[Rd] Best way to locate R executable from within R?
Hi, I'd like to spawn of a new R process from within R using system(), e.g. system(R -f myScript.R). However, just specifying R as in that example is not guaranteed to work, because R may not be on the OS's search path. What is the best way, from within a running R, to infer the command (basename or full path) for launching R in way that it works on any OS? I came up with the following alternatives, but I'm not sure if they'll work everywhere or not: 1. Rbin - commandArgs()[1]; 2. Rbin - file.path(R.home(), bin, R); Other suggestions that are better? /Henrik __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Best way to locate R executable from within R?
On Tue, May 22, 2012 at 10:34 AM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: Hi, I'd like to spawn of a new R process from within R using system(), e.g. system(R -f myScript.R). However, just specifying R as in that example is not guaranteed to work, because R may not be on the OS's search path. What is the best way, from within a running R, to infer the command (basename or full path) for launching R in way that it works on any OS? I came up with the following alternatives, but I'm not sure if they'll work everywhere or not: 1. Rbin - commandArgs()[1]; 2. Rbin - file.path(R.home(), bin, R); Other suggestions that are better? Rbin - file.path(Sys.getenv(R_HOME), bin, R) Dan /Henrik __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Best way to locate R executable from within R?
On Tue, May 22, 2012 at 10:47 AM, Dan Tenenbaum dtene...@fhcrc.org wrote: On Tue, May 22, 2012 at 10:34 AM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: Hi, I'd like to spawn of a new R process from within R using system(), e.g. system(R -f myScript.R). However, just specifying R as in that example is not guaranteed to work, because R may not be on the OS's search path. What is the best way, from within a running R, to infer the command (basename or full path) for launching R in way that it works on any OS? I came up with the following alternatives, but I'm not sure if they'll work everywhere or not: 1. Rbin - commandArgs()[1]; 2. Rbin - file.path(R.home(), bin, R); Other suggestions that are better? Rbin - file.path(Sys.getenv(R_HOME), bin, R) I don't see how Sys.getenv(R_HOME) would be better than R.home() - any reasons? Your reply triggered me to read up on help(R.home), where I noticed the passage: A character string giving the R home directory or path to a particular component. Normally the components are all subdirectories of the R home directory, but this may not be the case in a Unix-like installation. [...] The return value for modules and on Windows bin is to a sub-architecture-specific location. So, now I'd say that: 4. Rbin - file.path(R.home(bin), R); is better than (2). I'm still not sure whether to use (1) or (4), though. /Henrik Dan /Henrik __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Best way to locate R executable from within R?
On May 22, 2012, at 1:47 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: On Tue, May 22, 2012 at 10:34 AM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: Hi, I'd like to spawn of a new R process from within R using system(), e.g. system(R -f myScript.R). However, just specifying R as in that example is not guaranteed to work, because R may not be on the OS's search path. What is the best way, from within a running R, to infer the command (basename or full path) for launching R in way that it works on any OS? I came up with the following alternatives, but I'm not sure if they'll work everywhere or not: 1. Rbin - commandArgs()[1]; 2. Rbin - file.path(R.home(), bin, R); Other suggestions that are better? Rbin - file.path(Sys.getenv(R_HOME), bin, R) That is certainly worse, not better. 1. doesn't work because it may be a relative path. 2. Sounds pretty good - since the environment will be set by the current R. Dan /Henrik __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Best way to locate R executable from within R?
On Tue, May 22, 2012 at 1:34 PM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: Hi, I'd like to spawn of a new R process from within R using system(), e.g. system(R -f myScript.R). However, just specifying R as in that example is not guaranteed to work, because R may not be on the OS's search path. What is the best way, from within a running R, to infer the command (basename or full path) for launching R in way that it works on any OS? I came up with the following alternatives, but I'm not sure if they'll work everywhere or not: 1. Rbin - commandArgs()[1]; 2. Rbin - file.path(R.home(), bin, R); Other suggestions that are better? At least on Windows one could run R via R.exe, Rterm.exe or Rgui.exe amd #2 would not pick up the differences. On the other hand if I do this on the Windows command line on my Vista system with R 2.15.0 patched: cd \program files\R\R-2.15.x\bin\i386 Rterm.exe and then enter commandArgs() into R, the output is Rterm.exe with no path. The fact that one can have 32 bit and 64 bit R executables on the same system complicates things too. Thus, on Windows something like this might work: file.path(R.home(bin), R.version$arch, basename(commandArgs()[[1]])) If there are cases that I missed then this might pick up those too: R - commandArgs()[[1]] if (R == basename(R)) R - file.path(R.home(bin), R.version$arch, R) -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Best way to locate R executable from within R?
