I just want to add the perspective that I often browse package
documentation & vignettes from the website rather than accessing it from
the R command line. Sometimes it's just easier or more convenient to
view it in a browser. So, when doing this, I sometimes accidentally get
the wrong documentation (devel instead of release or vice versa) and end
up wondering why the vignette isn't working on my system.
So it's just just a problem of downloading the source code.
----- Original Message -----
From: "Andrzej Oleś" <andrzej.o...@gmail.com>
To: "James W. MacDonald" <jmac...@uw.edu>
Cc: "Dan Tenenbaum" <dtene...@fhcrc.org>, "Julian Gehring" <julian.gehr...@embl.de>,
"Michael Lawrence"
<lawrence.mich...@gene.com>, bioc-devel@r-project.org
Sent: Tuesday, July 22, 2014 10:14:05 AM
Subject: Re: [Bioc-devel] Distinction between release and devel package websites
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.
Why would you want to do that? That's the kind of thing that gets people into
trouble.
Anyway, the packages would still be downloadable, and the link location could
be figured out, but I don't think we need to make it easier for people to do
the wrong thing by providing links.
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.
There are also design considerations; I'm not sure a different background color
would look good.
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
These are all great ideas for making the release and devel pages look different
from each other, and maybe we'll consider some of them, but the real problem is
people downloading packages from these pages--and they could run into the same
problems by downloading packages from the release landing page (if, for
example, they are running BioC devel, or some version that's earlier than the
current release).
I don't think any of the measures will be as effective as simply removing the
links and replacing them with instructions on installing the package via
biocLite().
Dan
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
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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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