[Bioc-devel] zzz.R in GenoView

[Dan Tenenbaum]

I'm not sure I like that idea, because then we are propagating packages that do not build and/or check (even though there's a big fat warning when you load them).

Also I don't like the idea of modifying the build system so close to the release, and I don't have a lot of time to do that. We could look into doing it after the release if it's decided to do this.

Dan


----- Original Message -----
> From: "Hervé Pagès" <hpages at fredhutch.org>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Cc: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Monday, October 5, 2015 4:57:38 PM
> Subject: Re: zzz.R in GenoView
> 
> Hi Dan,
> 
> What about modifying the build system to propagate deprecated
> packages
> that install? That also means that the build system should also be
> modified to always perform the INSTALL step for a deprecated package.
> 
> H.
> 
> On 10/05/2015 03:31 PM, Dan Tenenbaum wrote:
> > Yes, this is part of a larger problem we need to think about.
> >
> > I marked several packages as deprecated. In each case, the package
> > has not built successfully (and propagated) in some time. So the
> > deprecation message will not propagate to the end user, and the
> > special landing page text will not be present (if the web site
> > code sees "PackageStatus: Deprecated" in a DESCRIPTION file it
> > will add some special text to the landing page, saying the package
> > is deprecated, with further instructions, but again that only
> > shows up if the package builds succesfully).
> >
> > Most of the time when we mark a package as deprecated we are doing
> > it because it does not build (and we can't reach the maintainer).
> > So there is this paradox that the deprecation warning we insert
> > will rarely be seen by end users.
> >
> > This seems to be at odds with the intent of what we are trying to
> > do.
> >
> > So instead what will happen when the end user tries to install one
> > of these packages (now or after the release) is:
> >
> > - if the package did not build at all during the release cycle (or
> > if we flushed our
> >    internal repos, a normal step leading up to release), biocLite()
> >    won't find it
> > - if it did build during the release cycle, the last good build
> > will be installed, and will
> >    not show the deprecation warning
> >
> > Maybe this is all ok. In the rare case where a package still builds
> > but we decide to mark it as deprecated for another reason, the
> > warning will be seen as intended.
> >
> > FYI
> > Dan
> >
> > PS. Hervé, I fixed the Collate field for GenoView.
> >
> > ----- Original Message -----
> >> From: "Hervé Pagès" <hpages at fredhutch.org>
> >> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> >> Sent: Monday, October 5, 2015 3:21:27 PM
> >> Subject: zzz.R in GenoView
> >>
> >> FYI
> >>
> >>
> >> http://bioconductor.org/checkResults/3.2/bioc-LATEST/GenoView/linux1.bioconductor.org-buildsrc.html
> >>
> >> Looks like zzz.R needs to be added to the Collate field.
> >>
> >> That will still not make the new version propagate though (because
> >> its
> >> vignette is broken, I think) so something else would need to be
> >> done
> >> if
> >> we want the Deprecation message to reach the end user and/or the
> >> package
> >> landing page.
> >>
> >> H.
> >>
> 
> --
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>