On May 22, 2012, at 2:39 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Tue, May 22, 2012 at 1:34 PM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: Hi, I'd like to spawn of a new R process from within R using system(), e.g. system(R -f myScript.R). However, just specifying R as in that example is not guaranteed to work, because R may not be on the OS's search path. What is the best way, from within a running R, to infer the command (basename or full path) for launching R in way that it works on any OS? I came up with the following alternatives, but I'm not sure if they'll work everywhere or not: 1. Rbin - commandArgs()[1]; 2. Rbin - file.path(R.home(), bin, R); Other suggestions that are better? At least on Windows one could run R via R.exe, Rterm.exe or Rgui.exe amd #2 would not pick up the differences. On the other hand if I do this on the Windows command line on my Vista system with R 2.15.0 patched: cd \program files\R\R-2.15.x\bin\i386 Rterm.exe and then enter commandArgs() into R, the output is Rterm.exe with no path. The fact that one can have 32 bit and 64 bit R executables on the same system complicates things too. Thus, on Windows something like this might work: file.path(R.home(bin), R.version$arch, basename(commandArgs()[[1]])) If there are cases that I missed then this might pick up those too: R - commandArgs()[[1]] if (R == basename(R)) R - file.path(R.home(bin), R.version$arch, R) Typically, when you want another subprocess of R it is not the same as the process you're in - e.g. you certainly don't want to use Rgui to run a script, so the above is not useful for Henrik's purpose. Besides, it won't even work since arg1 can as well be a symlink in a completely different place. Cheers, Simon -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Best way to locate R executable from within R?
On Tue, May 22, 2012 at 11:39 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Tue, May 22, 2012 at 1:34 PM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: Hi, I'd like to spawn of a new R process from within R using system(), e.g. system(R -f myScript.R). However, just specifying R as in that example is not guaranteed to work, because R may not be on the OS's search path. What is the best way, from within a running R, to infer the command (basename or full path) for launching R in way that it works on any OS? I came up with the following alternatives, but I'm not sure if they'll work everywhere or not: 1. Rbin - commandArgs()[1]; 2. Rbin - file.path(R.home(), bin, R); Other suggestions that are better? At least on Windows one could run R via R.exe, Rterm.exe or Rgui.exe amd #2 would not pick up the differences. On the other hand if I do this on the Windows command line on my Vista system with R 2.15.0 patched: cd \program files\R\R-2.15.x\bin\i386 Rterm.exe and then enter commandArgs() into R, the output is Rterm.exe with no path. Thanks, I overlooked this need. For my particular use case, I'm interested in launching R in batch mode, so R will do (but not Rgui). The fact that one can have 32 bit and 64 bit R executables on the same system complicates things too. Thus, on Windows something like this might work: file.path(R.home(bin), R.version$arch, basename(commandArgs()[[1]])) If there are cases that I missed then this might pick up those too: R - commandArgs()[[1]] if (R == basename(R)) R - file.path(R.home(bin), R.version$arch, R) FYI, R.home(bin) is not the same as file.path(R.home(), bin), cf. help(R.home). R.home(bin) will pick up the current architecture directory (by using .Platform$r_arch), e.g. R.home(bin) [1] C:/PROGRA~1/R/R-2.15.0patched/bin/x64 /Henrik -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Best way to locate R executable from within R?
