, "Martin
> > Morgan"
> > 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
- Original Message -
> From: "Vincent Carey"
> To: "Dan Tenenbaum"
> Cc: "Tim Triche, Jr." , bioc-devel@r-project.org, "Gabe
> Becker" , "Martin
> Morgan"
> Sent: Wednesday, August 5, 2015 6:09:02 PM
> Subject: Re
che, Jr." , bioc-devel@r-project.org,
> "Gabe Becker" , "Martin
> > Morgan"
> > Sent: Tuesday, July 7, 2015 1:12:26 PM
> > Subject: Re: [Bioc-devel] Short URLs for packages?
> >
> >
> > OK, thanks. Should we add a little bit to
- Original Message -
> From: "Vincent Carey"
> To: "Dan Tenenbaum"
> Cc: "Tim Triche, Jr." , bioc-devel@r-project.org, "Gabe
> Becker" , "Martin
> Morgan"
> Sent: Tuesday, July 7, 2015 1:12:26 PM
> Subject: Re: [B
Tim Triche, Jr." , bioc-devel@r-project.org,
> "Gabe Becker"
> > 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:
- Original Message -
> From: "Vincent Carey"
> To: "Martin Morgan"
> Cc: "Tim Triche, Jr." , bioc-devel@r-project.org, "Gabe
> Becker"
> Sent: Tuesday, July 7, 2015 12:49:24 PM
> Subject: Re: [Bioc-devel] Short URLs for
Has there been a solution to the short URL question?
On Tue, Mar 24, 2015 at 7:14 AM, Martin Morgan
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 URLs to people?
>>
Thanks Dan.
robert.
On 04/30/2015 05:34 PM, Dan Tenenbaum wrote:
- Original Message -
From: "Robert Castelo"
To: "Dan Tenenbaum"
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,
- Original Message -
> From: "Robert Castelo"
> To: "Dan Tenenbaum"
> 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 th
e page starting with 'www' or 'master'.
cheers,
robert.
On 04/28/2015 08:08 PM, Dan Tenenbaum wrote:
- Original Message -
From: "Wolfgang Huber" To:
bioc-devel@r-project.org Sent: Monday, March 23, 2015 3:17:03 AM
Subject: [Bioc-devel] Short URLs for
- Original Message -
> From: "Steve Lianoglou"
> To: "Dan Tenenbaum"
> Cc: "Wolfgang Huber" , bioc-devel@r-project.org
> Sent: Tuesday, April 28, 2015 3:57:25 PM
> Subject: Re: [Bioc-devel] Short URLs for packages?
>
> Awe
, Dan Tenenbaum wrote:
>
>
> - Original Message -
>> From: "Wolfgang Huber"
>> 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 p
- Original Message -
> From: "Wolfgang Huber"
> 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
> like
>
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" b
There are still problems with completely reproducing old analyses partly
due to our (current) inability to reproduce an exact version (as Martin
says).
But I don't think we should muddle the waters and mix URL schemas with
versioning.
What Wolfgang is asking for is something I think makes total s
On Tue, Mar 24, 2015 at 7:28 AM, Wolfgang Huber 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 (version
> 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 (version) of the thread.
But we already have dynamic resolution. Eve
#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
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)
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 arti
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,
http://www.bioconductor.org/packages/3.0/limma
On Mon, Mar 23, 2015 at 9:25 AM, Tim Triche, Jr.
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, as a
> project,
On March 23, 2015 9:18:57 AM PDT, "Tim Triche, Jr."
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 the existing
> 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.
> 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 ex
On Mon, Mar 23, 2015 at 9:00 AM, Tim Triche, Jr.
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.
>
It makes finding w
.../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
alw
On Mon, Mar 23, 2015 at 8:05 AM, Fischer, Bernd <
b.fisc...@dkfz-heidelberg.de> wrote:
>
> 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 the first
> release, the
> link (e.g. www.bioconductor.org/) s
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
Just so we don't lose the thoughts that have come before, here is a link to
a similar proposal from last year.
https://stat.ethz.ch/pipermail/bioc-devel/2014-February/005292.html
Sean
On Mon, Mar 23, 2015 at 6:17 AM, Wolfgang Huber wrote:
> I wonder whether it’d possible to have the website
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/
>
> This could resolve to
> http://www.bioconductor.org/packages/release/bioc/html/.html
> or
> http://www.bioconductor.org/packages/devel/
I wonder whether it’d possible to have the website understand URLs like
http://www.bioconductor.org/
This could resolve to
http://www.bioconductor.org/packages/release/bioc/html/.html
or
http://www.bioconductor.org/packages/devel/bioc/html/.html
depending on whether the package was yet re
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