Determine path of the executing script

Question

I have a script called foo R that includes another script other R  which is in the same directory      usr bin env Rscript message  Hello   source  other R     But I want R to find that other R no matter what the current working directory    In other words  foo R needs to know its own path  How can I do that

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I have wrapped up and extended the answers to this question into a new function thisfile   in rprojroot  Also works for knitting with knitr

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You can wrap the r script in a bash script and retrieve  the script s path as a bash variable like so      bin bash         environment variables can be set here       path to script   dirname  0        R --slave lt  lt EOF         source   path to script other R         EOF

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See findSourceTraceback   of the R utils package  which     Finds all  srcfile  objects generated by source   in all call frames     This makes it possible to find out which files are currently scripted by source

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You can use the commandArgs function to get all the options that were passed by Rscript to the actual R interpreter and search them for --file   If your script was launched from the path or if it was launched with a full path  the script name below will start with a      Otherwise  it must be relative to the cwd and you can concat the two paths to get the full path   Edit  it sounds like you d only need the script name above and to strip off the final component of the path  I ve removed the unneeded cwd   sample and cleaned up the main script and posted my other R  Just save off this script and the other R script into the same directory  chmod  x them  and run the main script   main R      usr bin env Rscript initial options  lt - commandArgs trailingOnly   FALSE  file arg name  lt -  --file   script name  lt - sub file arg name      initial options grep file arg name  initial options    script basename  lt - dirname script name  other name  lt - file path script basename   other R   print paste  Sourcing  other name  from  script name   source other name    other R   print  hello     output   burner firefighter    main R  1   Sourcing  home burner bin other R from  home burner bin main R   1   hello  burner firefighter    bin main R  1   Sourcing bin other R from bin main R   1   hello  burner firefighter    cd bin burner firefighter   bin  main R  1   Sourcing   other R from   main R   1   hello    This is what I believe dehmann is looking for

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usr bin env Rscript print  Hello      sad workaround but works    programDir  lt - dirname sys frame 1  ofile  source paste programDir  other R  sep       source paste programDir  other-than-other R  sep

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This works for me  library rstudioapi      rstudioapi  getActiveDocumentContext   path

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Steamer25 s approach works  but only if there is no whitespace in the path  On macOS at least the cmdArgs match  returns something like  base some   dir   with   whitespace  for  base some  dir  with  whitespace    I worked around this by replacing the       with a simple whitespace before returning it   thisFile  lt - function       cmdArgs  lt - commandArgs trailingOnly   FALSE    needle  lt -  --file     match  lt - grep needle  cmdArgs    if  length match   gt  0          Rscript     path  lt - cmdArgs match      path  lt - gsub                   path      return normalizePath sub needle      path        else          source d via R console     return normalizePath sys frames    1   ofile           Obviously you can still extend the else block like aprstar did

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frame files  lt - lapply sys frames    function x  x ofile  frame files  lt - Filter Negate is null   frame files  PATH  lt - dirname frame files  length frame files       Don t ask me how it works though  because I ve forgotten

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I liked steamer25 s solution as it seems the most robust for my purposes  However  when debugging in RStudio  in windows   the path would not get set properly  The reason being that if a breakpoint is set in RStudio  sourcing the file uses an alternate  debug source  command which sets the script path a little differently  Here is the final version which I am currently using which accounts for this alternate behavior within RStudio when debugging       return full path to this script get script path  lt - function         cmdArgs   commandArgs trailingOnly   FALSE      needle    --file       match   grep needle  cmdArgs      if  length match   gt  0              Rscript         return normalizePath sub needle      cmdArgs match           else           ls vars   ls sys frames    1            if   fileName   in  ls vars                  Source d via RStudio             return normalizePath sys frames    1   fileName              else                 Source d via R console             return normalizePath sys frames    1   ofile

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This works for me  Just greps it out of the command line arguments  strips off the unwanted text  does a dirname and finally gets the full path from that   args  lt - commandArgs trailingOnly   F    scriptPath  lt - normalizePath dirname sub   --file        args grep   --file    args

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99  of the cases you might simply use   sys calls    1     2     It will not work for crazy calls where the script is not the first argument  i e   source some args  file  myscript    Use  hadley s in these fancy cases