On Tue, May 22, 2012 at 3:05 PM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: On Tue, May 22, 2012 at 11:39 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Tue, May 22, 2012 at 1:34 PM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: Hi, I'd like to spawn of a new R process from within R using system(), e.g. system(R -f myScript.R). However, just specifying R as in that example is not guaranteed to work, because R may not be on the OS's search path. What is the best way, from within a running R, to infer the command (basename or full path) for launching R in way that it works on any OS? I came up with the following alternatives, but I'm not sure if they'll work everywhere or not: 1. Rbin - commandArgs()[1]; 2. Rbin - file.path(R.home(), bin, R); Other suggestions that are better? At least on Windows one could run R via R.exe, Rterm.exe or Rgui.exe amd #2 would not pick up the differences. On the other hand if I do this on the Windows command line on my Vista system with R 2.15.0 patched: cd \program files\R\R-2.15.x\bin\i386 Rterm.exe and then enter commandArgs() into R, the output is Rterm.exe with no path. Thanks, I overlooked this need. For my particular use case, I'm interested in launching R in batch mode, so R will do (but not Rgui). The fact that one can have 32 bit and 64 bit R executables on the same system complicates things too. Thus, on Windows something like this might work: file.path(R.home(bin), R.version$arch, basename(commandArgs()[[1]])) If there are cases that I missed then this might pick up those too: R - commandArgs()[[1]] if (R == basename(R)) R - file.path(R.home(bin), R.version$arch, R) FYI, R.home(bin) is not the same as file.path(R.home(), bin), cf. help(R.home). R.home(bin) will pick up the current architecture directory (by using .Platform$r_arch), e.g. R.home(bin) [1] C:/PROGRA~1/R/R-2.15.0patched/bin/x64 /Henrik Then perhaps something like this which is still not 100% foolproof but should work most of the time: Find(file.exists, c( commandArgs()[[1]], file.path(R.home(bin), commandArgs()[[1]]), file.path(R.home(bin), R) )) -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Best way to locate R executable from within R?
On Tue, May 22, 2012 at 3:28 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Tue, May 22, 2012 at 3:05 PM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: On Tue, May 22, 2012 at 11:39 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Tue, May 22, 2012 at 1:34 PM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: Hi, I'd like to spawn of a new R process from within R using system(), e.g. system(R -f myScript.R). However, just specifying R as in that example is not guaranteed to work, because R may not be on the OS's search path. What is the best way, from within a running R, to infer the command (basename or full path) for launching R in way that it works on any OS? I came up with the following alternatives, but I'm not sure if they'll work everywhere or not: 1. Rbin - commandArgs()[1]; 2. Rbin - file.path(R.home(), bin, R); Other suggestions that are better? At least on Windows one could run R via R.exe, Rterm.exe or Rgui.exe amd #2 would not pick up the differences. On the other hand if I do this on the Windows command line on my Vista system with R 2.15.0 patched: cd \program files\R\R-2.15.x\bin\i386 Rterm.exe and then enter commandArgs() into R, the output is Rterm.exe with no path. Thanks, I overlooked this need. For my particular use case, I'm interested in launching R in batch mode, so R will do (but not Rgui). The fact that one can have 32 bit and 64 bit R executables on the same system complicates things too. Thus, on Windows something like this might work: file.path(R.home(bin), R.version$arch, basename(commandArgs()[[1]])) If there are cases that I missed then this might pick up those too: R - commandArgs()[[1]] if (R == basename(R)) R - file.path(R.home(bin), R.version$arch, R) FYI, R.home(bin) is not the same as file.path(R.home(), bin), cf. help(R.home). R.home(bin) will pick up the current architecture directory (by using .Platform$r_arch), e.g. R.home(bin) [1] C:/PROGRA~1/R/R-2.15.0patched/bin/x64 /Henrik Then perhaps something like this which is still not 100% foolproof but should work most of the time: Find(file.exists, c( commandArgs()[[1]], file.path(R.home(bin), commandArgs()[[1]]), file.path(R.home(bin), R) )) So that the last one tried works on Windows too it should be: Find(file.exists, c( commandArgs()[[1]], file.path(R.home(bin), commandArgs()[[1]]), file.path(R.home(bin), R), file.path(R.home(bin), R.exe) )) -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Best way to locate R executable from within R?
