[Bioc-devel] BioC 3.1 branch created

Dan Tenenbaum dtenenba at fredhutch.org
Fri Apr 17 16:32:19 CEST 2015



----- Original Message -----
> From: "Kevin Rue-Albrecht" <kevin.rue at ucdconnect.ie>
> To: "Tiphaine Martin" <tiphaine.martin at kcl.ac.uk>
> Cc: "Dan Tenenbaum" <dtenenba at fredhutch.org>, "bioc-devel" <bioc-devel at r-project.org>
> Sent: Friday, April 17, 2015 4:30:24 AM
> Subject: Re: [Bioc-devel] BioC 3.1 branch created
> 
> 
> 
> 
> 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 will probably remove the 3.0 bridges as we are not building that version anymore and commits
to that branch are disabled.


>     * 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?
> 


Yes. Delete your 3.0 bridge first.
Dan


> 
> 
> 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
> >> 
> > 
> >_______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> 
> 
> --
> 
> 
> 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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