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Amazing there is no   0  type structure in R  You can do it with a system   call to a bash script written in R   write table c  readlink -e  0    file  scriptpath sh  col F  row F  quote F  thisscript  lt - system  sh scriptpath sh   intern   TRUE    Then just split out the scriptpath sh name for other R  splitstr  lt - rev strsplit thisscript          1    otherscript  lt - paste0 paste rev splitstr 2 length splitstr    collapse        other R

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My all in one    --01 09 2019 updated to deal with RStudio Console      current script file  in full path      description current script file  in full path      examples    works with Rscript  source   or in RStudio Run selection  RStudio Console     export ez csf  lt - function           http   stackoverflow com a 32016824 2292993     cmdArgs   commandArgs trailingOnly   FALSE      needle    --file       match   grep needle  cmdArgs      if  length match   gt  0              Rscript via command line         return normalizePath sub needle      cmdArgs match           else           ls vars   ls sys frames    1            if   fileName   in  ls vars                  Source d via RStudio             return normalizePath sys frames    1   fileName             else               if   is null sys frames    1   ofile                   Source d via R console             return normalizePath sys frames    1   ofile                 else                     RStudio Run Selection                   http   stackoverflow com a 35842176 2292993                 pth   rstudioapi  getActiveDocumentContext   path                 if  pth                            return normalizePath pth                     else                         RStudio Console                     tryCatch                               pth   rstudioapi  getSourceEditorContext   path                             pth   normalizePath pth                             error   function e                                  normalizePath     issues warning error                             pth                                                                          return pth

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I like this approach   this file  lt - sys frame tail grep  source  sys calls    n 1   ofile this dir  lt - dirname this file

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I tried almost everything from this question  Getting path of an R script  Get the path of current script  Find location of current  R file and R command for setting working directory to source file location in Rstudio  but at the end found myself manually browsing the CRAN table and found   scriptName library  which provides current filename   function  which returns proper full path of the script when sourcing in RStudio and also when invoking via R or RScript executable

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I had issues with the implementations above as my script is operated from a symlinked directory  or at least that s why I think the above solutions didn t work for me  Along the lines of  ennuikiller s answer  I wrapped my Rscript in bash  I set the path variable using pwd -P  which resolves symlinked directory structures  Then pass the path into the Rscript   Bash sh     bin bash    set path variable path  pwd -P    Run Rscript with path argument Rscript foo R  path   foo R  args  lt - commandArgs trailingOnly TRUE  setwd args 1   source other R

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I just worked this out myself   To ensure portability of your script always begin it with   wd  lt - setwd      setwd wd    It works because     translates like the Unix command  PWD  Assigning this string to a character object allows you to then insert that character object into setwd   and Presto your code will always run with its current directory as the working directory  no matter whose machine it is on or where in the file structure it is located   Extra bonus  The wd object can be used with file path    ie  file path wd   output directory   to allow for the creation of a standard output directory regardless of the file path leading to your named directory   This does require you to make the new directory before referencing it this way but that  too  can be aided with the wd object   Alternately  the following code performs the exact same thing   wd  lt - getwd   setwd wd    or  if you don t need the file path in an object you can simply   setwd

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If rather than the script  foo R  knowing its path location  if you can change your code to always reference all source d paths from a common root then these may be a great help    https   github com r-lib rprojroot  or https   rprojroot r-lib org  https   here r-lib org     Given     app deeply nested foo R  app other R   This will work     usr bin env Rscript library here  source here  other R      See https   rprojroot r-lib org  for how to define project roots

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By looking at the call stack we can get the filepath of each script being executed  the two most useful will probably either be the currently executing script  or the first script to be sourced  entry     script dir executing    function   return  if length sys parents     1  getwd   else dirname  Filter is character lapply rev sys frames    function x  x ofile    1           script dir entry    function   return  if length sys parents     1  getwd   else dirname sys frame 1  ofile

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The answer of rakensi from Getting path of an R script is the most correct and really brilliant IMHO  Yet  it s still a hack incorporating a dummy function  I m quoting it here  in order to have it easier found by others      sourceDir  lt - getSrcDirectory function dummy   dummy     This gives the directory of the file where the statement was placed  where the dummy function is defined   It can then be used to set the working direcory and use relative paths e g   setwd sourceDir  source  other R     or to create absolute paths   source paste sourceDir    other R   sep

