[R] Genuine relative paths with R

Olivier GIVAUDAN o||v|er_g|v@ud@n @end|ng |rom hotm@||@com
Wed Oct 10 21:51:19 CEST 2018 

Well, no idea...

I just created a file 'TestPWD', made it executable, inserted in it these lines and moved the file in various places:

#!/bin/bash

echo $PWD
read -p ""
________________________________
De : Duncan Murdoch <murdoch.duncan using gmail.com>
Envoyé : mercredi 10 octobre 2018 15:20
À : Olivier GIVAUDAN; Jeff Newmiller
Cc : r-help using r-project.org
Objet : Re: [R] Genuine relative paths with R

On 10/10/2018 11:18 AM, Olivier GIVAUDAN wrote:
> Hi Duncan,
>
> Yes, if you need to display the content of $PWD you obviously need to
> type 'echo' before this variable.
>
> It prints the user's working directory if run from a terminal but if run
> from a bash file it prints the working directory of the script.
> At least for me (I am running on the last version of Ubuntu)...

Not for me.  Always prints the user's working directory.

Duncan Murdoch


>
> Best regards,
>
> Olivier
> ------------------------------------------------------------------------
> *De :* Duncan Murdoch <murdoch.duncan using gmail.com>
> *Envoyé :* mercredi 10 octobre 2018 14:51
> *À :* Olivier GIVAUDAN; Jeff Newmiller
> *Cc :* r-help using r-project.org
> *Objet :* Re: [R] Genuine relative paths with R
> On 10/10/2018 10:37 AM, Olivier GIVAUDAN wrote:
>> Hi Jeff,
>> ​
>>> That is, there is not always a file in a particular directory even involved in the executing code.​​
>> ​
>> True. I'm only asking in the case where some R code is run from an R file. This function 'MyOwnPath()' (say) should only work (i.e. return a useful result) in this case.​
>> ​
>>> The R interpreter does not make assumptions about where the code it is running came from.​
>> ​
>> That's precisely the reproach I have in case the code comes from a file.​
>> ​
>>> You also keep referring to "this feature" being in many languages, though you seem to be mistaken about most of them...​
>> ​
>> 'Most of them' is largely exaggerated (plus I corrected myself): I only mixed between the 'cd' variable / command in Windows and Linux shells (you would certainly agree it's a bit vicious).​
>> ​
>>> $PWD is the same as getwd()​
>> ​
>> Wrong. As I already said, if I create an R script located somewhere on my computer with the only line 'getwd()' and run this script, I won't get the directory of this R script, contrary to a shell file with the only line '$PWD'.​
>
> What system are you talking about?  On Unix-alikes, you'd need an "echo"
> ahead of that, and it would print the user's working directory, not the
> working directory of the script.
>
> Duncan Murdoch
>
>> ​
>>> __FILE__ in C relates to the source code directory that is usually not where the executable is ​located and may not even exist on the computer it is running on​
>> ​
>> Yes, and? What is the issue here? So '__FILE__' does the job. Invoking '__FILE__' in a .C file (I never said in its related executable) will return the absolute path of this C source file.​
>> '__DIR__' in PHP also does the job. No to forget the good old VBA (Excel in this case) 'ActiveWorkbook.Path'.​
>>
>> Thank you for the 2 references you provided.
>> However it seems that some manual settings are still required to be able to use Rscript.
>> But I like the solution of the .RData file: I simply created an empty .RData file at the root of my project and by double-clicking on this file (as you said), the R GUI opens and 'getwd()' returns the path of this .RData file. It seems to be a good alternative  to .Rproj file to be opened with RStudio.
>> ​
>>> However, by far the best approach is to teach your users to fish... if you give them an RStudio project directory they can double-click on the .Rproj ​file to set the current directory and enter the world of R.​​
>> ​
