On Thu, Jul 24, 2014 at 5:34 PM, Hervé Pagès <hpa...@fhcrc.org> wrote: > Hi Henrik, > > > On 07/24/2014 06:03 AM, Henrik Bengtsson wrote: >> >> On Thu, Jul 24, 2014 at 3:16 AM, Hervé Pagès <hpa...@fhcrc.org> wrote: >>> >>> Hi Andrzej, >>> >>> >>> On 07/22/2014 02:28 PM, Andrzej Oleś wrote: >>>> >>>> >>>> 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... >>> >>> >>> >>> Done: >>> >>> http://bioconductor.org/checkResults/3.0/bioc-LATEST/index.html >>> >>> >>> http://bioconductor.org/checkResults/3.0/data-experiment-LATEST/index.html >>> >>> Will revert back if there is too much complaining about this... >> >> >> Thanks for all updates. The latter hurts my eyes though - > > > I didn't modify the data experiment report to use a less bright logo > yet. It should auto-update the next time the report is generated though.
Ok. > > >> may I >> instead suggest to use a left/right side bar with text "Bioconductor >> developer version (3.0)" written sideways. > > > We need to deal with a space problem. The report is already too wide. > > >> Alternatively, add >> "developer" and "release" tag after each package's version, e.g. >> "affycompData 1.2.0 (BioC release 2.14)" and "affycompData 1.3.0 (BioC >> developer 3.0)" (possible on a separate line). > > > Space problem again. Ok. > > >> >> BTW, the BioC version is nowhere to be seen on the current check >> results pages; it's only from the URL you can infer this. > > > It's in the title! What to say... touche. > > >> >> While at it, it would be great to have links on the check pages that >> quickly takes to the corresponding devel/release versions. > > > The check page for devel has links to the devel landing pages and the > check page for release has links to the release release landing pages. > Just click on the name of the package and it will take you to the > corresponding landing page. > > >> Also, if >> one could jump directly to a particular package, that would also be >> great, e.g. >> http://bioconductor.org/checkResults/3.0/data-experiment-LATEST/index.html#gageData > > > http://bioconductor.org/checkResults/3.0/bioc-LATEST/aroma.light/ After all these years I didn't know that one existed. ...which brings me to the last item of my wishlist; a link to this from the package page, e.g. http://bioconductor.org/packages/3.0/bioc/html/aroma.light.html -> http://bioconductor.org/checkResults/3.0/bioc-LATEST/aroma.light/. Thxs Henrik > > Cheers, > H. > > >> >> Thxs, >> >> Henrik >> >>> >>> Cheers, >>> >>> H. >>> >>>> >>>> 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 >>> >>> >>> >>> -- >>> 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 > > > -- > 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
