[R-pkg-devel] implications of staged install for data processing packages

[Florian Oswald]

brilliant! thanks a lot, and yes, will come back with more in case I'm
stuck.

F

On Fri, 28 Jun 2019 at 17:44, Tomas Kalibera <tomas.kalibera using gmail.com>
wrote:

> On 6/28/19 5:16 PM, Florian Oswald wrote:
> > oh ok i see: so i will always be able to do
> >
> > clean(path = "~/data.csv")
> >
> > for example? in that case I completely misunderstood this and there must
> > indeed be some system.file call buried somewhere. will check. thanks!
>
> In case it is hard to find manually, there is a script at
> https://github.com/kalibera/rstagedinst (described also in the blog post
> about staged install), which finds variables holding hard-coded paths to
> the temporary installation directory. Please give a reproducible example
> (e.g. the package, output from the script, output from the installation
> with the error, etc) if you needed more help.
>
> Best
> Tomas
>
> >
> > Florian
> >
> > On Fri, 28 Jun 2019 at 17:11, Georgi Boshnakov <
> > georgi.boshnakov using manchester.ac.uk> wrote:
> >
> >> You need to give details what exactly gets you into trouble and about
> your
> >> use case, since any advice would be conditional on making assumptions
> about
> >> that. It is usually a bad a idea to have a function working on a
> hardcoded
> >> full filename. You will thank yourself later if you at least make it
> >> argument to your function(s). It can have for default value the one
> that is
> >> currently hardcoded.
> >>
> >> Please note that your use case does not seem inherently related to
> staged
> >> installation.
> >> "Hardcoded" in the context of staged installation does not refer to any
> >> hardcoded path
> >> but to those paths that contain the temporary installation directory.
> Such
> >> paths can be obtained,
> >> for example, with calls to system.path(), as illustrated by Tomas.
> >>
> >> Georgi Boshnakov
> >>
> >>
> >>
> >> -----Original Message-----
> >> From: R-package-devel [mailto:r-package-devel-bounces using r-project.org] On
> >> Behalf Of Florian Oswald
> >> Sent: 28 June 2019 09:17
> >> To: r-package-devel using r-project.org
> >> Subject: [R-pkg-devel] implications of staged install for data
> processing
> >> packages
> >>
> >> Hi all
> >>
> >> I ran into trouble with the changes starting to come in with R3.6
> stemming
> >> from the new staged installation, which checks and errors on hard coded
> >> paths in R code. I understand there is an opt out, but still want to
> know.
> >> here's the blog post:
> >> https://developer.r-project.org/Blog/public/2019/02/14/staged-install/
> >>
> >> I have several packages which look like that:
> >>
> >>     1. large messy dataset stored on disk as `filename`, maybe a csv.
> >>     2. R package has a function `clean(filename)` which reads the data
> and
> >>     brings it into useable form
> >>     3. R package does analysis
> >>     4. R package exports results
> >>
> >> `filename` is hard coded. What is the proper way to do this instead?
> Should
> >> I store the inital raw data inside the R package in `/inst`? These
> things
> >> are typically very large, so I like to decouple the raw data from the
> >> package (easier to share).
> >>
> >> thanks for any suggestions!
> >>
> >>          [[alternative HTML version deleted]]
> >>
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> >>
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> >
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>
>

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