[Bioc-devel] development vs release version

[Laurent Gatto]

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/src/base-prerelease/

Or, closer to you

  http://ftp.heanet.ie/mirrors/cran.r-project.org/

> 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,
> bioc-sync
> <https://github.com/kevinrue/GOexpress/commits/master?author=bioc-sync>
> updated the release number, but I haven't seen that happen yet in either
> the release or the devel branches.

That will be done by the Bioc team as part of the release. 

> Is there any other place I should think of committing/pushing changes if I
> spot a typo/bug in the next few days?

Keep on committing your changes to the svn server (directly or via the
git-svn bridge), and you'll be fine.

Best wishes,

Laurent

> Thanks a million !
> Kevin
>
>
> On 22 March 2015 at 18:57, Dan Tenenbaum <dtenenba at fredhutch.org> wrote:
>
>>
>>
>> ----- Original Message -----
>> > From: "Vincent Carey" <stvjc at channing.harvard.edu>
>> > To: "Eric Frichot" <eric.frichot at gmail.com>
>> > Cc: bioc-devel at r-project.org
>> > Sent: Sunday, March 22, 2015 11:42:52 AM
>> > Subject: Re: [Bioc-devel] development vs release version
>> >
>> > On Sun, Mar 22, 2015 at 2:27 PM, Eric Frichot
>> > <eric.frichot at gmail.com>
>> > wrote:
>> >
>> > > Ok. Thanks for your help. It worked with the r-devel
>> > >
>> > > I assume that my package will be available with the current version
>> > > of R
>> > > after the next bioconductor release ?
>> > >
>> > >
>> > The next Bioconductor release will follow on the transition of
>> > R-release/R-patched to
>> > the 3.2.x series.
>> >
>> >
>> > > If I add a new version for my package, after the release, people
>> > > will also
>> > > have to install the r-devel to access this new version ?
>> > >
>> > >
>> > The current R-devel, 3.2.x, will be the released version in a couple
>> > of
>> > weeks.
>>
>>
>> Actually, R-devel is currently version 3.3.0. You should not use this
>> version, instead you should use what's currently R-alpha (3.2.0).
>>
>>
>> > That is
>> > what folks will have to use to get your package in the release
>> > version.
>> > Those using
>> > R-devel later on can get the devel version of your package as it
>> > evolves.
>> >
>> > Some relevant concepts are at
>> >
>> > http://master.bioconductor.org/developers/how-to/version-numbering/
>> >
>> > but ... there is likely a more transparent discussion of the
>> > release/devel
>> > distinctions
>> > somewhere that I am not finding currently.  If questions remain
>> > please let
>> > us know.
>> >
>>
>> It's discussed a bit at
>> http://bioconductor.org/developers/how-to/source-control/ under "where to
>> commit.
>>
>> See also http://bioconductor.org/developers/package-submission/#acceptance
>> .
>>
>> Dan
>>
>>
>>
>> >
>> > > Thanks,
>> > >
>> > > Eric Frichot
>> > >
>> > >
>> > > On Sun, Mar 22, 2015 at 7:01 PM Vincent Carey
>> > > <stvjc at channing.harvard.edu>
>> > > wrote:
>> > >
>> > >> The message means that you should use R-devel to get your package.
>> > >> R 3.1.3 is currently regarded as R-patched.
>> > >>
>> > >> On Sun, Mar 22, 2015 at 1:44 PM, Eric Frichot
>> > >> <eric.frichot at gmail.com>
>> > >> wrote:
>> > >>
>> > >>> Hi everyone,
>> > >>>
>> > >>> I am new in the bioconductor community. I just finished the
>> > >>> bioconductor
>> > >>> review of my package called LEA. By the way, all your feedbacks
>> > >>> are more
>> > >>> than welcome about it.
>> > >>>
>> > >>> I am not sure to understand how the release of a new version
>> > >>> works in
>> > >>> bioconductor. I have few questions you may help me with.
>> > >>>
>> > >>> I just downloaded my package through bioconductor. So, it is
>> > >>> under
>> > >>> development. I tried to install my package using biocLite
>> > >>> function. I got
>> > >>> the error message
>> > >>>
>> > >>> package ‘LEA’ is not available (for R version 3.1.3)
>> > >>>
>> > >>> Does it mean that I have to wait the next bioconductor release ?
>> > >>>
>> > >>> If it is the case, imagine that I add new features for my
>> > >>> package, do I
>> > >>> have to wait the next release (every 6 month) for these features
>> > >>> to be
>> > >>> available ?
>> > >>>
>> > >>> Thanks a lot for your help,
>> > >>>
>> > >>> Eric Frichot
>> > >>>
>> > >>>         [[alternative HTML version deleted]]
>> > >>>
>> > >>> _______________________________________________
>> > >>> Bioc-devel at r-project.org mailing list
>> > >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> > >>>
>> > >>
>> > >>
>> >
>> >       [[alternative HTML version deleted]]
>> >
>> > _______________________________________________
>> > Bioc-devel at r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>>
>> _______________________________________________
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>>

-- 
Laurent Gatto
http://cpu.sysbiol.cam.ac.uk/