[Bioc-devel] zzz.R in GenoView

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. Herv?, I fixed the Collate field for GenoView.

----- Original Message -----

From: "Herv? Pag?s" <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.