Re: [Bioc-devel] BioC 3.1 branch created
On Apr 16, 2015 9:44 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Henrik Bengtsson henrik.bengts...@ucsf.edu To: Dan Tenenbaum dtene...@fredhutch.org Cc: bioc-devel bioc-devel@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 dtene...@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/Rpacks/ 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. Confirmed. And no worries. Thanks for your great work. Henrik 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/ef10d93df696d018de3e426bc6c2c1b8256a9b06 (1.40.0) https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/affxparser/DESCRIPTION (1.40.0) https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affxparser/DESCRIPTION (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/64b2bbef5b81baebc5da548110a0bf1c25d208e2 (2.4.0) https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/aroma.light/DESCRIPTION (2.4.0) https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/aroma.light/DESCRIPTION (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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [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@ucdconnect.iemailto:kevin@ucdconnect.ie Date: Friday, 17 April 2015 11:30 To: Tiphaine Martin tiphaine.mar...@kcl.ac.ukmailto:tiphaine.mar...@kcl.ac.uk Cc: Dan Tenenbaum dtene...@fredhutch.orgmailto:dtene...@fredhutch.org, bioc-devel bioc-devel@r-project.orgmailto:bioc-devel@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.mar...@kcl.ac.ukmailto:tiphaine.mar...@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 dtene...@fredhutch.orgmailto:dtene...@fredhutch.org wrote: - Original Message - From: Henrik Bengtsson henrik.bengts...@ucsf.edumailto:henrik.bengts...@ucsf.edu To: Dan Tenenbaum dtene...@fredhutch.orgmailto:dtene...@fredhutch.org Cc: bioc-devel bioc-devel@r-project.orgmailto:bioc-devel@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 dtene...@fredhutch.orgmailto:dtene...@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@r-project.orgmailto:Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.orgmailto:Bioc-devel@r-project.org
Re: [Bioc-devel] BioC 3.1 branch created
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 dtene...@fredhutch.org wrote: - Original Message - From: Henrik Bengtsson henrik.bengts...@ucsf.edu To: Dan Tenenbaum dtene...@fredhutch.org Cc: bioc-devel bioc-devel@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 dtene...@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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BioC 3.1 branch created
- Original Message - From: Kevin Rue-Albrecht kevin@ucdconnect.ie To: Tiphaine Martin tiphaine.mar...@kcl.ac.uk Cc: Dan Tenenbaum dtene...@fredhutch.org, bioc-devel bioc-devel@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.mar...@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 dtene...@fredhutch.org wrote: - Original Message - From: Henrik Bengtsson henrik.bengts...@ucsf.edu To: Dan Tenenbaum dtene...@fredhutch.org Cc: bioc-devel bioc-devel@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 dtene...@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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc
Re: [Bioc-devel] BioC 3.1 branch created
- Original Message - From: Henrik Bengtsson henrik.bengts...@ucsf.edu To: Dan Tenenbaum dtene...@fredhutch.org Cc: bioc-devel bioc-devel@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 dtene...@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/Rpacks/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/ef10d93df696d018de3e426bc6c2c1b8256a9b06 (1.40.0) https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/affxparser/DESCRIPTION (1.40.0) https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affxparser/DESCRIPTION (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/64b2bbef5b81baebc5da548110a0bf1c25d208e2 (2.4.0) https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/aroma.light/DESCRIPTION (2.4.0) https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/aroma.light/DESCRIPTION (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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BioC 3.1 branch created
On Thu, Apr 16, 2015 at 1:23 PM, Dan Tenenbaum dtene...@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/Rpacks/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?! 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/ef10d93df696d018de3e426bc6c2c1b8256a9b06 (1.40.0) https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/affxparser/DESCRIPTION (1.40.0) https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affxparser/DESCRIPTION (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/64b2bbef5b81baebc5da548110a0bf1c25d208e2 (2.4.0) https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/aroma.light/DESCRIPTION (2.4.0) https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/aroma.light/DESCRIPTION (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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