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I also had this problem  and none of the above solutions worked for me  Maybe with the source or things like that  but it was not clear enough   I found this  for me elegant  solution   paste0 gsub            fileSnapshot   path  fixed TRUE         The important thing in that is the fileSnapshot   that gives you a lot of information about a file  It returns a list of 8 elements  When you pick path as the list element  the path is returned with    as separator  so the rest of the code is just to change that   I hope this helps

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A slimmed down variant of Supressingfire s answer   source local  lt - function fname       argv  lt - commandArgs trailingOnly   FALSE      base dir  lt - dirname substring argv grep  --file    argv    8       source paste base dir  fname  sep

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Note that the getopt package provides the get Rscript filename function  which just uses the same solution presented here  but is already written for you in a standard R module  so you don t have to copy and paste the  get script path  function into every script you write

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I couldn t get Suppressingfire s solution to work when  source ing from the R console  I couldn t get hadley s solution to work when using Rscript   Best of both worlds   thisFile  lt - function             cmdArgs  lt - commandArgs trailingOnly   FALSE          needle  lt -  --file           match  lt - grep needle  cmdArgs          if  length match   gt  0                      Rscript                 return normalizePath sub needle      cmdArgs match               else                      source d via R console                 return normalizePath sys frames    1   ofile

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Here there is a simple solution for the problem  This command   script dir  lt - dirname sys frame 1  ofile    returns the path of the current script file  It works after the script was saved

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I would use a variant of  steamer25  s approach  The point is that I prefer to obtain the last sourced script even when my session was started through Rscript  The following snippet  when included on a file  will provided a variable thisScript containing the normalized path of the script  I confess the  ab use of source ing  so sometimes I invoke Rscript and the script provided in the --file argument sources another script that sources another one    Someday I will invest in making my messy code turns into a package   thisScript  lt -  function       lastScriptSourced  lt - tail unlist lapply sys frames    function env  env ofile    1     if  is null lastScriptSourced           No script sourced  checking invocation through Rscript     cmdArgs  lt - commandArgs trailingOnly   FALSE      needle  lt -  --file       match  lt - grep needle  cmdArgs      if  length match   gt  0          return normalizePath sub needle      cmdArgs match    winslash  Platform file sep  mustWork TRUE             else          source d via R console     return normalizePath lastScriptSourced  winslash  Platform file sep  mustWork TRUE

