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Olivier GIVAUDAN

2018-Oct-10 14:57 UTC

[R] Genuine relative paths with R

Dear Eik,

Thank you for your message.

Yes, I already got to know this package and this discussion (while I found the
'here' package). But thanks.

Best regards,

Olivier
________________________________
De : Eik Vettorazzi <E.Vettorazzi at uke.de>
Envoy? : lundi 8 octobre 2018 11:30
? : Olivier GIVAUDAN; r-help at r-project.org
Objet : Re: [R] Genuine relative paths with R

Dear Olivier,
you may find the rprojroot package useful, see
https://github.com/r-lib/rprojroot

and a discussion

https://gist.github.com/jennybc/362f52446fe1ebc4c49f#file-2014-10-12_stop-working-directory-insanity-md

Cheers

Am 06.10.2018 um 13:48 schrieb Olivier GIVAUDAN:> 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.
>
--
Eik Vettorazzi

Department of Medical Biometry and Epidemiology
University Medical Center Hamburg-Eppendorf

Martinistrasse 52
building W 34
20246 Hamburg

Phone: +49 (0) 40 7410 - 58243
Fax:   +49 (0) 40 7410 - 57790
Web: www.uke.de/imbe<http://www.uke.de/imbe>
--

_____________________________________________________________________

Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen Rechts;
Gerichtsstand: Hamburg | www.uke.de
Vorstandsmitglieder: Prof. Dr. Burkhard G?ke (Vorsitzender), Prof. Dr. Dr. Uwe
Koch-Gromus, Joachim Pr?l?, Martina Saurin (komm.)
_____________________________________________________________________

SAVE PAPER - THINK BEFORE PRINTING

	[[alternative HTML version deleted]]

Tierney, Luke

2018-Oct-10 15:48 UTC

head link

[R] Genuine relative paths with R

If you are always running your main script as 'Rscript myscript.R'
then your file argument will appear as '--file=myscript.R' in
commandArgs(). So you can use something like

scriptFile <- function()
{
     pat <- "^--file="
     args <- commandArgs()
     file <- args[grepl(pat, args, args)]
     normalizePath(sub(pat, "", file))
}

Then scriptFile() will give you something to work with.

Best,

luke



On Wed, 10 Oct 2018, Olivier GIVAUDAN wrote:
> Dear Eik,
>
> Thank you for your message.
>
> Yes, I already got to know this package and this discussion (while I found
the 'here' package). But thanks.
>
> Best regards,
>
> Olivier
> ________________________________
> De : Eik Vettorazzi <E.Vettorazzi at uke.de>
> Envoy??? : lundi 8 octobre 2018 11:30
> ??? : Olivier GIVAUDAN; r-help at r-project.org
> Objet : Re: [R] Genuine relative paths with R
>
> Dear Olivier,
> you may find the rprojroot package useful, see
> https://github.com/r-lib/rprojroot
>
> and a discussion
>
>
https://gist.github.com/jennybc/362f52446fe1ebc4c49f#file-2014-10-12_stop-working-directory-insanity-md
>
> Cheers
>
> Am 06.10.2018 um 13:48 schrieb Olivier GIVAUDAN:
>> 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.
>>
>
> --
> Eik Vettorazzi
>
> Department of Medical Biometry and Epidemiology
> University Medical Center Hamburg-Eppendorf
>
> Martinistrasse 52
> building W 34
> 20246 Hamburg
>
> Phone: +49 (0) 40 7410 - 58243
> Fax:   +49 (0) 40 7410 - 57790
> Web: www.uke.de/imbe<http://www.uke.de/imbe>
> --
>
> _____________________________________________________________________
>
> Universit???tsklinikum Hamburg-Eppendorf; K???rperschaft des ???ffentlichen
Rechts; Gerichtsstand: Hamburg | www.uke.de
> Vorstandsmitglieder: Prof. Dr. Burkhard G???ke (Vorsitzender), Prof. Dr.
Dr. Uwe Koch-Gromus, Joachim Pr???l???, Martina Saurin (komm.)
> _____________________________________________________________________
>
> SAVE PAPER - THINK BEFORE PRINTING
>
> 	[[alternative HTML version deleted]]
>
>
-- 
Luke Tierney
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa                  Phone:             319-335-3386
Department of Statistics and        Fax:               319-335-3017
    Actuarial Science
241 Schaeffer Hall                  email:   luke-tierney at uiowa.edu
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu

