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

Henrik Bengtsson hb at biostat.ucsf.edu
Thu Jul 24 19:58:55 CEST 2014 

On Thu, Jul 24, 2014 at 5:34 PM, Hervé Pagès <hpages at fhcrc.org> wrote:
> 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.

Ok.

>
>
>> 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.

Ok.

>
>
>>
>> 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!

What to say... touche.

>
>
>>
>> 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/

After all these years I didn't know that one existed.  ...which brings
me to the last item of my wishlist; a link to this from the package
page, e.g. http://bioconductor.org/packages/3.0/bioc/html/aroma.light.html
-> http://bioconductor.org/checkResults/3.0/bioc-LATEST/aroma.light/.

Thxs

Henrik

>
> 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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