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

[Tomas Kalibera]

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!
>>
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