I hope the "package source" link is not on the proposed list of links to
remove. I often use these links to browse through the source code of
packages to learn from others' work. Also, it seems that making the source
code (even slightly) less accessible would go against the principle of open
source software.

Best,
Matt



On Tue, Jul 22, 2014 at 1:22 PM, Michael Lawrence <lawrence.michael@gene.com
> wrote:

> Agreed. Disabling the links is a good idea. There's really no good reason
> for someone to install packages manually. If a user really wants to mix
> release/devel, it is still technically possible but this change would
> strongly discourage it.
>
> For ensuring the user notices that a page is for the devel version , I'm
> still in favor of the simple notification box. Probably without the option
> to hide forever.
>
>
> On Tue, Jul 22, 2014 at 9:26 AM, James W. MacDonald <jmacdon@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@embl.de>
> >>> To: "Hervé Pagès" <hpages@fhcrc.org>, "Michael Lawrence" <
> >>> lawrence.michael@gene.com>, "Vincent Carey"
> >>> <stvjc@channing.harvard.edu>
> >>> Cc: bioc-devel@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@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@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@r-project.org mailing list
> >>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>>>>>
> >>>>>>>
> >>>>>>           [[alternative HTML version deleted]]
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> Bioc-devel@r-project.org mailing list
> >>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>>>>
> >>>>>>
> >>>>>      [[alternative HTML version deleted]]
> >>>>>
> >>>>> _______________________________________________
> >>>>> Bioc-devel@r-project.org mailing list
> >>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>>>
> >>>>>
> >>>>
> >>> _______________________________________________
> >>> Bioc-devel@r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>
> >>>
> >> _______________________________________________
> >> Bioc-devel@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
> >
>
>         [[alternative HTML version deleted]]
>
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>


-- 
Matthew N McCall, PhD
112 Arvine Heights
Rochester, NY 14611
Cell: 202-222-5880

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