>> Yes, using an .Rproj file to be opened with RStudio also seems to me to be a reasonable solution (the one I chose until now), although it is still a workaround and requires RStudio.​
>> Actually in this case, the package 'here'​ I previously mentioned is useless to get the current working directory of the project as 'When a project is opened within RStudio the following actions are taken: [...] The current working directory is set to the  project directory.', as stated on this page:
> https://support.rstudio.com/hc/en-us/articles/200526207-Using-Projects.
>> So 'getwd()' returns exactly the same as 'here()' does.
>>
>> Best regards,​
>> ​
>> Olivier
>>
>> ________________________________
>> De : Jeff Newmiller <jdnewmil using dcn.davis.ca.us>
>> Envoyé : dimanche 7 octobre 2018 20:48
>> À : Olivier GIVAUDAN
>> Cc : Dénes Tóth; r-help using r-project.org
>> Objet : RE: [R] Genuine relative paths with R
>>
>> On Sun, 7 Oct 2018, Olivier GIVAUDAN wrote:
>>
>>> Hello Denes,
>>>
>>>> Yes, the path to the "root" folder of your project. You seem to have a
>>> really esoteric context if you want to run an R script without knowing
>>> its path in the file system.
>>>
>>> I don't have any esoteric context: I'm just looking for the most generic, automatic and reproducible solution.
>>> Of course you always know where an R script is located, nevertheless it doesn't imply you want to manually write its path in this
>>> R script. The issue is to have to hardcode an absolute path: I don't want that.
>>>
>>>> Because it is extremely rare that someone - who uses R for what it is
>>> worth and in a manner how R is supposed to be used - actually needs such
>>> a function.
>>>
>>
>>> First, the fact that it is rare doesn't mean this need is not legitimate
>>> and relevant: it is needed to make R projects fully movable (i.e.
>>> wherever you want). Second why a vast majority of languages does have
>>> this feature and not R? Why is it useful in these languages and not in
>>> R?
>>
>> The R interpreter does not make assumptions about where the code it is
>> running came from. You might be running it by using the source() function,
>> or by using the Rscript program, or by R CMD BATCH, or using eval() on
>> code you pasted together in an R function, or as byte-compiled code loaded
>> from an RData file. That is, there is not always a file in a particular
>> directory even involved in the executing code.
>>
>> You also keep referring to "this feature" being in many languages, though
>> you seem to be mistaken about most of them... in fact, they, too, know NOT
>> where the script is but where the current directory is ($PWD is the same
>> as getwd()) or where the compilation occurred (__FILE__ in C relates to
>> the source code directory that is usually not where the executable is
>> located and may not even exist on the computer it is running on).
>>
>> I have already pointed out that the solution is to let the OS set the
>> current directory. If you want the user to have access to R independent of
>> your code, the easiest way to leave them in Rgui after your code is done
>> is to use save.image() to create a "myApp.RData" file which can be
>> double-clicked [1]. The double-clicking action by default (as defined by
>> the installation of R) causes the operating system to set the current
>> directory to the one containing the file you double-clicked on and then
>> executes the Rgui program.
>>
>> If you don't want the user to interact with your session, you can use the
>> Rscript executable (also mentioned briefly at the bottom of [1]). In both
>> cases, the user has (unknowingly) set the current directory before running
>> your code, and there is no need to encode where the script is or was
>> inside the script.
>>
>> You can also create a windows shortcut to invoke Rscript yourself by
>> bootstrapping the RData file and invoking the
>> R.utils::createWindowsShortcut() [2] function.
>>
>> However, by far the best approach is to teach your users to fish... if you
