[R-pkg-devel] Fwd: Re-creating vignettes after update of data or different mechanism to create reports?

[Rainer Krug]

> On 11 May 2017, at 14:59, Holger Hoefling <hhoeflin at gmail.com> wrote:
> 
> Hi Rainer,
> 
> thanks for the explanation.

No problem.

> You probably already considered this - but you could version-bump the analysis package with every data package update (and make the latest data package the minimum requirement). Given how large the data package is - the overhead of an analysis package version bum seems small. Then people would update the analysis package - which would trigger the data package update and the vignette would be built correctly.

That would certainly work. Considering the main distribution channel at the moment, which is source Packages as .tar.gz, this would not be as elegant.
Given possible distribution channels (GitHub likely), I think a different solution might be better. Also, I don’t know if CRAN would be to happy to have regular version bumps just to re-create the vignette…

Thanks,

Rainer

> 
> That being said - how exactly this would work may also depend on how you plan to host this large package (CRAN would likely not accept it). Bioconductor on the other hand requires version bumps for every package for every release anyway - so this concurs with my suggestion.
> 
> Best
> 
> Holger
> 
> On Thu, May 11, 2017 at 2:43 PM, Rainer Krug <Rainer at krugs.de <mailto:Rainer at krugs.de>> wrote:
> Sorry - forgot to cc the list
> 
> > Begin forwarded message:
> >
> > From: Rainer Krug <Rainer at krugs.de <mailto:Rainer at krugs.de>>
> > Subject: Re: [R-pkg-devel] Re-creating vignettes after update of data or different mechanism to create reports?
> > Date: 11 May 2017 at 14:41:03 GMT+2
> > To: Holger Hoefling <hhoeflin at gmail.com <mailto:hhoeflin at gmail.com>>
> >
> >
> >> On 11 May 2017, at 14:35, Holger Hoefling <hhoeflin at gmail.com <mailto:hhoeflin at gmail.com> <mailto:hhoeflin at gmail.com <mailto:hhoeflin at gmail.com>>> wrote:
> >>
> >> Hi Rainer,
> >>
> >> could you elaborate a little more on why you split this into two packages in the first place? If you all kept it in one, you would have to update this package regularly - but rebuilding the vignette would not be a problem.
> >>
> >> As you designed it with 2 packages - you also have to update the data package regularly.
> >>
> >> I guess I just don't understand what you gain by splitting the packages.
> >
> > I am aware that I wouldn’t have this problem with a single package, but there are some reasons why I would like to keep them separate (see below):
> >
> > 1) The dataset will be huge. So combining it with the analysis package is not a good idea in case that the analysis package needs to be updated and the data package stays the same.
> >
> > 2) I like the separation between data package and analysis package - it is cleaner
> >
> > 3) The data is not (but will hopefully be sometime later) public. So we can have two versions of the data package: one for internal usage, and one witch dummy data which can be made publicly available, as we want to make the code of the analysis public.
> >
> > Hope this explains why I want to keep them separate,
> >
> > Rainer
> >
> >>
> >> Best
> >>
> >> Holger
> >>
> >> On Thu, May 11, 2017 at 2:31 PM, Rainer Krug <Rainer at krugs.de <mailto:Rainer at krugs.de> <mailto:Rainer at krugs.de <mailto:Rainer at krugs.de>>> wrote:
> >> Hi
> >>
> >> I am building two packages:
> >>
> >> - a data package which contains the data and function to extract it (several datasets, linked, like an sql database) and
> >> - an analysis package which contains functions to analyse the data in the data package and depends on the data package.
> >>
> >> The data package is updated often as the data is updated regularly, while the analysis package will (hopefully) be more static.
> >>
> >> Now I created a report which I put in the vignette of the analysis package, which works nicely and the report is created when the analysis package is installed, but when the data package is updated, the user has to re-install the analysis package to re-create the report (vignette) of the updated dataset.
> >>
> >> I know that I am abusing the vignette, but it works nicely.
> >>
> >> My question:  Is there a way of re-creating the vignette by a user after they installed a newer version of the data package, or is there a better way of creating the report(s)?
> >>
> >> Thanks,
> >>
> >> Rainer
> >>
> >> --
> >> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
> >>
> >> University of Zürich
> >>
> >> Cell:       +41 (0)78 630 66 57 <tel:%2B41%20%280%2978%20630%2066%2057> <tel:%2B41%20%280%2978%20630%2066%2057>
> >>
> >> Fax (D):    +49 - (0)3 21 21 25 22 44 <tel:%2B49%20-%20%280%293%2021%2021%2025%2022%2044> <tel:%2B49%20-%20%280%293%2021%2021%2025%2022%2044>
> >>
> >> email:      Rainer at krugs.de <mailto:Rainer at krugs.de> <mailto:Rainer at krugs.de <mailto:Rainer at krugs.de>>
> >>
> >> Skype:      RMkrug
> >>
> >>
> >> ______________________________________________
> >> R-package-devel at r-project.org <mailto:R-package-devel at r-project.org> <mailto:R-package-devel at r-project.org <mailto:R-package-devel at r-project.org>> mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-package-devel <https://stat.ethz.ch/mailman/listinfo/r-package-devel> <https://stat.ethz.ch/mailman/listinfo/r-package-devel <https://stat.ethz.ch/mailman/listinfo/r-package-devel>>
> >>
> >
> > --
> > Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
> >
> > University of Zürich
> >
> > Cell:       +41 (0)78 630 66 57 <tel:%2B41%20%280%2978%20630%2066%2057>
> >
> > Fax (D):    +49 - (0)3 21 21 25 22 44 <tel:%2B49%20-%20%280%293%2021%2021%2025%2022%2044>
> >
> > email:      Rainer at krugs.de <mailto:Rainer at krugs.de> <mailto:Rainer at krugs.de <mailto:Rainer at krugs.de>>
> >
> > Skype:      RMkrug
> >
> 
> --
> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
> 
> University of Zürich
> 
> Cell:       +41 (0)78 630 66 57 <tel:%2B41%20%280%2978%20630%2066%2057>
> 
> Fax (D):    +49 - (0)3 21 21 25 22 44 <tel:%2B49%20-%20%280%293%2021%2021%2025%2022%2044>
> 
> email:      Rainer at krugs.de <mailto:Rainer at krugs.de>
> 
> Skype:      RMkrug
> 
> 
> ______________________________________________
> R-package-devel at r-project.org <mailto:R-package-devel at r-project.org> mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel <https://stat.ethz.ch/mailman/listinfo/r-package-devel>
> 

--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)

University of Zürich

Cell:       +41 (0)78 630 66 57

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer at krugs.de

Skype:      RMkrug

-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 455 bytes
Desc: Message signed with OpenPGP
URL: <https://stat.ethz.ch/pipermail/r-package-devel/attachments/20170511/e7a833c1/attachment.sig>