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

James W. MacDonald jmacdon at uw.edu
Tue Jul 22 19:51:35 CEST 2014 

Hi Andrzej,

On 7/22/2014 1:14 PM, 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.

I'm not sure I think this is a compelling reason for keeping the links. 
If someone is sophisticated enough to install a devel version of a 
package into their release install, then surely they are sophisticated 
enough to get it from svn?

It has always struck me as odd that we try time and again to get people 
to use biocLite() to install packages, yet make it so easy for people to 
ignore this advice.

Best,

Jim




>
> 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 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

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

More information about the Bioc-devel mailing list