>> give them an RStudio project directory they can double-click on the .Rproj
>> file to set the current directory and enter the world of R.
>>
>> [1] https://www.r-bloggers.com/look-ma-no-typing-autorunning-code-on-r-startup/
>> [2] https://cran.r-project.org/web/packages/R.utils/R.utils.pdf
>>
>> End comment.
>>
>>> Best regards,
>>>
>>> Olivier
>>>
>>> _________________________________________________________________________________________________________________________________
>>> De : D?nes T?th <toth.denes using kogentum.hu>
>>> Envoy? : samedi 6 octobre 2018 23:36
>>> ? : Olivier GIVAUDAN; Jeff Newmiller; r-help using r-project.org
>>> Objet : Re: [R] Genuine relative paths with R
>>> Hi Olivier,
>>>
>>>
>>> On 10/07/2018 01:13 AM, Olivier GIVAUDAN wrote:
>>>> Hi Denes,
>>>>
>>>> Thank you for the possibility you shared: unfortunately it still uses
>>>> one hardcoded absolute path which I want to avoid.
>>>
>>> Yes, the path to the "root" folder of your project. You seem to have a
>>> really esoteric context if you want to run an R script without knowing
>>> its path in the file system.
>>>
>>>>
>>>> I just think that the solutions suggested are too complicated for my
>>>> simple need.
>>>>
>>>> The root cause being that R doesn't seem to have the Windows batch
>>>> equivalent of cd, or bash equivalent of $PWD, or PHP equivalent of __DIR__.
>>>> Hence the workarounds we are discussing.
>>>>
>>>> And finally we go back to my initial question: if such a function
>>>> doesn't exist in R, what are the reasons?
>>>
>>> Because it is extremely rare that someone - who uses R for what it is
>>> worth and in a manner how R is supposed to be used - actually needs such
>>> a function.
>>>
>>> Best,
>>> Denes
>>>
>>>
>>>
>>>>
>>>> Best regards,
>>>>
>>>> Olivier
>>>> ------------------------------------------------------------------------
>>>> *De :* D?nes T?th <toth.denes using kogentum.hu>
>>>> *Envoy? :* samedi 6 octobre 2018 23:05
>>>> *?:* Olivier GIVAUDAN; Jeff Newmiller; r-help using r-project.org
>>>> *Objet :* Re: [R] Genuine relative paths with R
>>>> Hi Olivier,
>>>>
>>>> I really think that Ista and Jeff gave you plenty of useful options how
>>>> you can avoid using absolute paths.
>>>>
>>>> One more possibility: you can use `source()` with the chdir = TRUE
>>>> argument (see ?source). If you have a master script which sources other
>>>> files which are located in a fixed hierarchy relative to the location of
>>>> the master script, the only time when you have to use an absolute path
>>>> is when you source your master script, e.g.:
>>>> source("/my/path/to/master.R", chdir = TRUE)
>>>>
>>>> Inside the master script, you can then source the other scripts by
>>>> relative paths, define your 'data' folders relative to the master script
>>>> and let the other scripts use those data paths, etc.
>>>>
>>>> Best,
>>>> Denes
>>>>
>>>>
>>>> On 10/06/2018 11:36 PM, Olivier GIVAUDAN wrote:
>>>>> Hi Jeff,
>>>>>
>>>>> Thanks for sharing your workaround.
>>>>>
>>>>> I guess my last answer to Ista answers your question as well.
>>>>>
>>>>> To me this function (an equivalent of 'cd', say) should be platform-independent.
>>>>>
>>>>> Best regards,
>>>>>
>>>>> Olivier
>>>>>
>>>>> ________________________________
>>>>> De : Jeff Newmiller <jdnewmil using dcn.davis.ca.us>
>>>>> Envoy??? : samedi 6 octobre 2018 19:31
>>>>> ??? : r-help using r-project.org; Olivier GIVAUDAN; r-help using r-project.org
>>>>> Objet : Re: [R] Genuine relative paths with R
>>>>>
>>>>> I stopped using hardcoded absolute paths inside R scripts years ago, and I suspect that is fairly common practice. That is, I
>>> almost never enter a path starting with "/" or "c:/" in an R script.
>>>>>
>>>>> The key concession you have to make is to start your R session in your working directory using OS-specific mechanisms, and
>>> then reference your code and data relative to that directory. RStudio project files offer one mechanism for doing this; using CD
