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

Dan Tenenbaum dtenenba at fhcrc.org
Tue Jul 22 19:57:39 CEST 2014 


----- Original Message -----
> From: "James W. MacDonald" <jmacdon at uw.edu>
> To: "Andrzej Oleś" <andrzej.oles at gmail.com>
> Cc: "Dan Tenenbaum" <dtenenba at fhcrc.org>, "Julian Gehring" <julian.gehring at embl.de>, "Michael Lawrence"
> <lawrence.michael at gene.com>, bioc-devel at r-project.org
> Sent: Tuesday, July 22, 2014 10:51:35 AM
> Subject: Re: [Bioc-devel] Distinction between release and devel package websites
> 
> 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?
> 

Or to know how to find the link to the tarball.

Dan


> 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
>

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