----- Original Message ----- > From: "Matthew McCall" <mcca...@gmail.com> > To: "Michael Lawrence" <lawrence.mich...@gene.com> > Cc: bioc-devel@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.mich...@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 > > <jmac...@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.gehr...@embl.de> > > >>> To: "Hervé Pagès" <hpa...@fhcrc.org>, "Michael Lawrence" < > > >>> lawrence.mich...@gene.com>, "Vincent Carey" > > >>> <st...@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 > > >>>>> <st...@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.gehr...@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 > > [[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
