[Bioc-devel] Distinction between release and devel package websites
Hervé Pagès
hpages at fhcrc.org
Tue Jul 22 22:04:48 CEST 2014
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
>>>>
>>>
>>> _______________________________________________
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>>> 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
>
> _______________________________________________
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> 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
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