[Bioc-devel] BioC 3.1 branch created

[Kevin Rue-Albrecht]

Hi Tiphaine,

I have followed both of your links,. and they both work for me. Probably
just a glitch in the connection ?

Hi Dan,

I have a quick question of my own,
I would like to bridge the new release branch to my Github "release"
repository, but:

   - In the dropdown of the bridge creation, release 3.0 is still listed. I
   supposed I should wait that 3.1 is listed there, to create the good bridge?
   - I had a GitHub repository bridged to the 3.0 release branch. Is it ok
   to use the same GitHub repository, and use "SVN wins" during the bridge
   creation? That should update GitHub with the new release code, right?

Many thanks,
Kevin

On 17 April 2015 at 11:43, Martin, Tiphaine <tiphaine.martin at kcl.ac.uk>
wrote:

> Hi Dan,
>
> When I try to access on my package, I have ³Internal Server Error². Maybe
> I make a mistake somewhere.
>
> https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/
> coMET
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/coMET
>
> Regards,
> Tiphaine
>
> On 17/04/2015 05:44, "Dan Tenenbaum" <dtenenba at fredhutch.org> wrote:
>
> >
> >
> >----- Original Message -----
> >> From: "Henrik Bengtsson" <henrik.bengtsson at ucsf.edu>
> >> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> >> Cc: "bioc-devel" <bioc-devel at r-project.org>
> >> Sent: Thursday, April 16, 2015 6:57:45 PM
> >> Subject: Re: [Bioc-devel] BioC 3.1 branch created
> >>
> >> On Thu, Apr 16, 2015 at 1:23 PM, Dan Tenenbaum
> >> <dtenenba at fredhutch.org> wrote:
> >> > The BioC 3.1 branch is now ready.
> >> >
> >> > Remember, you always have access to 2 versions of your package:
> >> > the "release" and the "devel" versions.
> >> >
> >> > Right now the "release" version of your package (which is not
> >> > officially released yet but will be tomorrow if
> >> > everything goes well) is in the 3.1 branch and accessible at:
> >> >
> >> >
> >>
> https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpack
> >>s/<PKGNAME>
> >> >
> >> > Only bug fixes and documentation improvements should go here.
> >> >
> >> > As always the "devel" version of your package is at:
> >> >
> >> >  https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/
> <PKGNAME>
> >> >
> >> > Similarly for experiment packages, where your package is available
> >> > in devel at
> >> >
> >> > https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/<PKGNAME>
> >> >
> >> > The release branch of it is in:
> >> >
> >> >
> >>
> https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_1/experiment/pkgs
> >>/<PKGNAME>
> >> >
> >> >
> >> > Normal development of your package can now resume here.
> >> >
> >> > Please let us know if you have any questions.
> >>
> >> Was the wrong version bump done for the GitHub-SVN bridges, because
> >> the 'bioc-sync' commits show release version numbers and not devel
> >> ones?!
> >>
> >
> >Not the wrong version bump, but it seems like the second one didn't come
> >through.
> >
> >Should be sorted now. Sorry for the inconvenience.
> >
> >Dan
> >
> >
> >
> >> For instance, the aroma.light GitHub repository (master branch),
> >> which
> >> should reflect the Bioc devel version, 'bioc-sync' made a commit
> >> bumping the version from 1.39.5 to 1.40.0.  Note that this version is
> >> the version for the Bioc release - not Bioc devel.  I would expect it
> >> to be a bump to 1.41.0. Details:
> >>
> >>
> >>
> https://github.com/HenrikBengtsson/affxparser/commit/ef10d93df696d018de3e
> >>426bc6c2c1b8256a9b06
> >> (1.40.0)
> >>
> >>
> https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpack
> >>s/affxparser/DESCRIPTION
> >> (1.40.0)
> >>
> >>
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affxparser/DE
> >>SCRIPTION
> >> (1.41.0)
> >>
> >> I've verified that the bridge is still to the Bioc devel SVN
> >> (trunk/madman), because when I tweaked the Date in DESCRIPTION (with
> >> the wrong Version field) and pushed to GitHub, that was reflected on
> >> Bioc devel SVN  (trunk/madman).
> >>
> >> I see the same for aroma.light as well:
> >>
> >>
> >>
> https://github.com/HenrikBengtsson/aroma.light/commit/64b2bbef5b81baebc5d
> >>a548110a0bf1c25d208e2
> >> (2.4.0)
> >>
> >>
> https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpack
> >>s/aroma.light/DESCRIPTION
> >> (2.4.0)
> >>
> >>
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/aroma.light/D
> >>ESCRIPTION
> >> (2.5.0)
> >>
> >> Holding back with pushes via GitHub until I resolved. Let me know if
> >> this is a FAQ.
> >>
> >> Thanks,
> >>
> >> Henrik
> >>
> >> >
> >> >
> >> > Thanks!
> >> >
> >> > Dan
> >> >
> >> > _______________________________________________
> >> > Bioc-devel at r-project.org mailing list
> >> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >
> >_______________________________________________
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>
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>



-- 
Kévin RUE-ALBRECHT
Wellcome Trust Computational Infection Biology PhD Programme
University College Dublin
Ireland
http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en

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