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

On Thu, Jul 24, 2014 at 3:16 AM, Herv? Pag?s <hpages at fhcrc.org> wrote:

Hi Andrzej,


On 07/22/2014 02:28 PM, Andrzej Ole? wrote:

Hi Herv?,

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 -

may I
instead suggest to use a left/right side bar with text "Bioconductor
developer version (3.0)" written sideways.

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).

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.

While at it, it would be great to have links on the check pages that
quickly takes to the corresponding devel/release versions.

 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

Thxs,

Henrik

Cheers,

H.

Cheers,
Andrzej

On Tue, Jul 22, 2014 at 10:04 PM, Herv? Pag?s <hpages at fhcrc.org> wrote:

Hi Andrzej,


On 07/22/2014 10:14 AM, Andrzej Ole? 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 <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: "Herv? Pag?s" <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, Herv? Pag?s 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

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James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
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--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
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--
Herv? Pag?s

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: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319