On May 22, 2012, at 3:34 PM, Gabor Grothendieck wrote: On Tue, May 22, 2012 at 3:28 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Tue, May 22, 2012 at 3:05 PM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: On Tue, May 22, 2012 at 11:39 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Tue, May 22, 2012 at 1:34 PM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: Hi, I'd like to spawn of a new R process from within R using system(), e.g. system(R -f myScript.R). However, just specifying R as in that example is not guaranteed to work, because R may not be on the OS's search path. What is the best way, from within a running R, to infer the command (basename or full path) for launching R in way that it works on any OS? I came up with the following alternatives, but I'm not sure if they'll work everywhere or not: 1. Rbin - commandArgs()[1]; 2. Rbin - file.path(R.home(), bin, R); Other suggestions that are better? At least on Windows one could run R via R.exe, Rterm.exe or Rgui.exe amd #2 would not pick up the differences. On the other hand if I do this on the Windows command line on my Vista system with R 2.15.0 patched: cd \program files\R\R-2.15.x\bin\i386 Rterm.exe and then enter commandArgs() into R, the output is Rterm.exe with no path. Thanks, I overlooked this need. For my particular use case, I'm interested in launching R in batch mode, so R will do (but not Rgui). The fact that one can have 32 bit and 64 bit R executables on the same system complicates things too. Thus, on Windows something like this might work: file.path(R.home(bin), R.version$arch, basename(commandArgs()[[1]])) If there are cases that I missed then this might pick up those too: R - commandArgs()[[1]] if (R == basename(R)) R - file.path(R.home(bin), R.version$arch, R) FYI, R.home(bin) is not the same as file.path(R.home(), bin), cf. help(R.home). R.home(bin) will pick up the current architecture directory (by using .Platform$r_arch), e.g. R.home(bin) [1] C:/PROGRA~1/R/R-2.15.0patched/bin/x64 /Henrik Then perhaps something like this which is still not 100% foolproof but should work most of the time: Find(file.exists, c( commandArgs()[[1]], file.path(R.home(bin), commandArgs()[[1]]), file.path(R.home(bin), R) )) So that the last one tried works on Windows too it should be: Find(file.exists, c( commandArgs()[[1]], file.path(R.home(bin), commandArgs()[[1]]), file.path(R.home(bin), R), file.path(R.home(bin), R.exe) )) Obviously, you don't want to do that for reasons discussed previously. -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Best way to locate R executable from within R?
I think the most reliable solution is something like system(paste(shQuote(file.path(R.home(bin),R)), ...)) it supports spaces in paths and works both on unix and Windows, picking the proper architecture. Cheers, Simon On May 22, 2012, at 3:05 PM, Henrik Bengtsson wrote: On Tue, May 22, 2012 at 11:39 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Tue, May 22, 2012 at 1:34 PM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: Hi, I'd like to spawn of a new R process from within R using system(), e.g. system(R -f myScript.R). However, just specifying R as in that example is not guaranteed to work, because R may not be on the OS's search path. What is the best way, from within a running R, to infer the command (basename or full path) for launching R in way that it works on any OS? I came up with the following alternatives, but I'm not sure if they'll work everywhere or not: 1. Rbin - commandArgs()[1]; 2. Rbin - file.path(R.home(), bin, R); Other suggestions that are better? At least on Windows one could run R via R.exe, Rterm.exe or Rgui.exe amd #2 would not pick up the differences. On the other hand if I do this on the Windows command line on my Vista system with R 2.15.0 patched: cd \program files\R\R-2.15.x\bin\i386 Rterm.exe and then enter commandArgs() into R, the output is Rterm.exe with no path. Thanks, I overlooked this need. For my particular use case, I'm interested in launching R in batch mode, so R will do (but not Rgui). The fact that one can have 32 bit and 64 bit R executables on the same system complicates things too. Thus, on Windows something like this might work: file.path(R.home(bin), R.version$arch, basename(commandArgs()[[1]])) If there are cases that I missed then this might pick up those too: R - commandArgs()[[1]] if (R == basename(R)) R - file.path(R.home(bin), R.version$arch, R) FYI, R.home(bin) is not the same as file.path(R.home(), bin), cf. help(R.home). R.home(bin) will pick up the current architecture directory (by using .Platform$r_arch), e.g. R.home(bin) [1] C:/PROGRA~1/R/R-2.15.0patched/bin/x64 /Henrik -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Best way to locate R executable from within R?
