2 strings together, while it is one string here).
Solve this by explicitly attaching input and output to those files.
If you would insist on using paste, you could use it for instance like this:
system(paste("iconv -f ISO-8859-1 -t UTF-8 ", getwd(), "/FileName.md > ",
getwd(), "/FileNameNew.md", sep=""))
Related
I want to open a file from within R.
I can launch the software (graphpad prism) with the following:
system2("C:/Program Files (x86)/GraphPad/Prism 7/prism.exe")
I expected this to open my prism file as if I were double clicking on it or running it from cmd, but it didn't:
system2("H:/Graphs/Shell/Templates/NASH4_Standard.pzfx")
I am receiving the message:
Warning message: running command
'H:/Graphs/Shell/Templates/NASH4_Standard.pzfx' had status 127
I see that this is not an error but just a warning. Am I unintentionally "shelling" the document in the background? How would I make sure it pops up as a window?
Status 127 was addressed here, but for launching the software, not opening the document with it.
In Windows environments, you need to call a command line interpreter like CMD prompt or PowerShell. Also, any file path that has spaces needs to be enclosed in double quotes above the quotes needed in R for string literals (the case for your .exe not specific file).
With system() send entire command in one string:
system('cmd /c "H:/Graphs/Shell/Templates/NASH4_Standard.pzfx"')
# POWER SHELL REQUIRES MORE QUOTE ESCAPING (ONLY ONE PAIR W/O SPACES)
system('powershell & """H:/Graphs/Shell/Templates/NASH4_Standard.pzfx"""')
With system2() use the args parameter:
# FILES
system2('cmd', args=c('/c', '"H:/Graphs/Shell/Templates/NASH4_Standard.pzfx"'))
system2('powershell', args=c(' & """H:/Graphs/Shell/Templates/NASH4_Standard.pzfx"""'))
# EXECUTABLES
system2('cmd', args=c('/c', '"C:/Program Files (x86)/GraphPad/Prism 7/prism.exe"'))
system2('powershell', args=c(' & """C:/Program Files (x86)/GraphPad/Prism 7/prism.exe"""'))
shell.exec("C:/Program Files (x86)/GraphPad/Prism 7/prism.exe")
does it work for you ?
ps. and shell.exec("MyWorkbook.xls") open file with default program
I am trying to invoke some system commands on R using system() calls. However, I am having the infamous problem with spaces in the directories.
For example, I am trying to use this directory:
odir <- '/Volumes/Macintosh HD 2/data/cmip5/historical/clt/models'
on this command:
system(paste('ls ', odir,sep=''))
and I receive the following error:
> system(paste('ls ', odir,sep=''))
ls: /Volumes/Macintosh: No such file or directory
ls: 2/data/cmip5/historical/clt/models: No such file or directory
ls: HD: No such file or directory
How can I overcome this?
Thanks!
Most command lines require that you escape spaces with a backslash. And when you make R strings, you need to escape backslashes with a backslash. Try
odir <- '/Volumes/Macintosh\\ HD\\ 2/data/cmip5/historical/clt/models'
I am new to programming and mainly I am able to do some scripts within R, but for my work I need to call an external program. For this program to work on the ubuntu's terminal I have to first use setenv and then execute the program. Googling I've found the system () and Sys.setenv() functions, but unfortunately I can make it function.
This is the code that does work in the ubuntu terminal:
$ export PATH=/home/meme/bin:$PATH
$ mast "/home/meme/meme.txt" "/home/meme/seqs.txt" -o "/home/meme/output" -comp
Where the first two arguments are input files, the -o argument is the output directory and the -comp is another parameter for the program to run.
The reason that I need to do it in R despite it already works in the terminal is because I need to run the program 1000 times with 1000 different files so I want to make a for loop where the input name changes in every loop and then analyze every output in R.