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I ve made a package for this as of 2020-12-03 available on CRAN called  quot this path quot   Install it using  install packages  quot this path quot   and then use it by  this path  this path   or library this path  this path   I still have my original answer below  though it is less functional than the version in the package  On a Unix-alike OS  strange characters  such as  quot   quot   in the  Rscript  command-line argument  file  are replaced  such as  quot     quot    R does this so that it is easier to use that filename for other system commands  but this isn t what we want  Given that we want a path usable in R  any such strange character sequences must be replaced  Original Answer  My answer is an improvement upon Jerry T s answer  The issue I found is that he is guessing whether a source call was made by checking if variable ofile is found in the first frame on the stack  This will not work with nested source calls  nor source calls made from a non-global environment  Additionally  a source call must be looked for before checking the command-line arguments  that has also been fixed  Here is my solution  this path  lt - function  verbose   getOption  quot verbose quot          where  lt - function x  if  verbose          cat  quot Source   quot   x   quot  n quot   sep    quot  quot           loop through functions that lead here from most recent to earliest looking           for an appropriate source call  a call to function base  source or base  sys source        an appropriate source call is a source call in which           argument  file  has been evaluated  forced        this means  for example  the following is an inappropriate source call            source this path          the argument  file  is stored as a promise           containing the expression  quot this path   quot        when the value of  file  is requested  it assigns the value           returned by evaluating  quot this path   quot  to variable  file        there are two functions on the calling stack at           this point being  source  and  this path        clearly  you don t want to request the  file  argument from that source           call because the value of  file  is under evaluation right now        the trick is to ask if variable   ofile  for base  source   exprs  for base  sys source            exists in that function s evaluation environment  this is because that           variable is created AFTER argument  file  has been forced       if that variable does exist  then argument  file  has been forced and the           source call is deemed appropriate  For base  source  the filename we want           is the variable  ofile  from that function s evaluation environment  For           base  sys source  the filename we want is the variable  file  from that           function s evaluation environment        if that variable does NOT exist  then argument  file  hasn t been forced and           the source call is deemed inappropriate  The  for  loop moves to the next           function up the calling stack  if available              unfortunately  there is no way to check the argument  fileName  has been forced           for  debugSource  since all the work is done internally in C  Instead            we have to use a  tryCatch  statement  When we ask for an object by name           using  get   R is capable of realizing if a variable is asking for its           own definition  a recursive definition   The exact error is  quot promise already           under evaluation quot  which indicates that the promise evaluation is requesting           its own value  So we use the  tryCatch  to get the argument  fileName            from the evaluation environment of  debugSource   and if it does not raise           an error  then we are safe to return that value  If not  the condition           returns false and the  for  loop moves to the next function up the calling           stack  if available        if   Platform GUI     quot RStudio quot           dbs  lt - get  quot debugSource quot   mode    quot function quot    quot tools rstudio quot               inherits   FALSE      for  n in seq int sys nframe    1L  -1L             if  identical sys function n   base  source   amp  amp              exists  quot ofile quot   envir   sys frame n   inherits   FALSE                 path  lt - get  quot ofile quot   envir   sys frame n   inherits   FALSE              if   is character path                   path  lt - summary connection path  description             where  quot call to function source quot               return normalizePath path  mustWork   TRUE                     else if  identical sys function n   base  sys source   amp  amp              exists  quot exprs quot   envir   sys frame n   inherits   FALSE                 path  lt - get  quot file quot   envir   sys frame n   inherits   FALSE              where  quot call to function sys source quot               return normalizePath path  mustWork   TRUE                     else if   Platform GUI     quot RStudio quot   amp  amp  identical sys function n   dbs   amp  amp              tryCatch                   path  lt - get  quot fileName quot   envir   sys frame n   inherits   FALSE                  TRUE                error   function c                    FALSE                               where  quot call to function debugSource in RStudio quot               return normalizePath path  mustWork   TRUE                           if the for loop is passed  no appropriate           source call was found up the calling stack       next  check if the user is running R from the command-line           on a Windows OS  the GUI is  quot RTerm quot            on a Unix    OS  the GUI is  quot X11 quot        if   Platform OS type     quot windows quot   amp  amp   Platform GUI     quot RTerm quot        running from Windows command-line          Platform OS type     quot unix quot   amp  amp   Platform GUI     quot X11 quot             running from Unix command-line             get all command-line arguments that start with  quot --file  quot            check the number of command-line arguments starting with  quot --file  quot                in case more or less than one were supplied           path  lt - grep  quot  --file  quot   commandArgs    value   TRUE          if  length path     1L                path  lt - sub  quot  --file  quot    quot  quot   path              where  quot Command-line argument  file  quot               return normalizePath path  mustWork   TRUE                     else if  length path                 stop  quot  this path  used in an inappropriate fashion n quot                    quot   no appropriate source call was found up the calling stack n quot                    quot   R is being run from the command-line and formal argument   quot --file   quot  matched by multiple actual arguments n quot                     else stop  quot  this path  used in an inappropriate fashion n quot                quot   no appropriate source call was found up the calling stack n quot                