Olivier GIVAUDAN

2018-Oct-10 20:13 UTC

head link

[R] Genuine relative paths with R

Thank you, Luke.

Unfortunately I don't use Rscript (it is not allowed to run shell scripts on
my professional computer).

Best regards,

Olivier
________________________________
De : Tierney, Luke <luke-tierney at uiowa.edu>
Envoy? : mercredi 10 octobre 2018 15:48
? : Olivier GIVAUDAN
Cc : Eik Vettorazzi; r-help at r-project.org
Objet : Re: [R] Genuine relative paths with R

If you are always running your main script as 'Rscript myscript.R'
then your file argument will appear as '--file=myscript.R' in
commandArgs(). So you can use something like

scriptFile <- function()
{
     pat <- "^--file="
     args <- commandArgs()
     file <- args[grepl(pat, args, args)]
     normalizePath(sub(pat, "", file))
}

Then scriptFile() will give you something to work with.

Best,

luke



On Wed, 10 Oct 2018, Olivier GIVAUDAN wrote:
> Dear Eik,
>
> Thank you for your message.
>
> Yes, I already got to know this package and this discussion (while I found
the 'here' package). But thanks.
>
> Best regards,
>
> Olivier
> ________________________________
> De : Eik Vettorazzi <E.Vettorazzi at uke.de>
> Envoy??? : lundi 8 octobre 2018 11:30
> ??? : Olivier GIVAUDAN; r-help at r-project.org
> Objet : Re: [R] Genuine relative paths with R
>
> Dear Olivier,
> you may find the rprojroot package useful, see
> https://github.com/r-lib/rprojroot
>
> and a discussion
>
>
https://gist.github.com/jennybc/362f52446fe1ebc4c49f#file-2014-10-12_stop-working-directory-insanity-md
>
> Cheers
>
> Am 06.10.2018 um 13:48 schrieb Olivier GIVAUDAN:
>> 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.
>>
>
> --
> Eik Vettorazzi
>
> Department of Medical Biometry and Epidemiology
> University Medical Center Hamburg-Eppendorf
>
> Martinistrasse 52
> building W 34
> 20246 Hamburg
>
> Phone: +49 (0) 40 7410 - 58243
> Fax:   +49 (0) 40 7410 - 57790
> Web: www.uke.de/imbe<http://www.uke.de/imbe>
> --
>
> _____________________________________________________________________
>
> Universit???tsklinikum Hamburg-Eppendorf; K???rperschaft des ???ffentlichen
Rechts; Gerichtsstand: Hamburg | www.uke.de
> Vorstandsmitglieder: Prof. Dr. Burkhard G???ke (Vorsitzender), Prof. Dr.
Dr. Uwe Koch-Gromus, Joachim Pr???l???, Martina Saurin (komm.)
> _____________________________________________________________________
>
> SAVE PAPER - THINK BEFORE PRINTING
>
>        [[alternative HTML version deleted]]
>
>
--
Luke Tierney
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa                  Phone:             319-335-3386
Department of Statistics and        Fax:               319-335-3017
    Actuarial Science
241 Schaeffer Hall                  email:   luke-tierney at uiowa.edu
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu

	[[alternative HTML version deleted]]

R help - Oct 2018 - Genuine relative paths with R

[R] Genuine relative paths with R

[R] Genuine relative paths with R

[R] Genuine relative paths with R