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

Dan Tenenbaum dtenenba at fhcrc.org
Tue Jul 22 19:10:41 CEST 2014 


----- Original Message -----
> From: "James W. MacDonald" <jmacdon at uw.edu>
> To: "Dan Tenenbaum" <dtenenba at fhcrc.org>, "Julian Gehring" <julian.gehring at embl.de>
> Cc: "Michael Lawrence" <lawrence.michael at gene.com>, bioc-devel at r-project.org
> Sent: Tuesday, July 22, 2014 9:26:13 AM
> Subject: Re: [Bioc-devel] Distinction between release and devel package websites
> 
> 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?

I tend to agree with this...

> 
> 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().
> 

There is such a note, but it's often ignored, as you point out.
Dan


> 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
>

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