Problems with spaces in paths when calling a batch file from R

Question

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

Answer 1

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.