quot   R is being run from the command-line and argument   quot --file   quot  is missing n quot             else if   Platform GUI     quot RStudio quot        running R from  RStudio              function  quot  rs api getActiveDocumentContext quot  from the environment  quot tools rstudio quot                returns a list of information about the document where your cursor is located                     function  quot  rs api getSourceEditorContext quot  from the environment  quot tools rstudio quot                returns a list of information about the document open in the current tab                     element  id  is a character string  an identification for the document           element  path  is a character string  the path of the document           adc  lt - get  quot  rs api getActiveDocumentContext quot               mode    quot function quot    quot tools rstudio quot   inherits   FALSE            if  adc id     quot  console quot                 path  lt - adc path             if  nzchar path                     where  quot active document in RStudio quot                   return normalizePath path  mustWork   TRUE                             else stop  quot  this path  used in an inappropriate fashion n quot                    quot   no appropriate source call was found up the calling stack n quot                    quot   active document in RStudio does not exist n quot                       sec  lt - get  quot  rs api getSourceEditorContext quot   mode    quot function quot                quot tools rstudio quot   inherits   FALSE            if   is null sec                 path  lt - sec path             if  nzchar path                     where  quot source document in RStudio quot                   return normalizePath path  mustWork   TRUE                             else stop  quot  this path  used in an inappropriate fashion n quot                    quot   no appropriate source call was found up the calling stack n quot                    quot   source document in RStudio does not exist n quot                     else stop  quot  this path  used in an inappropriate fashion n quot                quot   no appropriate source call was found up the calling stack n quot                quot   R is being run from RStudio with no documents open n quot             else if   Platform OS type     quot windows quot   amp  amp   Platform GUI     quot Rgui quot        running R from  RGui  on Windows             on a Windows OS only  the function  quot getWindowsHandles quot  from the base           package  quot utils quot  returns a list of external pointers containing the windows           handles  The thing of interest are the names of this list  these should           be the names of the windows belonging to the current R process  Since           RGui can have files besides R scripts open  such as images   a regular           expression is used to subset only windows handles with names that exactly           match the string  quot R Console quot  or end with  quot  - R Editor quot   I highly suggest           that you NEVER end a document s filename with  quot  - R Editor quot   From there            similar checks are done as in the above section for  RStudio            wh  lt - names utils  getWindowsHandles pattern    quot  R Console   - R Editor  quot               minimized   TRUE             if   length wh               stop  quot this error SHOULD be unreachable  as far as I know it s impossible to have an R n quot                    quot   process running without the R Console open  If you reached this error  please n quot                    quot   send a bug report to the package maintainer quot             path  lt - wh 1L          if  path     quot R Console quot                 path  lt - sub  quot  - R Editor  quot    quot  quot   path              if  path     quot Untitled quot                     where  quot active document in RGui quot                   return normalizePath path  mustWork   TRUE                             else stop  quot  this path  used in an inappropriate fashion n quot                    quot   no appropriate source call was found up the calling stack n quot                    quot   active document in RGui does not exist n quot                       path  lt - wh 2L          if   is na path                 path  lt - sub  quot  - R Editor  quot    quot  quot   path              if  path     quot Untitled quot                     where  quot source document in RGui quot                   return normalizePath path  mustWork   TRUE                             else stop  quot  this path  used in an inappropriate fashion n quot                    quot   no appropriate source call was found up the calling stack n quot                    quot   source document in RGui does not exist n quot                     else stop  quot  this path  used in an inappropriate fashion n quot                quot   no appropriate source call was found up the calling stack n quot                quot   R is being run from RGui with no documents open n quot             else if   Platform OS type     quot unix quot   amp  amp   Platform GUI     quot AQUA quot        running R from  RGui  on Unix         stop  quot  this path  used in an inappropriate fashion n quot                quot   no appropriate source call was found up the calling stack n quot                quot   R is being run from AQUA which requires a source call on the calling stack n quot             else stop  quot  this path  used in an inappropriate fashion n quot            quot   no appropriate source call was found up the calling stack n quot            quot   R is being run in an unrecognized manner n quot

User · Answer

I work in an HPC cluster environment   I develop my code in a different location from where I do my production runs   During development  I m usually calling R interactively from the command line  not using RStudio    There is lots of source  quot foo R quot   going on  During production runs  I usually write a bash script that tries different parameters and runs each set of parameters in a separate directory  The bash script utilizes the workload manager  i e  SLURM    In this environment  it is trivial to set an environmental variable   With this in mind  the below solution works best for me  other R my message  lt - function    return  quot R is awkward quot      foo R srcpath   Sys getenv  quot R SRC quot     Check if runnning w o setting R SRC - presumably done in directory of development  i e   path to R code if srcpath     quot  quot        srcpath  quot    quot    source sprintf  quot  s other R quot   srcpath   string   my message   print string   If running this from the R interactive shell and within  path to R code  simply do  gt  source  quot foo R quot    If running not from the interactive shell and not running from  path to R code  set the environmental variable R SRC first  then call Rscript   export R SRC  path to R code    Rscript  path to R code foo R

[r] Determine path of the executing script

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