[Bioc-devel] Distinction between release and devel package websites

Martin Morgan mtmorgan at fhcrc.org
Wed Jul 23 20:44:33 CEST 2014 

On 07/23/2014 11:33 AM, Martin Morgan wrote:
> Dan has implemented these changes. Go to the Bioconductor home page and in the
> search box at the top right enter
>
>    supraHex
>
> (winner of the ISMB 2014 Best Artwork Award! Check out the URL on the package
> landing page). You'll see that the first link is to supraHex, and the second to
> supraHex (development version).
>
> On the supraHex (development version) page you'll see text indicating that
> you're looking at the development version, and for the release you should go
> somewhere else.
>
> Further down the installation instructions are now in their own section, adding
> a little more emphasis.
>
> The Documentation section includes instructions -- browseVignettes("supraHex")
> -- for getting your version of the vignettes.
>
> The 'download' section is now called 'Package Archives'.
>
> The Package Archives section starts with a sentence pointing to Installation
> instructions.
>
> Mousing over one of the links pops up a tool tip encouraging you once again to
> use biocLite.
>
> Relevant changes also apply to release landing pages.
>
> As Vince mentioned, it is REALLY IMPORTANT that users do not mix release and
> devel versions of packages in a single library. Even if it 'works for package
> X', this invariably leads to incompatibilities and confusion. For those users
> wanting new features, tell them to switch to using the development version,
> e.g., as outlined at
>
>    http://bioconductor.org/packages/release/bioc/html/supraHex.html

