Hi Dan, all
Maybe a silly question, but: where is the R-alpha 3.2.0 ?
So far, I have only pushed to the devel branch (3.1.x), hoping that all my
commits (most recent: 19 Mar) will be integrated into the release version
(3.2.0).
This is only my second release cycle. I remember that the first time,
On 23 March 2015 09:46, Kevin Rue-Albrecht wrote:
> Hi Dan, all
>
> Maybe a silly question, but: where is the R-alpha 3.2.0 ?
>From the r-project.org page, choose 'download R', your local mirror and
'R alpha and beta releases':
Using the Cambridge CRAN mirror
http://mirrors.ebi.ac.uk/CRAN/sr
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
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/
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
Hi Nate,
Thanks a lot for your really quick help, your updated suggestions really
work great! I could not yet take advantage from the new version of
VariantAnnotation, since the changes have not been propagated to the
package archive. It seems that currently many packages are broken,
especial
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
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
.../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 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
> 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
> 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 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
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,
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 03/23/2015 09:55 AM, Gabe Becker wrote:>> >Thus it is more likely that a
person will do the right thing if it happens
>> >to be the most convenient thing IMHO. Anything to advance this strategy
>> >would be a step in the right direction
>> >
> Bioc core team: This may be getting a bit off topi
Martin,
On Mon, Mar 23, 2015 at 11:28 AM, Martin Morgan
wrote:
> On 03/23/2015 09:55 AM, Gabe Becker wrote:>> >Thus it is more likely that
> a person will do the right thing if it happens
> >> >to be the most convenient thing IMHO. Anything to advance this strategy
> >> >would be a step in the
Hi all,
I'm pleased to announce the availability of the coMET package
(http://bioconductor.org/packages/devel/bioc/html/coMET.html ,
https://github.com/TiphaineCMartin/coMET), which visualises regional
epigenome-wide association scan (EWAS) results and DNA co-methylation patterns.
The R packag
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