Re: [Bioc-devel] "Error: duplicate commits" when pushing FamAgg to Bioconductor git

[Rainer Johannes]

Thanks Nitesh for your quick reply!

> On 13 Feb 2018, at 16:47, Turaga, Nitesh  
> wrote:
> 
> Hi,
> 
> It seems that there are multiple levels of duplication on your repository. 
> 
> You seem to have issued the “merge” with not the current bioconductor devel 
> but the (now deprecated) GitHub- bioconductor mirror, multiple times. Please 
> correct me if this is not accurate. I’m wondering why the merge was issued so 
> many times? 
> 

could be that I pushed several time (wasn't aware of that) - eventually I was 
just puzzled that it didn't resolve the problem so I tried again...

> As far as the fix goes, it would take me a while to track down the “merge” 
> commits and then “cherry-pick" on to the master branch the commits that are 
> not duplicated. These seem to be stemming right from the beginning of your 
> development history. 
> 
> The steps you need are:
> 
> 1. Back up master branch (git branch master_backup)
> 2. Check merge commit SHA’s (git log --oneline maste)
> 3. Reset to commit before the merge, (git reset --hard )
> 4. Then, overlay commits on top that reset, with latest non-duplicated 
> commits (git cherry-pick )
> 
> You’d have to repeat these steps quite extensively depending on how many 
> merges you have.
> 
> Take a look at this manual as further help to do this, 
> http://sethrobertson.github.io/GitFixUm/fixup.html. 
> 
> Do these steps on your local repository and push to Github. Once you have 
> done that, let me know and I’ll take a look at your Github repo, and sync 
> with Bioconductor if history looks clean.
> 
> If you are unable to fix the repo, then the best way forward it to remove the 
> pre-receive hook from your repository and deal with the history as is. This 
> will not effect your package in anyway, just that the git history won’t be 
> clean. 
> 

honestly - I'm afraid my git-knowledge isn't good enough so that I can fix the 
duplicated commits (I think they still derive from the git git-svn setup). I 
could live with the git history not being clean. So, from my side, you could go 
ahead and remove the pre-receive hook.

funnily, I have also duplicated commits in ensembldb, but there I'm still able 
to push to Bioconductor git without problems.

best, jo

> 
> Best,
> 
> Nitesh 
> 
> 
>> On Feb 12, 2018, at 5:41 AM, Rainer Johannes  
>> wrote:
>> 
>> Dear all,
>> 
>> I'm unable to push my recent changes to FamAgg to the Bioconductor git repo 
>> (see below for the error message). I did try the suggested fix but without 
>> any success - seems the duplicated commits are in Bioconductor and not 
>> github.
>> 
>> thankful for any help or advise
>> 
>> The error message is:
>> 
>> macbookjo:FamAgg jo$ git push origin master
>> Everything up-to-date
>> macbookjo:FamAgg jo$ git push upstream master
>> Counting objects: 13, done.
>> Delta compression using up to 8 threads.
>> Compressing objects: 100% (13/13), done.
>> Writing objects: 100% (13/13), 2.17 KiB | 2.17 MiB/s, done.
>> Total 13 (delta 11), reused 0 (delta 0)
>> remote: Error: duplicate commits.
>> remote: 
>> remote: There are duplicate commits in your commit history, These cannot be
>> remote: pushed to the Bioconductor git server. Please make sure that this is
>> remote: resolved.
>> remote: 
>> remote: Take a look at the documentation to fix this,
>> remote: 
>> https://bioconductor.org/developers/how-to/git/sync-existing-repositories/,
>> remote: particularly, point #8 (force Bioconductor master to Github master).
>> remote: 
>> remote: For more information, or help resolving this issue, contact
>> remote: . Provide the error, the package name and
>> remote: any other details we might need.
>> remote: 
>> remote: Use
>> remote: 
>> remote: git show 397d05e8ba7d301a9145573210c277f1c6dd66a5
>> remote: git show 6a0c683477b78e231a7eb1b59171baa0bc582ef2
>> remote: 
>> remote: to see body of commits.
>> remote: 
>> To git.bioconductor.org:packages/FamAgg
>> ! [remote rejected] master -> master (pre-receive hook declined)
>> error: failed to push some refs to 
>> 'g...@git.bioconductor.org:packages/FamAgg'
>> 
>> 
>> macbookjo:FamAgg jo$ git show 397d05e8ba7d301a9145573210c277f1c6dd66a5
>> commit 397d05e8ba7d301a9145573210c277f1c6dd66a5
>> Author: Herve Pages 
>> Date:   Mon Apr 24 19:50:57 2017 +
>> 
>>   bump x.y.z versions to odd y after creation of 3_5 branch
>> 
>>   git-svn-id: 
>> file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/FamAgg@129129
>>  bc3139a8-67e5-0310-9ffc-ced21a209358
>> 
>> diff --git a/DESCRIPTION b/DESCRIPTION
>> index c9cb1b7..948b777 100644
>> --- a/DESCRIPTION
>> +++ b/DESCRIPTION
>> @@ -1,7 +1,7 @@
>> Package: FamAgg
>> Type: Package
>> Title: Pedigree Analysis and Familial Aggregation
>> -Version: 1.4.0
>> +Version: 1.5.0
>> Author: J. Rainer, D. Taliun, C.X. Weichenberger
>> Maintainer: Johannes Rainer 
>> URL: 