http://bioconductor.org/developers/how-to/useDevel/

>
> Thanks for your input,
>
> Martin
>
> On 07/22/2014 12:01 PM, Martin Morgan wrote:
>> Thanks everyone for the input.
>>
>> We'll make some changes (over the next day or so), and then iterate on those as
>> needed. Specifically
>>
>> 1. text after the package title indicating when the user is on the 'developer'
>> page, with link to a 'stable release version'.
>>
>> 2. more prominent Installation header
>>
>> 3. Rename 'Package Downloads' to something less appealing, add text to indicate
>> that the correct way to install a package is to follow Installation
>> instructions, add pop-up interstitial to each of the gz/zip/tgz links to try to
>> further clarify installation.
>>
>> We might tell google not to index devel packages (but then packages added during
>> a particular release cycle aren't indexed until the next release). We will not
>> change the color of the devel landing page (because color would not have meaning
>> to the uninitiated).
>>
>> Interesting also that one source of problem is the _vignettes_, not the landing
>> page. Maybe we could add a browseVignettes() code chunk.
>>
>> Martin
>>
>> On 07/22/2014 11:10 AM, Matthew McCall wrote:
>>> The current link to the source tarball is called "Package Source" hence the
>>> quotes. Yes, I could check out the package using svn, but when browsing
>>> through a Bioconductor workflow, there are these handy links to the package
>>> pages that let me download and browse the source tarball without having to
>>> type anything. I like the idea of replacing the source tarball link with a
>>> link to the package source in svn.
>>>
>>> Best,
>>> Matt
>>>
>>>
>>>
>>>
>>> On Tue, Jul 22, 2014 at 1:58 PM, Michael Lawrence <lawrence.michael at gene.com
>>>> wrote:
>>>
>>>> Just check out from svn to get the source... way easier to keep up to
>>>> date, and if you notice an issue, easier to make a patch.
>>>>
>>>>
>>>>
>>>>
>>>> On Tue, Jul 22, 2014 at 10:49 AM, Matthew McCall <mccallm at gmail.com>
>>>> wrote:
>>>>
>>>>> I hope the "package source" link is not on the proposed list of links to
>>>>> remove. I often use these links to browse through the source code of
>>>>> packages to learn from others' work. Also, it seems that making the source
>>>>> code (even slightly) less accessible would go against the principle of open
>>>>> source software.
>>>>>
>>>>> Best,
>>>>> Matt
>>>>>
>>>>>
>>>>>
>>>>> On Tue, Jul 22, 2014 at 1:22 PM, Michael Lawrence <
>>>>> lawrence.michael at gene.com> wrote:
>>>>>
>>>>>> Agreed. Disabling the links is a good idea. There's really no good reason
>>>>>> for someone to install packages manually. If a user really wants to mix
>>>>>> release/devel, it is still technically possible but this change would
>>>>>> strongly discourage it.
>>>>>>
>>>>>> For ensuring the user notices that a page is for the devel version , I'm
>>>>>> still in favor of the simple notification box. Probably without the
>>>>>> option
>>>>>> to hide forever.
>>>>>>
>>>>>>
>>>>>> On Tue, Jul 22, 2014 at 9:26 AM, James W. MacDonald <jmacdon at uw.edu>
>>>>>> wrote:
>>>>>>
>>>>>>> Given that we have an ongoing problem with people inadvisedly clicking
>>>>>> and
>>>>>>> installing things, is there a good rationale for allowing them to do
>>>>>> so?
>>>>>>>
>>>>>>> Perhaps the landing page for each package should be stripped of links
>>>>>> and
>>>>>>> replaced with some indication of the availability for each package on
>>>>>> the
>>>>>>> various operating systems. There could also be a note indicating that
>>>>>>> people can install using biocLite().
>>>>>>>
>>>>>>> Best,
>>>>>>>
>>>>>>> Jim
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 7/22/2014 11:48 AM, Dan Tenenbaum wrote:
>>>>>>>
>>>>>>>> Seems like there are two problems, first that the release and devel
>>>>>> pages
>>>>>>>> look similar, but more importantly that people are downloading and
>>>>>>>> installing from the package pages when they should be using
>>>>>> biocLite().
>>>>>>>>
>>>>>>>> I am open to the suggestions for making the release/devel pages look
>>>>>> more
>>>>>>>> different from each other, but I think something needs to be done
>>>>>> about the
>>>>>>>> second problem as well. Perhaps a popup that comes up when you click
>>>>>> on a
>>>>>>>> package tarball saying "The best way to install this is with
>>>>>> biocLite();
>>>>>>>> are you sure you want to download it?"
>>>>>>>>
>>>>>>>> Whatever we do probably won't happen until after BioC2014.
>>>>>>>>
>>>>>>>> Dan
>>>>>>>>
>>>>>>>>
>>>>>>>> ----- Original Message -----
>>>>>>>>
>>>>>>>>> From: "Julian Gehring" <julian.gehring at embl.de>
>>>>>>>>> To: "Hervé Pagès" <hpages at fhcrc.org>, "Michael Lawrence" <
>>>>>>>>> lawrence.michael at gene.com>, "Vincent Carey"
>>>>>>>>> <stvjc at channing.harvard.edu>
>>>>>>>>> Cc: bioc-devel at r-project.org
>>>>>>>>> Sent: Tuesday, July 22, 2014 8:07:29 AM
>>>>>>>>> Subject: Re: [Bioc-devel] Distinction between release and devel
>>>>>> package
>>>>>>>>> websites
>>>>>>>>>
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> Tooltips that appear while hovering over selected links are easy to
>>>>>>>>> miss.  This alone will likely not be clear enough.  We should convey
>>>>>>>>> the
>>>>>>>>> information that the entire website presents a different version of
>>>>>>>>> the
