[R] Genuine relative paths with R

Jeff Newmiller
Sun, 07 Oct 2018 20:48:06 -0000

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 at kogentum.hu>
> Envoy? : samedi 6 octobre 2018 23:36
> ? : Olivier GIVAUDAN; Jeff Newmiller; r-help at 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 at kogentum.hu>
> > *Envoy? :* samedi 6 octobre 2018 23:05
> > *?:* Olivier GIVAUDAN; Jeff Newmiller; r-help at 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 at dcn.davis.ca.us>
> >> Envoy??? : samedi 6 octobre 2018 19:31
> >> ??? : r-help at r-project.org; Olivier GIVAUDAN; r-help at
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 at 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 at 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 at 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.
> >>
>
>

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