[Bioc-devel] BioC 3.1 branch created
Hi Kevin, Thanks, I will try it later and check whether I have still this issue to connect it. Tiphaine From: Kevin Rue-Albrecht <kevin.rue at ucdconnect.ie<mailto:kevin.rue at ucdconnect.ie>> Date: Friday, 17 April 2015 11:30 To: Tiphaine Martin <tiphaine.martin at kcl.ac.uk<mailto:tiphaine.martin at kcl.ac.uk>> Cc: Dan Tenenbaum <dtenenba at fredhutch.org<mailto:dtenenba at fredhutch.org>>, bioc-devel <bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>> 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 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<mailto:tiphaine.martin at kcl.ac.uk>> wrote:
Hi Dan, When I try to access on my package, I have ?Internal Server Error?. 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<mailto:dtenenba at fredhutch.org>> wrote:
----- Original Message -----
From: "Henrik Bengtsson" <henrik.bengtsson at ucsf.edu<mailto:henrik.bengtsson at ucsf.edu>> To: "Dan Tenenbaum" <dtenenba at fredhutch.org<mailto:dtenenba at fredhutch.org>> Cc: "bioc-devel" <bioc-devel at r-project.org<mailto: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<mailto: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:
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:
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
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_______________________________________________ Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- K?vin 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