[Bioc-devel] git help
Nitesh, ? I have re-cloned it, everything looks good. Thanks for your help. Can you please make sure that the duplicate commit check has been re-enabled for this repo? It was previously disabled. Kevin
On 01/09/2018 10:03 AM, Turaga, Nitesh wrote:
Hi Kevin, Your repository should now be fixed. Please re-clone your repository. Best, Nitesh
On Jan 8, 2018, at 8:39 PM, Kevin Horan <khoran at cs.ucr.edu> wrote:
Nitesh,
Sorry, just saw your email now. You can go ahead and make those changes. Thanks for all your help.
Kevin
On 01/07/2018 11:22 AM, Turaga, Nitesh wrote:
Hi Kevin, One last message, give me a green light to fix your repository once you have had a chance to see my emails. Best, Nitesh
On Jan 7, 2018, at 2:17 PM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:
Now your version numbers don?t match. You skip versions without those commits
Your history is supposed to look like this,
commit 5a1ad6ff08747d1380875840fe96d3633c210ee2 (HEAD -> master)
Author: khoran <khoran at cs.ucr.edu>
Date: Sun Jan 7 09:44:16 2018 -0800
History was rolled back 6 months to remove dup commits.
All changes since then are being re-applied in this one commit.
commit fb7c8ed13eb09527038e1959737d556a15667771
Author: Herv? Pag?s <hpages at fredhutch.org>
Date: Mon Oct 30 12:52:08 2017 -0400
bump x.y.z versions to odd y after creation of RELEASE_3_6 branch
commit 73c4cb1d48d9f14598e63a28a9b9184e096f254e
Author: Herv? Pag?s <hpages at fredhutch.org>
Date: Mon Oct 30 12:39:24 2017 -0400
bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch
commit e3a8d2122a65305c478276e538faace277ea9ed6
Author: Kevin Horan <khoran at cs.ucr.edu>
Date: Fri Jun 30 20:12:52 2017 +0000
Merge branch 'master' into devel
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChemmineR at 130816 bc3139a8-67e5-0310-9ffc-ced21a209358
##########################
Same for the RELEASE branch.
##########################
commit 7111f07cc9c32977f1eca63a0f2a25cb1092f7be (HEAD -> RELEASE_3_6)
Author: khoran <khoran at cs.ucr.edu>
Date: Sun Jan 7 10:14:49 2018 -0800
set version for release branch
commit a2615e98aff83130f6129abc02132a65d99689b9
Author: Herv? Pag?s <hpages at fredhutch.org>
Date: Mon Oct 30 12:39:24 2017 -0400
bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch
commit e3a8d2122a65305c478276e538faace277ea9ed6
Author: Kevin Horan <khoran at cs.ucr.edu>
Date: Fri Jun 30 20:12:52 2017 +0000
Merge branch 'master' into devel
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChemmineR at 130816 bc3139a8-67e5-0310-9ffc-ced21a209358
I can make your commit history look like this, but I?m not sure if all the changes in your code are reflected accurately. You might have to make sure manually, and see if your code and package work like you expect.
Once they work as expected, please don?t do anything with the commit history. Just add the new changes on top of what exists. It becomes extremely complicated and time taking to fix the commit history manually.
Best,
Nitesh
On Jan 7, 2018, at 1:32 PM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote: Hi Kevin, It seems you have lost a few commits which are important in tracking RELEASE?s in Bioconductor. commit fb5868c2fdfa607b52e467881212b3619a8b0ae9 (HEAD -> master) Author: Herv? Pag?s <hpages at fredhutch.org> Date: Mon Oct 30 12:52:08 2017 -0400 bump x.y.z versions to odd y after creation of RELEASE_3_6 branch commit 46e0a56d1117cca6274fea3b8430eb8d6c7a9976 (RELEASE_3_6) Author: Herv? Pag?s <hpages at fredhutch.org> Date: Mon Oct 30 12:39:24 2017 -0400 bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch These commits are important. Please wait for further instructions while we figure out how to resolve this issue. Best, Nitesh
On Jan 7, 2018, at 1:20 PM, Kevin Horan <khoran at cs.ucr.edu> wrote: Nitesh, I have pushed changes to both the master and RELEASE_3_6 branches now. Kevin On 01/05/2018 11:14 AM, Turaga, Nitesh wrote:
Hi Kevin, Please overlay the commits so that we can get your package building on our build machines. Please do this soon. You also have to make RELEASE_3_6 branch now. We have skipped your package for now, and it won?t show up in the release report. Thanks Nitesh
On Jan 4, 2018, at 10:07 AM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote: Hi Kevin, I have your package reset to this commit e3a8d2122a65305c478276e538faace277ea9ed6. Please check. You will need to overlay all the commits including the new release on top of this (RELEASE_3_6). If you have any questions further on this, please ask before pushing to Bioconductor. Best, Nitesh
On Jan 3, 2018, at 7:10 PM, Kevin Horan <khoran at cs.ucr.edu> wrote: Nitesh, That sounds great, thanks. Kevin On 01/03/2018 01:53 PM, Turaga, Nitesh wrote:
Hi Kevin, I can help you with this. I can take you back to a state before August 18th and put that repository up on our Git server. From that point onwards you?d have to reapply all the changes on that repository from "commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389" and onwards. commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389 Merge: 643e470 f1785fb Author: tgirke <tgirke at citrus.ucr.edu> Date: Sat Aug 19 16:32:35 2017 -0700 resolved conflicts I can do this tomorrow and send you an email. Best, Nitesh
On Jan 3, 2018, at 4:28 PM, Kevin Horan <khoran at cs.ucr.edu> wrote: Nitesh, I tried to re-construct the repo starting from what is left in the SVN repository, but I couldn't get all the branches to come over and it just generally looks too different to easily replace the bioc repo. I was thinking though, if its easy for you to clobber the current bioc repo for ChemmineR and re-create it from the old SVN repo (ie, because you might have scripts from having done it the first time), then that might be an easier fix. Then I can check it out, apply the recent changes and push it back. But if you don't think that's a good idea, then I'll take your offer of help and we can try to figure out how to get rid of the duplicate commits. Thanks. Kevin On 01/03/2018 11:55 AM, Turaga, Nitesh wrote:
Hi Kevin, I?ll try to help you. I?ll take a look at your package and get back to you. Please forward this message to bioc-devel so that it?s public and other maintainers/users know that there is an issue with your package. Best, Nitesh
On Jan 3, 2018, at 2:31 PM, Kevin Horan <khoran at globalrecordings.net> wrote: Nitesh, I am one of the maintainers for the ChemmineR package on bioconductor. I have a bad duplicate commit problem I was wondering if you could help me with. Basically, it seems one string of 1000 or so commits has been duplicated twice in the repository, so that there are now 3 copies of each of these commits. This mess is already in the bioconductor repository because in order to allow me to get some last minute changes in for the last release, someone at boic disabled the duplicate commit check for me. That was before I understood the extend of the problem. I'm not sure if its really your job to help with this sort of thing, as I understand that it's not a bioconductor problem. So if not that is fine. I've spent 6 hours trying to fix it myself ( and I am generally good with GIT), but I've only succeeded in make more duplicates. So I think I'd need to toss all the history up to the last release, which I image I'd need your help to reset the repo on the bioc side as well. If you can help, there are more specifics I can give you, just let me know. Thanks. Kevin Horan
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