Re: [Bioc-devel] "Error: duplicate commits" when pushing FamAgg to Bioconductor git

[Turaga, Nitesh]

Hi,

It seems that there are multiple levels of duplication on your repository. 

You seem to have issued the “merge” with not the current bioconductor devel but 
the (now deprecated) GitHub- bioconductor mirror, multiple times. Please 
correct me if this is not accurate. I’m wondering why the merge was issued so 
many times? 

As far as the fix goes, it would take me a while to track down the “merge” 
commits and then “cherry-pick" on to the master branch the commits that are not 
duplicated. These seem to be stemming right from the beginning of your 
development history. 

The steps you need are:

1. Back up master branch (git branch master_backup)
2. Check merge commit SHA’s (git log --oneline maste)
3. Reset to commit before the merge, (git reset --hard )
4. Then, overlay commits on top that reset, with latest non-duplicated commits 
(git cherry-pick )

You’d have to repeat these steps quite extensively depending on how many merges 
you have.

Take a look at this manual as further help to do this, 
http://sethrobertson.github.io/GitFixUm/fixup.html. 

Do these steps on your local repository and push to Github. Once you have done 
that, let me know and I’ll take a look at your Github repo, and sync with 
Bioconductor if history looks clean.

If you are unable to fix the repo, then the best way forward it to remove the 
pre-receive hook from your repository and deal with the history as is. This 
will not effect your package in anyway, just that the git history won’t be 
clean. 


Best,

Nitesh 


> On Feb 12, 2018, at 5:41 AM, Rainer Johannes  
> wrote:
> 
> Dear all,
> 
> I'm unable to push my recent changes to FamAgg to the Bioconductor git repo 
> (see below for the error message). I did try the suggested fix but without 
> any success - seems the duplicated commits are in Bioconductor and not github.
> 
> thankful for any help or advise
> 
> The error message is:
> 
> macbookjo:FamAgg jo$ git push origin master
> Everything up-to-date
> macbookjo:FamAgg jo$ git push upstream master
> Counting objects: 13, done.
> Delta compression using up to 8 threads.
> Compressing objects: 100% (13/13), done.
> Writing objects: 100% (13/13), 2.17 KiB | 2.17 MiB/s, done.
> Total 13 (delta 11), reused 0 (delta 0)
> remote: Error: duplicate commits.
> remote: 
> remote: There are duplicate commits in your commit history, These cannot be
> remote: pushed to the Bioconductor git server. Please make sure that this is
> remote: resolved.
> remote: 
> remote: Take a look at the documentation to fix this,
> remote: 
> https://bioconductor.org/developers/how-to/git/sync-existing-repositories/,
> remote: particularly, point #8 (force Bioconductor master to Github master).
> remote: 
> remote: For more information, or help resolving this issue, contact
> remote: . Provide the error, the package name and
> remote: any other details we might need.
> remote: 
> remote: Use
> remote: 
> remote: git show 397d05e8ba7d301a9145573210c277f1c6dd66a5
> remote: git show 6a0c683477b78e231a7eb1b59171baa0bc582ef2
> remote: 
> remote: to see body of commits.
> remote: 
> To git.bioconductor.org:packages/FamAgg
> ! [remote rejected] master -> master (pre-receive hook declined)
> error: failed to push some refs to 'g...@git.bioconductor.org:packages/FamAgg'
> 
> 
> macbookjo:FamAgg jo$ git show 397d05e8ba7d301a9145573210c277f1c6dd66a5
> commit 397d05e8ba7d301a9145573210c277f1c6dd66a5
> Author: Herve Pages 
> Date:   Mon Apr 24 19:50:57 2017 +
> 
>bump x.y.z versions to odd y after creation of 3_5 branch
> 
>git-svn-id: 
> file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/FamAgg@129129
>  bc3139a8-67e5-0310-9ffc-ced21a209358
> 
> diff --git a/DESCRIPTION b/DESCRIPTION
> index c9cb1b7..948b777 100644
> --- a/DESCRIPTION
> +++ b/DESCRIPTION
> @@ -1,7 +1,7 @@
> Package: FamAgg
> Type: Package
> Title: Pedigree Analysis and Familial Aggregation
> -Version: 1.4.0
> +Version: 1.5.0
> Author: J. Rainer, D. Taliun, C.X. Weichenberger
> Maintainer: Johannes Rainer 
> URL: https://github.com/jotsetung/FamAgg
> 
> macbookjo:FamAgg jo$ git show 6a0c683477b78e231a7eb1b59171baa0bc582ef2
> commit 6a0c683477b78e231a7eb1b59171baa0bc582ef2
> Author: hpa...@fhcrc.org 
> 
> Date:   Mon Apr 24 19:50:57 2017 +
> 
>bump x.y.z versions to odd y after creation of 3_5 branch
> 
>git-svn-id: 
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/FamAgg@129129 
> bc3139a8-67e5-0310-9ffc-ced21a209358
> 
> diff --git a/DESCRIPTION b/DESCRIPTION
> index c9cb1b7..948b777 100644
> --- a/DESCRIPTION
> +++ b/DESCRIPTION
> @@ -1,7 +1,7 @@
> Package: FamAgg
> Type: Package
> Title: Pedigree Analysis and Familial Aggregation
> -Version: 1.4.0
> +Version: 1.5.0
> Author: J. Rainer, D. Taliun, C.X. Weichenberger
> Maintainer: Johannes Rainer 
> 

