:02 PM
Subject: Re: [Bioc-devel] Short URLs for packages?
It seems that the short URLs on devel landing pages refer to release
pages. Intended?
Yes. If you mouse over the short url it says:
Canonical url for use in publications, etc., will always redirect to current
release version
becker.g...@gene.com, Martin
Morgan mtmor...@fredhutch.org
Sent: Wednesday, August 5, 2015 6:09:02 PM
Subject: Re: [Bioc-devel] Short URLs for packages?
It seems that the short URLs on devel landing pages refer to release
pages. Intended?
Yes. If you mouse over the short url it says
Subject: Re: [Bioc-devel] Short URLs for packages?
OK, thanks. Should we add a little bit to each package landing page
indicating how to link?
Done. For example go to
http://bioconductor.org/packages/release/bioc/html/a4.html and scroll to the
bottom, the short url appears just before
Has there been a solution to the short URL question?
On Tue, Mar 24, 2015 at 7:14 AM, Martin Morgan mtmor...@fredhutch.org
wrote:
On 03/24/2015 02:31 AM, Wolfgang Huber wrote:
Before we start a religious war, can we make progress on the pragmatic
goal of making it possible to provide such
Cc: Tim Triche, Jr. ttri...@usc.edu, bioc-devel@r-project.org,
Gabe Becker becker.g...@gene.com
Sent: Tuesday, July 7, 2015 12:49:24 PM
Subject: Re: [Bioc-devel] Short URLs for packages?
Has there been a solution to the short URL question?
Yes: https://stat.ethz.ch/pipermail/bioc-devel
- Original Message -
From: Vincent Carey st...@channing.harvard.edu
To: Martin Morgan mtmor...@fredhutch.org
Cc: Tim Triche, Jr. ttri...@usc.edu, bioc-devel@r-project.org, Gabe
Becker becker.g...@gene.com
Sent: Tuesday, July 7, 2015 12:49:24 PM
Subject: Re: [Bioc-devel] Short URLs
- Original Message -
From: Robert Castelo robert.cast...@upf.edu
To: Dan Tenenbaum dtene...@fredhutch.org
Cc: bioc-devel@r-project.org
Sent: Thursday, April 30, 2015 12:57:36 AM
Subject: Re: [Bioc-devel] Short URLs for packages?
hi Dan,
one question about this, just to know
Tenenbaum dtene...@fredhutch.org wrote:
- Original Message -
From: Wolfgang Huber whu...@embl.de
To: bioc-devel@r-project.org
Sent: Monday, March 23, 2015 3:17:03 AM
Subject: [Bioc-devel] Short URLs for packages?
I wonder whether it'd possible to have the website understand URLs
- Original Message -
From: Steve Lianoglou lianoglou.st...@gene.com
To: Dan Tenenbaum dtene...@fredhutch.org
Cc: Wolfgang Huber whu...@embl.de, bioc-devel@r-project.org
Sent: Tuesday, April 28, 2015 3:57:25 PM
Subject: Re: [Bioc-devel] Short URLs for packages?
Awesome, thank you
#5 is what I was thinking of when I responded. A simple RewriteRule, if anyone
still uses Apache.
Release vs devel and/or 3.0 vs 3.1 vs 3.2, e.g.
http://bioconductor.org/release/BiocGenerics/
Pointing analogously to
http://bioconductor.org/3.0/BiocGenerics/
seems like a good minimal
Before we start a religious war, can we make progress on the pragmatic goal of
making it possible to provide such URLs to people?
There are two concepts
- ‘the package' - a specific version, running in a specific environment,
‘frozen’, etc. (Gabe)
- ‘the package’ - as a concept and a living
On 03/24/2015 02:31 AM, Wolfgang Huber wrote:
Before we start a religious war, can we make progress on the pragmatic goal of
making it possible to provide such URLs to people?
There are two concepts
- ‘the package' - a specific version, running in a specific environment,
‘frozen’, etc. (Gabe)
On Tue, Mar 24, 2015 at 7:28 AM, Wolfgang Huber whu...@embl.de wrote:
5. At the end of the day I find myself casting my lot for landing pages
with the form
http://bioconductor.org/release/BiocGenerics/
which leads to a little less typing but not the dynamic resolution that
started this
I just think there are a couple of subtleties here. I certainly don't
begrudge people wanting to type less and find packages easier. But if a
naive user with a default (read: release) Bioc installation goes to
http://bioconductor.org/CoolAwesomePkg and see's that it is available in
bioconductor
The cited htaccess rule just links the release version of the package. Since
this would already be an improvement, it is not sufficient for links in papers.
During the production process of the paper we want to link to the accompanying
BioC package that is in devel, but not yet in release. Before
.../release/... silently changes every six months or so, as does .../devel/...,
so I don't see how this changes anything beyond that. It does make finding the
packages a lot easier in general, and more mnemonic.
If you want to document the versions of packages used in an analysis, there's
I guess my problem is that there is even an if at the beginning of that
sentence. That's not an attack on you, I know that the above reflects the
current state of affairs, I'm simply saying that perhaps Bioconductor, as a
project, can help/encourage people to do better.
Quite true.
On Mon, Mar 23, 2015 at 9:00 AM, Tim Triche, Jr. tim.tri...@gmail.com
wrote:
.../release/... silently changes every six months or so, as does
.../devel/..., so I don't see how this changes anything beyond that. It
does make finding the
packages a lot easier in general, and more mnemonic.
On 23 March 2015 10:17, Wolfgang Huber wrote:
I wonder whether it’d possible to have the website understand URLs like
http://www.bioconductor.org/pkgname
This could resolve to
http://www.bioconductor.org/packages/release/bioc/html/pkgname.html
or
I wonder whether it’d possible to have the website understand URLs like
http://www.bioconductor.org/pkgname
This could resolve to
http://www.bioconductor.org/packages/release/bioc/html/pkgname.html
or
http://www.bioconductor.org/packages/devel/bioc/html/pkgname.html
depending on whether
Packages are (read: should be, IMHO) published, citable pieces of research,
though. Imagine if a paper you cite were silently updated without the
doi/citation changing. That wouldn't be good
I don't disagree, but the existing setup does nothing to address that.
Citation('limma'), for
On March 23, 2015 9:18:57 AM PDT, Tim Triche, Jr. tim.tri...@gmail.com
wrote:
Packages are (read: should be, IMHO) published, citable pieces of
research, though. Imagine if a paper you cite were silently updated
without the doi/citation changing. That wouldn't be good
I don't disagree, but
On Mon, Mar 23, 2015 at 9:25 AM, Tim Triche, Jr. tim.tri...@gmail.com
wrote:
I guess my problem is that there is even an if at the beginning of that
sentence. That's not an attack on you, I know that the above reflects the
current state of affairs, I'm simply saying that perhaps Bioconductor,
I just meant that the mnemonic link
http://www.bioconductor.org/limma/ (SEO version of limma ;-))
could dump people at something like
http://www.bioconductor.org/release/limma/3.22.7/ (I'd prefer this)
or if need be for backwards compatibility,
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