On Tue, May 22, 2012 at 6:04 PM, Simon Urbanek simon.urba...@r-project.org wrote: On May 22, 2012, at 3:34 PM, Gabor Grothendieck wrote: On Tue, May 22, 2012 at 3:28 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Tue, May 22, 2012 at 3:05 PM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: On Tue, May 22, 2012 at 11:39 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Tue, May 22, 2012 at 1:34 PM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: Hi, I'd like to spawn of a new R process from within R using system(), e.g. system(R -f myScript.R). However, just specifying R as in that example is not guaranteed to work, because R may not be on the OS's search path. What is the best way, from within a running R, to infer the command (basename or full path) for launching R in way that it works on any OS? I came up with the following alternatives, but I'm not sure if they'll work everywhere or not: 1. Rbin - commandArgs()[1]; 2. Rbin - file.path(R.home(), bin, R); Other suggestions that are better? At least on Windows one could run R via R.exe, Rterm.exe or Rgui.exe amd #2 would not pick up the differences. On the other hand if I do this on the Windows command line on my Vista system with R 2.15.0 patched: cd \program files\R\R-2.15.x\bin\i386 Rterm.exe and then enter commandArgs() into R, the output is Rterm.exe with no path. Thanks, I overlooked this need. For my particular use case, I'm interested in launching R in batch mode, so R will do (but not Rgui). The fact that one can have 32 bit and 64 bit R executables on the same system complicates things too. Thus, on Windows something like this might work: file.path(R.home(bin), R.version$arch, basename(commandArgs()[[1]])) If there are cases that I missed then this might pick up those too: R - commandArgs()[[1]] if (R == basename(R)) R - file.path(R.home(bin), R.version$arch, R) FYI, R.home(bin) is not the same as file.path(R.home(), bin), cf. help(R.home). R.home(bin) will pick up the current architecture directory (by using .Platform$r_arch), e.g. R.home(bin) [1] C:/PROGRA~1/R/R-2.15.0patched/bin/x64 /Henrik Then perhaps something like this which is still not 100% foolproof but should work most of the time: Find(file.exists, c( commandArgs()[[1]], file.path(R.home(bin), commandArgs()[[1]]), file.path(R.home(bin), R) )) So that the last one tried works on Windows too it should be: Find(file.exists, c( commandArgs()[[1]], file.path(R.home(bin), commandArgs()[[1]]), file.path(R.home(bin), R), file.path(R.home(bin), R.exe) )) Obviously, you don't want to do that for reasons discussed previously. In most cases with a link the complete path would be passed in which case the first arg of Find would be chosen and be correct. If not it would fail through to further choices one of which would likely be correct and if none of them are then its likely that file.path(R.home(bin), R) isn't either since that is already one of the choices. While its not 100% foolproof the cases where it does not work are quite pathological whereas the cases where file.path(R.home(bin), R) fails to use the same executable include common cases such as R being called as Rterm or Rscript. -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Best way to locate R executable from within R?
On May 22, 2012, at 7:37 PM, Gabor Grothendieck wrote: On Tue, May 22, 2012 at 6:04 PM, Simon Urbanek simon.urba...@r-project.org wrote: On May 22, 2012, at 3:34 PM, Gabor Grothendieck wrote: On Tue, May 22, 2012 at 3:28 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Tue, May 22, 2012 at 3:05 PM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: On Tue, May 22, 2012 at 11:39 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Tue, May 22, 2012 at 1:34 PM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: Hi, I'd like to spawn of a new R process from within R using system(), e.g. system(R -f myScript.R). However, just specifying R as in that example is not guaranteed to work, because R may not be on the OS's search path. What is the best way, from within a running R, to infer the command (basename or full path) for launching R in way that it works on any OS? I came up with the following alternatives, but I'm not sure if they'll work everywhere or not: 1. Rbin - commandArgs()[1]; 2. Rbin - file.path(R.home(), bin, R); Other suggestions that are better? At least on Windows one could run R via R.exe, Rterm.exe or Rgui.exe amd #2 would not pick up the differences. On the other hand if I do this on the Windows command line on my Vista system with R 2.15.0 patched: cd \program files\R\R-2.15.x\bin\i386 Rterm.exe and then enter commandArgs() into R, the output is Rterm.exe with no path. Thanks, I overlooked this need. For my particular use case, I'm interested in launching R in batch mode, so R will do (but not Rgui). The fact that one can have 32 bit and 64 bit R executables on the same system complicates things too. Thus, on Windows something like this might work: file.path(R.home(bin), R.version$arch, basename(commandArgs()[[1]])) If there are cases that I missed then this might pick up those too: R - commandArgs()[[1]] if (R == basename(R)) R - file.path(R.home(bin), R.version$arch, R) FYI, R.home(bin) is not the same as file.path(R.home(), bin), cf. help(R.home). R.home(bin) will pick up the current architecture directory (by using .Platform$r_arch), e.g. R.home(bin) [1] C:/PROGRA~1/R/R-2.15.0patched/bin/x64 /Henrik Then perhaps something like this which is still not 100% foolproof but should work most of the time: Find(file.exists, c( commandArgs()[[1]], file.path(R.home(bin), commandArgs()[[1]]), file.path(R.home(bin), R) )) So that the last one tried works on Windows too it should be: Find(file.exists, c( commandArgs()[[1]], file.path(R.home(bin), commandArgs()[[1]]), file.path(R.home(bin), R), file.path(R.home(bin), R.exe) )) Obviously, you don't want to do that for reasons discussed previously. In most cases with a link the complete path would be passed in which case the first arg of Find would be chosen and be correct. If not it would fail through to further choices one of which would likely be correct and if none of them are then its likely that file.path(R.home(bin), R) isn't either since that is already one of the choices. While its not 100% foolproof the cases where it does not work are quite pathological whereas the cases where file.path(R.home(bin), R) fails to use the same executable include common cases such as R being called as Rterm or Rscript. Except that you may not have noticed that no one asked about that since that makes no sense (arguments differ etc.). The question was how to start R and your suggestions make it only worse and unusable - fortunately Henrik asked about better solutions so we can safely close this discussion. Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Best way to locate R executable from within R?
