[Bioc-devel] Distinction between release and devel package websites

Dan Tenenbaum dtenenba at fhcrc.org
Tue Jul 22 23:11:26 CEST 2014 

Hi Andrzej,

----- Original Message -----
> From: "Andrzej Oleś" <andrzej.oles at gmail.com>
> To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> Cc: "James W. MacDonald" <jmacdon at uw.edu>, "Julian Gehring" <julian.gehring at embl.de>, "Michael Lawrence"
> <lawrence.michael at gene.com>, bioc-devel at r-project.org
> Sent: Tuesday, July 22, 2014 2:06:25 PM
> Subject: Re: [Bioc-devel] Distinction between release and devel package websites
> 
> Dear Dan, James, Michael, Matt,
> 
> thank you, I see your point but I'm afraid I must disagree with you.
> I've had this situation numerous times that I have added/fixed
> something in the devel branch of a package and had to advice the
> users
> to use this latest version. Needless to say, they were typically
> using
> the release branch, and it was a relatively painless procedure for
> them to pick the tarball from the devel landing page and proceed with
> manual installation. Of course, this could be also achieved by
> installing from the svn, however, this is not very welcome from the
> user's perspective.
> 
> Please correct me if I'm wrong, but to my knowledge there is no
> build-in mechanism in 'biocLite' facilitating the above described
> scenario. Therefore, I think that it could be useful to have an
> 'useDevel' argument to biocLite() allowing for the installation of a
> specific package(s) from the devel rather than from the release
> branch
> without having to switch to devel completely. As this would be an
> optional argument defaulting to FALSE I wouldn't be worried by
> potential abuse, at least not more than by having the devel packages
> exposed on the website. As an additional precaution measure we could
> issue a warning and ask the user to confirm that (s)he is aware of
> the
> risks and wants to proceed.

If a user wants to use a devel package they should be using BioC-devel. We explain on the web site how to run both BioC-devel and BioC-release on the same machine. Installing a devel package into an otherwise release installation is going to cause problems and defeats the entire purpose of having a devel branch.


> 
> As Matt pointed out, direct links to "package source" tarballs are
> very useful for quick and lightweight inspection of package code.
> This
> approach combined with opening the files directly with an archive
> browser is particularly appealing, as it saves one from dealing with
> manual svn checkout and the cleanup afterwards. Please note that
> replacing the prebuild tarball with a link to the SVN has the caveat
> of getting potantially broken code. Tarballs which make it through to
> the website guarantee that the package at least builds.
> 

I think we're going to leave the links there but put in some sort of popup explaining that you should really use biocLite() unless you have some special reason for downloading the tarball.

Dan


> Best,
> Andrzej
> 
> On Tue, Jul 22, 2014 at 7:57 PM, Dan Tenenbaum <dtenenba at fhcrc.org>
> wrote:
> >
> >
> > ----- Original Message -----
> >> From: "James W. MacDonald" <jmacdon at uw.edu>
> >> To: "Andrzej Oleś" <andrzej.oles at gmail.com>
> >> Cc: "Dan Tenenbaum" <dtenenba at fhcrc.org>, "Julian Gehring"
> >> <julian.gehring at embl.de>, "Michael Lawrence"
> >> <lawrence.michael at gene.com>, bioc-devel at 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
> >> > <jmacdon at 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.gehring at embl.de>
> >> >>>> To: "Hervé Pagès" <hpages at fhcrc.org>, "Michael Lawrence"
> >> >>>> <lawrence.michael at gene.com>, "Vincent Carey"
> >> >>>> <stvjc at channing.harvard.edu>
> >> >>>> Cc: bioc-devel at 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
> >> >>>>>> <stvjc at 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.gehring at 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 at r-project.org mailing list
> >> >>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >> >>>>>>>>
> >> >>>>>>>
> >> >>>>>>>            [[alternative HTML version deleted]]
> >> >>>>>>>
> >> >>>>>>> _______________________________________________
> >> >>>>>>> Bioc-devel at r-project.org mailing list
> >> >>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >> >>>>>>>
> >> >>>>>>
> >> >>>>>>       [[alternative HTML version deleted]]
> >> >>>>>>
> >> >>>>>> _______________________________________________
> >> >>>>>> Bioc-devel at r-project.org mailing list
> >> >>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >> >>>>>>
> >> >>>>>
> >> >>>>
> >> >>>> _______________________________________________
> >> >>>> Bioc-devel at r-project.org mailing list
> >> >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >> >>>>
> >> >>>
> >> >>> _______________________________________________
> >> >>> Bioc-devel at 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 at 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
> >>
>

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