Hej,
When I try to call QIIME with a system call from R, i.e
system2("macqiime")
R stops responding. It's no problem with other command line programs though.
can certain programs not be called from R via system2() ?
MacQIIME version:
MacQIIME 1.8.0-20140103
Sourcing MacQIIME environment variables...
This is the same as a normal terminal shell, except your default
python is DIFFERENT (/macqiime/bin/python) and there are other new
QIIME-related things in your PATH.
(note that I am primarily interested to call QIIME from R Markdown with engine = "sh" which fails, too. But I strongly suspect the problems are related)
In my experience, when you call Qiime from unix command line, it usually creates a virtual shell of it`s own to run its commands which is different from regular system commands like ls or mv. I suspect you may not be able to run Qiime from within R unless you emulate that same shell or configuration Qiime requires. I tried to run it from a python script and was not successful.
Related
I have exe file which was built on C++. The exe file needs an input argument.
Now i want to launch multiple exe file from Rstudio by changing the input arguments so that i can run different scenarios in parallel. When i use system/shell/system2 commands, the model starts running inside the Rstudio environment itself, but i want to make it to run outside Rstudio environment, so that i can run multiple models at a time.
system("xyz.exe scenario1")
system("xyz.exe scenario2")
system("xyz.exe scenario3")
Looking at ?system you can see that there is an argument wait. Quoting from the help file:
[wait is] a logical (not NA) indicating whether the R interpreter should wait
for the command to finish, or run it asynchronously. This will be
ignored (and the interpreter will always wait) if intern = TRUE.
So using wait=TRUE would cause the behaviour that you require.
Is it possible to determine - from within the script - whether the script is running in the R-GUI (specifically R.app on OS X) or whether it has been called from Terminal/command line (i.e. R --vanilla -f script.R)? If so, how is this possible?
I'm asking because I have a script that can run parallelized (using the doMC library), which should not be used from the GUI. Sometimes I need to further process the data calculated in the script, so I'd like to call the script from the GUI on these occasions.
Perhaps you are looking for interactive()?
In C, you would use the isatty function. If you could find an equivalent function in R (probably in a UNIX or file system library), that should help.
I want to launch Rcmdr as a command from bash (or any unix shell), perhaps as an alias. R accepts the CMD argument and I could also pipe a script in with <. I would like the R console to stay open, and an interactive RCommander session to be started (Rcmdr is a popular GUI for R, for any newbies reading along, and it seems that you start up R, type library(Rcmdr) and then Commander() to start it up).
I am aware of how to add Rcmdr to my profile, and it appears to always start up if I include library(Rcmdr) in my .Rprofile, on my Linux workstation.
If I pipe my input in with < then this script works up to the point where it says that Commander GUI is launched only in interactive sessions:
library(Rcmdr);
Commander();
However if I run R CMD BATCH ./rcommander.r it just starts up and shuts down immediately, probably giving me some warning about interactive sessions that I didn't see, because CMD BATCH puts R into non-interactive mode and is thus useless for the purpose of "injecting" Rcmdr into an interactive R session.
It appears impossible to "source a file on the command line but run interactively" in R. It also appears that there are command line options to ignore the global and the user profile, but not to specify a custom profile like R --profile-custom ./.Rprofile2
Either I would like to specify a profile that means "Right now I want to start up and use RCmdr" and still be able to run R without it sometimes.
Working on an Ubuntu machine here, I was able to use the advice provided by Dirk in this mailing list post:
nathan#nathan-laptop:~/tmp$ cat rcommander.r
#!/bin/bash
r -lRcmdr -e'while(TRUE) Commander();'
nathan#nathan-laptop:~/tmp$ cat rcommander2.r
#!/bin/bash
Rscript --default-packages=Rcmdr -e 'while(TRUE) Commander();'
The first script uses Dirk's littler package, available on CRAN, and the second uses the standard Rscript executable. As noted, you can kill the process with ctrl + c from your terminal.
How does R's built-in system() function know where to look to invoke some arbitrary OS command specified by the command argument? For example, if I homebrew install some_command_line_program, how does R's system() function know where it is located when I type:
cmd <- "some_complicated_code_from_some_command_line_program"
system(cmd, wait=FALSE)
In other words, how is R smart enough to know where to look without any user input? If I compile from source via Github (instead of homebrew install), would system() also recognize the command?
What system does depends on your OS, you've not told us (although you've given us some clues...).
On unix-alike systems, it executes it as a command in a bash shell, which searches for the first match in the directories on the $PATH environment variable. You can see what that is in R:
> Sys.getenv("PATH")
[1] "/usr/local/heroku/bin:/usr/local/heroku/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/nobackup/rowlings/NEST4B"
In Windows, it does something else.
You can get a full path to whatever it might run with Sys.which, which uses the systems' which command on unixes and fakes it on Windows. Read the help for more.
If you compile something from source then it will be found if the file that runs the command (a shell script, an executable, a #!-script in any language) is placed in a folder in your $PATH. You can create a folder yourself, say /home/user/bin, put your executables in there, add that to your $PATH, and (possibly after logging out an in again, or restarting R, or just firing up a new shell...) then R will find it.
I am using RStudio and at times I want to remove some files in the working directory (e.g., previously generated .csv files).
It is quite inconvenient to frequently switch to bash and execute rm. Is there any way of invoking commands in the R console?
See here
Use system (or shell) as agstudy's comment says
e.g. system("pwd")
If you are just removing files, rather than executing arbitrary commands on the shell, you would be better off following Thomas's suggestion:
?file.remove
Using this function instead of shell("rm example.csv") is safer and more portable.