The current link to the source tarball is called "Package Source" hence the quotes. Yes, I could check out the package using svn, but when browsing through a Bioconductor workflow, there are these handy links to the package pages that let me download and browse the source tarball without having to type anything. I like the idea of replacing the source tarball link with a link to the package source in svn.
Best, Matt On Tue, Jul 22, 2014 at 1:58 PM, Michael Lawrence <lawrence.mich...@gene.com > wrote: > 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 >> >> > -- Matthew N McCall, PhD 112 Arvine Heights Rochester, NY 14611 Cell: 202-222-5880 [[alternative HTML version deleted]]
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