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

Dan Tenenbaum dtenenba at fhcrc.org
Tue Jul 22 19:57:18 CEST 2014 


----- Original Message -----
> From: "Matthew McCall" <mccallm at gmail.com>
> To: "Michael Lawrence" <lawrence.michael at gene.com>
> Cc: bioc-devel at r-project.org
> Sent: Tuesday, July 22, 2014 10:49:39 AM
> Subject: Re: [Bioc-devel] Distinction between release and devel package	websites
> 
> 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.

There is no package source link (unless you mean the source tarball) but I think it would be good to add a link directly to the package source in svn. That would make the source even easier to browse than it is now (you would now have to download and untar a tarball first).

Dan


> 
> Best,
> Matt
> 
> 
> 
> On Tue, Jul 22, 2014 at 1:22 PM, Michael Lawrence
> <lawrence.michael at 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 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
> > >
> >
> >         [[alternative HTML version deleted]]
> >
> >
> > _______________________________________________
> > Bioc-devel at 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
> 
> 	[[alternative HTML version deleted]]
> 
> 
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