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

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

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

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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