[Bioc-devel] "Error: duplicate commits" when pushing FamAgg to Bioconductor git

[Rainer Johannes]

Dear all,

I'm unable to push my recent changes to FamAgg to the Bioconductor git repo 
(see below for the error message). I did try the suggested fix but without any 
success - seems the duplicated commits are in Bioconductor and not github.

thankful for any help or advise

The error message is:

macbookjo:FamAgg jo$ git push origin master
Everything up-to-date
macbookjo:FamAgg jo$ git push upstream master
Counting objects: 13, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (13/13), done.
Writing objects: 100% (13/13), 2.17 KiB | 2.17 MiB/s, done.
Total 13 (delta 11), reused 0 (delta 0)
remote: Error: duplicate commits.
remote: 
remote: There are duplicate commits in your commit history, These cannot be
remote: pushed to the Bioconductor git server. Please make sure that this is
remote: resolved.
remote: 
remote: Take a look at the documentation to fix this,
remote: 
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/,
remote: particularly, point #8 (force Bioconductor master to Github master).
remote: 
remote: For more information, or help resolving this issue, contact
remote: . Provide the error, the package name and
remote: any other details we might need.
remote: 
remote: Use
remote: 
remote: git show 397d05e8ba7d301a9145573210c277f1c6dd66a5
remote: git show 6a0c683477b78e231a7eb1b59171baa0bc582ef2
remote: 
remote: to see body of commits.
remote: 
To git.bioconductor.org:packages/FamAgg
 ! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to 'g...@git.bioconductor.org:packages/FamAgg'


macbookjo:FamAgg jo$ git show 397d05e8ba7d301a9145573210c277f1c6dd66a5
commit 397d05e8ba7d301a9145573210c277f1c6dd66a5
Author: Herve Pages 
Date:   Mon Apr 24 19:50:57 2017 +

bump x.y.z versions to odd y after creation of 3_5 branch

git-svn-id: 
file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/FamAgg@129129
 bc3139a8-67e5-0310-9ffc-ced21a209358

diff --git a/DESCRIPTION b/DESCRIPTION
index c9cb1b7..948b777 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: FamAgg
 Type: Package
 Title: Pedigree Analysis and Familial Aggregation
-Version: 1.4.0
+Version: 1.5.0
 Author: J. Rainer, D. Taliun, C.X. Weichenberger
 Maintainer: Johannes Rainer 
 URL: https://github.com/jotsetung/FamAgg

macbookjo:FamAgg jo$ git show 6a0c683477b78e231a7eb1b59171baa0bc582ef2
commit 6a0c683477b78e231a7eb1b59171baa0bc582ef2
Author: hpa...@fhcrc.org 
Date:   Mon Apr 24 19:50:57 2017 +

bump x.y.z versions to odd y after creation of 3_5 branch

git-svn-id: 
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/FamAgg@129129 
bc3139a8-67e5-0310-9ffc-ced21a209358

diff --git a/DESCRIPTION b/DESCRIPTION
index c9cb1b7..948b777 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: FamAgg
 Type: Package
 Title: Pedigree Analysis and Familial Aggregation
-Version: 1.4.0
+Version: 1.5.0
 Author: J. Rainer, D. Taliun, C.X. Weichenberger
 Maintainer: Johannes Rainer 
 URL: https://github.com/jotsetung/FamAgg

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