[Bioc-devel] zzz.R in GenoView

[Hervé Pagès]

On 10/05/2015 05:45 PM, Dan Tenenbaum wrote:
> 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).

Right but if the package was passing build and check, there wouldn't be 
much reason to deprecate it in the first place.

>
> 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.

Agreed. Not a change you want to do now. The change to the build system
is too big to make it 1 week before a release.

H.

>
> 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
>>

-- 
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