I'm having some problems using the function System() in R.
I don't really know exactly what kind of commands that I use in ms-dos is possible to
use in System(). Probably I can use anything but I don't know how.
I have used a few examples on the internet, for example:
To launch a file
system("notepad myfile.txt")
To launch a shell
system(Sys.getenv("COMSPEC"))
However, I wanted to use the command SET in order to try to get the user input (I know I could use readline() in R but it won't be useful in my code).
Is it possible to use SET with system()?
I tried to use:
system("SET /P uname=Please enter your name:")
system(SET /P uname=Please enter your name:)
system(paste("SET /P uname=Please enter your name:"),wait=FALSE)
None of them worked. Does anyone know how to do this?
Related
I have the following code that should open the Recode.xlsx inside the subf folder but doesn't
write_xlsx(mtcars, "subf/Recode.xlsx")
shell("subf/Recode.xlsx", wait=FALSE)
The following code works, so if anyone has an idea on why it doesn't work it would help me
write_xlsx(mtcars, "Recode.xlsx")
shell("Recode.xlsx", wait=FALSE)
Here’s what the documentation of the shell function says (emphasis mine):
shell is a more user-friendly wrapper for system. To make use of Windows file associations, use shell.exec.
And here is another bit of relevant information from the shell.exec documentation:
To be interpreted as relative, the path also needs to use backslashes as separators (at least in Windows 10).
So the following is the correct usage:
shell.exec("subf\\Recode.xlsx")
Can this be done in R? where am R script can be run without interruption by any function.
This Do you want to proceed? [y/N]: was generated from renv::restore(), but regardless, can all promotes be ignored.
Any input is helpful, Thanks.
Afaik all renv commands (restore() definitely) have the prompt argument:
prompt
Boolean; prompt the user before taking any action? For backwards compatibility, confirm is accepted as an alias for prompt.
Use prompt=FALSE (default is interactive()) to turn off the prompting.
I am trying to run the following command from Julia:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/user/.julia/v0.3/Smile/deps/downloads
When I run it as-is it tries to replace $LD_LIBRARY_PATH with a local variable.
When I escape the $, it puts quotes around the command, which invalidates it.
julia> cmd = `export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/tim/.julia/v0.3/Smile/deps/downloads`
ERROR: LD_LIBRARY_PATH not defined
julia> cmd = `export LD_LIBRARY_PATH=\$LD_LIBRARY_PATH:/home/tim/.julia/v0.3/Smile/deps/downloads`
`export 'LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/tim/.julia/v0.3/Smile/deps/downloads'`
I would like to run the command in a form similar to:
run(`export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$newpath`)
How do I properly handle the dollar sign?
Thank you
*note: pasting the command directly into terminal and running it does work
In Julia, backticks are not completely equivalent to running the corresponding command at the shell. You can't interpolate environmental variables with $ (although $(get(ENV, "varname", "") should match the shell's behavior), and export is a shell built-in, not a command, so I don't think you can run it. Also, even if backticks shelled out, export would only change the environment of the subshell, not the calling process.
You should be able to set LD_LIBRARY_PATH from Julia as:
ENV["LD_LIBRARY_PATH"] = "$(get(ENV, "LD_LIBRARY_PATH", "")):$newpath"
but you should avoid this if possible. If your intent is to ccall a specific library, you can pass the library path directly to ccall, perhaps using find_library as you indicated in a comment if you don't know the full path advance. If you need to set LD_LIBRARY_PATH because the library needs to load other libraries, I'm not sure if there's a better way, but note that LD_LIBRARY_PATH is platform-specific. You might be able to dlopen the dependent libraries first, but I haven't tested that.
I have some problems to call a command line program called molconvert from R using system() in Windows. molconvert is located in "C:\Program Files\ChemAxon\MarvinBeans\bin"
I would then like to invoke system() or shell() to mimick what I would achieve by typing
molconvert pdb "C:\molecule conversions\cembrene A.mol"
at the command prompt and collect the resulting output back to R as in
out=system(...,intern=T)
I seem to have trouble though with the backslashes and the spaces in the paths.
I tried with
dirmolconvert="C:\\Program Files\\ChemAxon\\MarvinBeans\\bin"
shell(shQuote(paste(dirmolconvert,"\\molconvert pdb "C:\\cembrene A.mol",sep="")))
but that gives me "Error: unexpected symbol in ..." and escaping the " also doesn't help. Any thoughts on how I should resolve this?
or
system(paste(dirmolconvert,"\\molconvert pdb \"C:\\cembrene A.mol\"",sep=""), intern=T)
but that gives me
'C:\Program' not found
Any thoughts?
Edit:
Based on the answer below the right way to do this apparently is
inputdir="C:/Users/Ento/Documents/GCMS/molconvert test"
molconvertdir="C:/Program Files/ChemAxon/MarvinBeans/bin"
molecule="cembrene A.mol"
out=system(paste(shQuote(file.path(molconvertdir, "molconvert.bat")),
"pdb",
shQuote(file.path(inputdir,molecule))),intern=T)
You want to use shQuote to quote the path to the executable, not the entire command line. Depending on what your molconvert program expects, you may also want to quote paths that are arguments to it.
system(paste(shQuote(file.path(dirmolconvert, "molconvert.exe")),
"pdb",
shQuote("C:\\molecule conversions\\cembrene A.mol"))
the easiest way to fix this is to use short paths:
for %%a in ("C:\molecule conversions\cembrene A.mol") set "sh_path=%%~dpfnxsa"
or
for %%a in ("C:\Program Files\ChemAxon\MarvinBeans\bin") do set "pf_sh_path=%%~dpfnxsa"
and then to pass %sh_path% and %pf_sh_path% as parameter.
I'm new to zsh and am using the ZSH_THEME="jnrowe", which works great for a little while.
It starts out and I get a prompt that looks like this:
Ξ ~ →
but if I run a command like: ssh it becomes:
↑255 ~ →
I suspect something is messing up the character that was creating the triple bar in the first one, but have no clue really as to what's going on. I could just pick a different theme, but I've noticed most of them with a fancy character in the prompt do the same thing.
Is this a special error code or something? Or is something just borking out?
I don't know the prompt theme "jnrowe" (it's not part of the default zsh distribution afaics), but I suspect this prompt includes the error code of the last command in its output.
Try to run "ls" or "true" and the number will disapper. Run "false" and it will be 1, run ssh without arguments and it will be 255. zsh preserves this value until you run the next command, so pressing ENTER many times will not clear it.
(This will be the same value that is stored in the shell variable "$?")