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

Hervé Pagès hpages at fhcrc.org
Thu Jul 24 17:34:00 CEST 2014 

Hi Henrik,

On 07/24/2014 06:03 AM, Henrik Bengtsson wrote:
> On Thu, Jul 24, 2014 at 3:16 AM, Hervé Pagès <hpages at fhcrc.org> wrote:
>> 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...
>
> Thanks for all updates. The latter hurts my eyes though -

I didn't modify the data experiment report to use a less bright logo
yet. It should auto-update the next time the report is generated though.

> may I
> instead suggest to use a left/right side bar with text "Bioconductor
> developer version (3.0)" written sideways.

We need to deal with a space problem. The report is already too wide.

> Alternatively, add
> "developer" and "release" tag after each package's version, e.g.
> "affycompData 1.2.0 (BioC release 2.14)" and "affycompData 1.3.0 (BioC
> developer 3.0)" (possible on a separate line).

Space problem again.

>
> BTW, the BioC version is nowhere to be seen on the current check
> results pages; it's only from the URL you can infer this.

It's in the title!

>
> While at it, it would be great to have links on the check pages that
> quickly takes to the corresponding devel/release versions.

The check page for devel has links to the devel landing pages and the
check page for release has links to the release release landing pages.
Just click on the name of the package and it will take you to the
corresponding landing page.

>  Also, if
> one could jump directly to a particular package, that would also be
> great, e.g. http://bioconductor.org/checkResults/3.0/data-experiment-LATEST/index.html#gageData

http://bioconductor.org/checkResults/3.0/bioc-LATEST/aroma.light/

Cheers,
H.

>
> Thxs,
>
> Henrik
>
>>
>> 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
>>
>> _______________________________________________
>> 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

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