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

Tue Jul 22 23:28:10 CEST 2014

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...

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