On Tue, May 22, 2012 at 7:50 PM, Simon Urbanek simon.urba...@r-project.org wrote: On May 22, 2012, at 7:37 PM, Gabor Grothendieck wrote: On Tue, May 22, 2012 at 6:04 PM, Simon Urbanek simon.urba...@r-project.org wrote: On May 22, 2012, at 3:34 PM, Gabor Grothendieck wrote: On Tue, May 22, 2012 at 3:28 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Tue, May 22, 2012 at 3:05 PM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: On Tue, May 22, 2012 at 11:39 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Tue, May 22, 2012 at 1:34 PM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: Hi, I'd like to spawn of a new R process from within R using system(), e.g. system(R -f myScript.R). However, just specifying R as in that example is not guaranteed to work, because R may not be on the OS's search path. What is the best way, from within a running R, to infer the command (basename or full path) for launching R in way that it works on any OS? I came up with the following alternatives, but I'm not sure if they'll work everywhere or not: 1. Rbin - commandArgs()[1]; 2. Rbin - file.path(R.home(), bin, R); Other suggestions that are better? At least on Windows one could run R via R.exe, Rterm.exe or Rgui.exe amd #2 would not pick up the differences. On the other hand if I do this on the Windows command line on my Vista system with R 2.15.0 patched: cd \program files\R\R-2.15.x\bin\i386 Rterm.exe and then enter commandArgs() into R, the output is Rterm.exe with no path. Thanks, I overlooked this need. For my particular use case, I'm interested in launching R in batch mode, so R will do (but not Rgui). The fact that one can have 32 bit and 64 bit R executables on the same system complicates things too. Thus, on Windows something like this might work: file.path(R.home(bin), R.version$arch, basename(commandArgs()[[1]])) If there are cases that I missed then this might pick up those too: R - commandArgs()[[1]] if (R == basename(R)) R - file.path(R.home(bin), R.version$arch, R) FYI, R.home(bin) is not the same as file.path(R.home(), bin), cf. help(R.home). R.home(bin) will pick up the current architecture directory (by using .Platform$r_arch), e.g. R.home(bin) [1] C:/PROGRA~1/R/R-2.15.0patched/bin/x64 /Henrik Then perhaps something like this which is still not 100% foolproof but should work most of the time: Find(file.exists, c( commandArgs()[[1]], file.path(R.home(bin), commandArgs()[[1]]), file.path(R.home(bin), R) )) So that the last one tried works on Windows too it should be: Find(file.exists, c( commandArgs()[[1]], file.path(R.home(bin), commandArgs()[[1]]), file.path(R.home(bin), R), file.path(R.home(bin), R.exe) )) Obviously, you don't want to do that for reasons discussed previously. In most cases with a link the complete path would be passed in which case the first arg of Find would be chosen and be correct. If not it would fail through to further choices one of which would likely be correct and if none of them are then its likely that file.path(R.home(bin), R) isn't either since that is already one of the choices. While its not 100% foolproof the cases where it does not work are quite pathological whereas the cases where file.path(R.home(bin), R) fails to use the same executable include common cases such as R being called as Rterm or Rscript. Except that you may not have noticed that no one asked about that since that makes no sense (arguments differ etc.). The question was how to start R and your suggestions make it only worse and unusable - fortunately Henrik asked about better solutions so we can safely close this discussion. Cheers, Simon So far he has excluded Rgui but that still leaves Rterm, Rscript and R (and littler on UNIX) -- all of which are valid ways to launch R. If its sufficient to always launch it as R then your solution is briefer but it is subsumed in the one I posted which handles it in full generality. Its really a matter of usage case at this point. -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
