Hi Hervé, thank you for the demo! Yes, this is definitely much more clear than just a different color. Maybe we could first implement this idea on the build/check report websites and see how the uptake will be? I always keep getting confused by the colors which keep changing with every release cycle anyway...
Cheers, Andrzej On Tue, Jul 22, 2014 at 10:04 PM, Hervé Pagès <hpa...@fhcrc.org> wrote: > Hi Andrzej, > > > On 07/22/2014 10:14 AM, 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. >> >> 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 was thinking of something like this: > > http://www.bioconductor.org/checkResults/3.0/data-experiment-LATEST/ > > Just a demo. This will be reset to the usual background tomorrow. > > Cheers, > H. > > >> 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 >> >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpa...@fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