>>>>>>>>> package.
>>>>>>>>>
>>>>>>>>> The idea of a notification box that can be made visible by the
>>>>>>>>> individual user seems tempting.  One can combine this with an
>>>>>>>>> optional
>>>>>>>>> cookie, to remember the state between browser sessions.
>>>>>>>>>
>>>>>>>>> Changing the layout of the devel page itself will also be helpful to
>>>>>>>>> make the distinction more pronounced.  Hopefully we could approach
>>>>>>>>> this
>>>>>>>>> in a way that maintains the nice design of the bioc website.
>>>>>>>>>
>>>>>>>>> Best
>>>>>>>>> Julian
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 21.07.2014 21:50, Hervé Pagès wrote:
>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>>
>>>>>>>>>> In addition to these suggestions, how about using a special
>>>>>>>>>> background
>>>>>>>>>> color for package landing pages in devel?
>>>>>>>>>>
>>>>>>>>>> Cheers,
>>>>>>>>>> H.
>>>>>>>>>>
>>>>>>>>>> On 07/21/2014 07:32 PM, Michael Lawrence wrote:
>>>>>>>>>>
>>>>>>>>>>> Or an unobtrusive "notification box" that drops down from the top
>>>>>>>>>>> of the
>>>>>>>>>>> page, saying something like "this is devel"; there would be a
>>>>>>>>>>> dismiss
>>>>>>>>>>> button and a checkbox for whether to show again. The user is free
>>>>>>>>>>> to
>>>>>>>>>>> simply
>>>>>>>>>>> ignore it and proceed as normal.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Mon, Jul 21, 2014 at 7:10 PM, Vincent Carey
>>>>>>>>>>> <stvjc at channing.harvard.edu>
>>>>>>>>>>> wrote:
>>>>>>>>>>>
>>>>>>>>>>>   how about a tooltip that reads "installation via biocLite() is
>>>>>>>>>>>> the
>>>>>>>>>>>> recommended approach to Bioconductor software
>>>>>>>>>>>> acquisition, other approaches may lead to inconsistent
>>>>>>>>>>>> package-sets"
>>>>>>>>>>>> that
>>>>>>>>>>>> appears when a reader hovers over a tarball.  i would imagine
>>>>>>>>>>>> that
>>>>>>>>>>>> this is
>>>>>>>>>>>> how the "wrong package" gets installed, by manually using an
>>>>>>>>>>>> inappropriate
>>>>>>>>>>>> tarball.
>>>>>>>>>>>>
>>>>>>>>>>>> wrong documentation is not so easy but the doc on the devel
>>>>>>>>>>>> branch might
>>>>>>>>>>>> have a different tooltip cautioning the readers to be sure they
>>>>>>>>>>>> want to
>>>>>>>>>>>> read the doc on the devel version.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On Mon, Jul 21, 2014 at 9:39 PM, Julian Gehring
>>>>>>>>>>>> <julian.gehring at embl.de>
>>>>>>>>>>>> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>   Hi,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Can we make the package websites for the devel and release
>>>>>>>>>>>>> version of a
>>>>>>>>>>>>> package more distinguishable?
>>>>>>>>>>>>>
>>>>>>>>>>>>> To elaborate on this: In the past, I have seen several users
>>>>>>>>>>>>> having
>>>>>>>>>>>>> problems with using bioconductor because they ended up on the
>>>>>>>>>>>>> wrong
>>>>>>>>>>>>> page
>>>>>>>>>>>>> (mostly the devel page when they would have needed the release).
>>>>>>>>>>>>>    This
>>>>>>>>>>>>> resulted in getting the wrong documentation or installing the
>>>>>>>>>>>>> wrong
>>>>>>>>>>>>> package.  The pages are well designed, and there is no reason to
>>>>>>>>>>>>> change
>>>>>>>>>>>>> this.  However, the websites for the devel and release version
>>>>>>>>>>>>> of a
>>>>>>>>>>>>>
>>>>>>>>>>>> package
>>>>>>>>>>>>
>>>>>>>>>>>>> look almost identical, and that these two get confused seems to
>>>>>>>>>>>>> happen to
>>>>>>>>>>>>> many users (me included).
>>>>>>>>>>>>>
>>>>>>>>>>>>> If you search for a package within the bioc website, the release
>>>>>>>>>>>>> version
>>>>>>>>>>>>> always comes first in the search results.  If you are coming
>>>>>>>>>>>>> from the
>>>>>>>>>>>>> outside (e.g. google), this may not be the case.  In fact,
>>>>>>>>>>>>> googling
>>>>>>>>>>>>> a few
>>>>>>>>>>>>> packages names often returned only the devel page in the top 10
>>>>>>>>>>>>> search
>>>>>>>>>>>>> results.
>>>>>>>>>>>>>
>>>>>>>>>>>>> What are the feelings regarding this? We could add a header
>>>>>>>>>>>>> section on
>>>>>>>>>>>>>
>>>>>>>>>>>> the
>>>>>>>>>>>>
>>>>>>>>>>>>> devel page that states that this is an unstable version not
>>>>>>>>>>>>> meant to be
>>>>>>>>>>>>> used in production settings, and provide a link to the
>>>>>>>>>>>>> respective
>>>>>>>>>>>>> release
>>>>>>>>>>>>> version?
>>>>>>>>>>>>>
>>>>>>>>>>>>> Best wishes
>>>>>>>>>>>>> Julian
>>>>>>>>>>>>>
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>            [[alternative HTML version deleted]]
>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>       [[alternative HTML version deleted]]
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>>>>
>>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>>>
>>>>>>>>
>>>>>>> --
>>>>>>> James W. MacDonald, M.S.
>>>>>>> Biostatistician
>>>>>>> University of Washington
>>>>>>> Environmental and Occupational Health Sciences
>>>>>>> 4225 Roosevelt Way NE, # 100
>>>>>>> Seattle WA 98105-6099
>>>>>>>
>>>>>>
>>>>>>          [[alternative HTML version deleted]]
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioc-devel at r-project.org mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Matthew N McCall, PhD
>>>>> 112 Arvine Heights
>>>>> Rochester, NY 14611
>>>>> Cell: 202-222-5880
>>>>>
>>>>>
>>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>>
>
>


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