>>> from  the OS command line is another, and using the file-browser
>>>> double-click mechanism on .RData files is another (though I prefer to
>>>> avoid that these days due to potential global environment contamination).
>>>>>
>>>>> Perhaps you can be more specific about what facilities you are expecting to find. You should also mention what OS you
>>> typically use and how you normally start R.
>>>>>
>>>>> On October 6, 2018 4:48:44 AM PDT, Olivier GIVAUDAN <olivier_givaudan using hotmail.com> wrote:
>>>>>> Dear R users,
>>>>>>
>>>>>> I would like to work with genuine relative paths in R for obvious
>>>>>> reasons: if I move all my scripts related to some project as a whole to
>>>>>> another location of my computer or someone else's computer, if want my
>>>>>> scripts to continue to run seamlessly.
>>>>>>
>>>>>> What I mean by "genuine" is that it should not be necessary to hardcode
>>>>>> one single absolute path (making the code obviously not "portable" - to
>>>>>> another place - anymore).
>>>>>>
>>>>>> For the time being, I found the following related posts, unfortunately
>>>>>> never conclusive or even somewhat off-topic:
>>>>>> https://stackoverflow.com/questions/1815606/rscript-determine-path-of-the-executing-script
>>>>>> https://stackoverflow.com/questions/47044068/get-the-path-of-current-script/47045368
>>>>>> http://r.789695.n4.nabble.com/Script-auto-detecting-its-own-path-td2719676.html
>>>>>>
>>>>>> So I found 2 workarounds, more or less satisfactory:
>>>>>>
>>>>>>
>>>>>> 1.  Either create a variable "ScriptPath" in the first lines of each of
>>>>>> my R scripts and run a batch (or shell, etc.) to replace every single
>>>>>> occurrence of "ScriptPath <-" by "ScriptPath <- [Absolute path of the R
>>>>>> script]" in all the R scripts located in the folder (and possibly
>>>>>> subfolders) of the batch file.
>>>>>> 2.  Or create an R project file with RStudio and use the package "here"
>>>>>> to get the absolute path of the R project file and put all the R
>>>>>> scripts related to this project in the R project directory, as often
>>>>>> recommended.
>>>>>>
>>>>>> But I am really wondering why R doesn't have (please tell me if I'm
>>>>>> wrong) this basic feature as many other languages have it (batch,
>>>>>> shell, C, LaTeX, SAS with macro-variables, etc.)?
>>>>>> Do you know whether the language will have this kind of function in a
>>>>>> near future? What are the obstacles / what is the reasoning for not
>>>>>> having it already?
>>>>>>
>>>>>> Do you know other workarounds?
>>>>>>
>>>>>> Best regards,
>>>>>>
>>>>>> Olivier
>>>>>>
>>>>>>         [[alternative HTML version deleted]]
>>>>>>
>>>>>> ______________________________________________
>>>>>> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>>> PLEASE do read the posting guide
>>>>>> http://www.R-project.org/posting-guide.html
>>>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>>
>>>>> --
>>>>> Sent from my phone. Please excuse my brevity.
>>>>>
>>>>>         [[alternative HTML version deleted]]
>>>>>
>>>>>
>>>>>
>>>>> ______________________________________________
>>>>> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>>
>>>
>>>
>>
>> ---------------------------------------------------------------------------
>> Jeff Newmiller                        The     .....       .....  Go Live...
>> DCN:<jdnewmil using dcn.davis.ca.us>        Basics: ##.#.       ##.#.  Live Go...
>>                                         Live:   OO#.. Dead: OO#..  Playing
>> Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
>> /Software/Embedded Controllers)               .OO#.       .OO#.  rocks...1k
>> ---------------------------------------------------------------------------
>>
>>        [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>


	[[alternative HTML version deleted]]

More information about the R-help mailing list