I have already tried to use:
Sys.setenv(PATH="/home/meme/bin"); system(mast "/home/meme/meme.txt" "/home/meme/seqs.txt" -o "/home/meme/output" -comp )
and
system(Sys.setenv(PATH="/home/meme/bin") && mast "/home/meme/meme.txt" "/home/meme/seqs.txt" -o "/home/meme/output" -comp )
but always received:
Error: unexpected constant string in "system(mast "/home/meme/meme.txt""
or
Error: unexpected symbol in "system(Sys.setenv(PATH="/home/meme/bin") && mast "/home/meme/meme.txt""
At this point I have run out of ideas to make this work. If this has already been answered, then my googling have just been poor and I would appreciate any links to its response.
Thank you very much for your time.
Carlos
Additional details:
I use Ubuntu 12.04 64-bits version, RStudio version 0.97.551, R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" Platform: x86_64-pc-linux-gnu (64-bit).
The program I use (MAST) finds a sequence pattern in a list of letters and is part of the MEME SUIT version 4.9.1 found in http://meme.nbcr.net/meme/doc/meme-install.html and run through command line. The command-line usage for mast is:
mast <motif file> <sequence file> [options]
Construct the string you want to execute with paste and feed that to system:
for(i in 1:10){
cmd=paste("export FOO=",i," ; echo \"$FOO\" ",sep='')
system(cmd)
}
Note the use of sep='' to stop paste putting spaces in, and back-quoting quote marks in the string to preserve them.
Test before running by using print(cmd) instead of system(cmd) to make sure you are getting the right command built. Maybe do:
if(TESTING){print(cmd)}else{system(cmd)}
and set TESTING=TRUE or FALSE in R before running.
If you are going to be running more than one shell command per system call, it might be better to put them all in one shell script file and call that instead, passing parameters from R. Something like:
cmd = paste("/home/me/bin/dojob.sh ",i,i+1)
system(cmd)
and then dojob.sh is a shell script that parses the args. You'll need to learn a bit more shell scripting.
Is there a way to write my R errors to a file? I run R on bash via:
R --vanilla < myprogram > myprogram.out &
When my program encounters an error (not a syntax error...like an illegal replacement or something) it stops but the error line isn't written to the output file and I don't know what the program was and a lot of the time I log out from the server while it runs.
Thanks,
Josh
Use the R CMD BATCH <infile> <outfile> syntax instead.
This command:
/usr/bin/mysqldump --add-drop-table -u myuser -pmypass mydb > "/home/myuser/dbBackups/"`date +%Y%m%d`".sql"
works fine from the command line but whenb cron runs it I get
/bin/sh: -c: line 0: unexpected EOF while looking for matching ``'
/bin/sh: -c: line 1: syntax error: unexpected end of file
The command is all on one line in the crontab as well so I'm confused by the line 0 and line 1 references...
Can anyone advise me as to what I am doing wrong there?
It's the obvious dumb question, but do you have the matching backquote in your crontab (crontab -l)?
The line one, line zero stuff isn't referring to the lines in the crontab, only to the 'lines' in the one-line script.
Updated:
Ah, I think I've got it. This is from crontab(5):
Percent-signs (%) in the command, unless escaped with backslash (\),
will be changed into newline characters, and all data after the
first % will be sent to the command as standard input.
So the percent characters in your date spec are being interpreted as newlines, which means the backquote isn't terminated before the newline, which would produce your error message.
So escape the percent characters. I'd forgotten that about crontab....
The easiest fix is probably to put the whole command in a shell script and just have that be run. So make a scriptName.sh file that contains the command you listed and have crontab call that script. That gets around all these odd problems.
Commands executed from cron do not have access to the environment variables from your login shell, including the path. So try the following (adding fully qualified path to date):
/usr/bin/mysqldump --add-drop-table -u myuser -pmypass mydb > "/home/myuser/dbBackups/"`/usr/bin/date +%Y%m%d`".sql"
Of course, verify if your date command is located elsewhere by running which date then adjust the path if necessary.