----- Original Message ----- > From: "James W. MacDonald" <jmac...@uw.edu> > To: "Andrzej Oleś" <andrzej.o...@gmail.com> > Cc: "Dan Tenenbaum" <dtene...@fhcrc.org>, "Julian Gehring" > <julian.gehr...@embl.de>, "Michael Lawrence" > <lawrence.mich...@gene.com>, bioc-devel@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 > > <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 > >> > >> > >> _______________________________________________ > >> 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 > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
