Just check out from svn to get the source... way easier to keep up to date, and if you notice an issue, easier to make a patch.
On Tue, Jul 22, 2014 at 10:49 AM, Matthew McCall <mcca...@gmail.com> wrote: > 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. > > 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]]
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