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

Hervé Pagès hpages at fhcrc.org
Thu Jul 24 03:16:51 CEST 2014 

Hi Andrzej,

On 07/22/2014 02:28 PM, Andrzej Oleś wrote:
> Hi Hervé,
>
> thank you for the demo! Yes, this is definitely much more clear than
> just a different color. Maybe we could first implement this idea on
> the build/check report websites and see how the uptake will be? I
> always keep getting confused by the colors which keep changing with
> every release cycle anyway...

Done:

   http://bioconductor.org/checkResults/3.0/bioc-LATEST/index.html
 
http://bioconductor.org/checkResults/3.0/data-experiment-LATEST/index.html

Will revert back if there is too much complaining about this...

Cheers,
H.

>
> Cheers,
> Andrzej
>
> On Tue, Jul 22, 2014 at 10:04 PM, Hervé Pagès <hpages at fhcrc.org> wrote:
>> Hi Andrzej,
>>
>>
>> On 07/22/2014 10:14 AM, Andrzej Oleś wrote:
>>>
>>> Hi all,
>>>
>>> I think having links is useful, e.g. for someone who uses BioC release
>>> but wants to install by hand a particular package from the devel
>>> branch.
>>>
>>> Distinct colors between release and devel make sense only if one
>>> understands their meaning, which in the end might prove not to be very
>>> useful.
>>
>>
>> I was thinking of something like this:
>>
>>    http://www.bioconductor.org/checkResults/3.0/data-experiment-LATEST/
>>
>> Just a demo. This will be reset to the usual background tomorrow.
>>
>> Cheers,
>> H.
>>
>>
>>> I would rather recommend emphasizing the distinction between
>>> release and devel in clear text across the package landing page,
>>> possibly in multiple places, e.g. somewhere close to the actual
>>> package version number; for instance, add the word "devel" after the
>>> version number with a tooltip which will give some explanation/warning
>>> that this is not the stable release version.
>>>
>>> The concept of a notification box is far from ideal because it tends
>>> to be annoing to the user and once dismissed 'forever' the user won't
>>> be warned in the future.
>>>
>>> I think that the actual problem arises from the fact that the release
>>> landing pages are not clearly prioritized over the devel ones. Maybe
>>> this could be  addressed by preventing the devel pages from being
>>> harvested by google? It could make also sense to emphasize (bold face,
>>> color, ...) the package release landing page on the result list
>>> returned by the search engine on the BioC website. Currently, the
>>> results for release and devel differ only in their relative path,
>>> which can be easily overlooked, and both say "<Package> Home", see
>>> example below:
>>>
>>> Bioconductor - DESeq2 - /packages/release/bioc/html/DESeq2.html
>>>             Bioconductor - DESeq2 Home
>>> Bioconductor - DESeq2 - /packages/devel/bioc/html/DESeq2.html
>>>             Bioconductor - DESeq2 Home
>>>
>>>
>>> Cheers,
>>> Andrzej
>>>
>>> On Tue, Jul 22, 2014 at 6:26 PM, 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
>>>>
>>>>
>>>> _______________________________________________
>>>> 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
>>>
>>
>> --
>> 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 fhcrc.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 fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

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