[Bioc-devel] Duplicate commits for hpar was [Re: Duplicate commits in Bioconductor commit history]

2 messages · Turaga, Nitesh

Original

Fri, Jan 19, 2018 9:43 AM #

Hi Laurent,

If you check the package ?hpar? with a fresh clone from git at git.bioconductor, you?ll see that it doesn?t have any duplicate commits now. 

I think only your local repository has duplicate commits. You?d have to fix this issue on your side. 

Best regards,

Nitesh

On Jan 19, 2018, at 11:37 AM, Laurent Gatto <lg390 at cam.ac.uk> wrote:


Dear Nitesh,

I have the exact same issue with hpar:

Counting objects: 454, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (167/167), done.
Writing objects: 100% (359/359), 1.87 MiB | 0 bytes/s, done.
Total 359 (delta 225), reused 314 (delta 186)
remote: Resolving deltas: 100% (225/225), completed with 26 local objects.
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: <bioc-devel at r-project.org>. Provide the error, the package name and
remote: any other details we might need.
remote: 
remote: Use
remote: 
remote:     git show c7e7f60cf62745d1ef56c6e4afa2e125583bafb2
remote:     git show dfb82cec06e8b56d4b01ab0c313c658240ad1bae
remote: 
remote: to see body of commits.
remote: 
To git at git.bioconductor.org:packages/hpar.git
! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to 'git at git.bioconductor.org:packages/hpar.git'


I believe this is due to the old git-svn bridge, that resulted in the
duplicated commits - via the git-svn bridge and then me merging into
master on github.

Could you sort this out on your end so that I can fix my package,
please.

Thank you very much in advance.

Best wishes,

Laurent

On 17 January 2018 17:40, Turaga, Nitesh wrote:

Hi Laurent,

After checking your package, it?s very hard to get rid of the duplicate commits at this stage of development. I don?t think it should effect the build process of your package. 

The only thing it might effect is, when you look back at a later time to specific commit which is duplicated there might be confusion for developers. Just as a helpful tip, duplicate commits happen when you ?merge? different sources. So, be careful while merging in the future from a remote.

I?ve enabled you to push to your repository, so this does not hold up your development. 

Best,

Nitesh

On Jan 16, 2018, at 10:15 AM, Laurent Gatto <lg390 at cam.ac.uk> wrote:


Dear all,

There are duplicated commit in the Bioconductor commit history of the
qcmetrics package, which stop me from pushing additional changes. Here
is an illustration of the problem:

$ git clone git at git.bioconductor.org:packages/qcmetrics.git
Cloning into 'qcmetrics'...
cd remote: Counting objects: 973, done.
remote: Compressing objects: 100% (429/429), done.
remote: Total 973 (delta 614), reused 800 (delta 510)
Receiving objects: 100% (973/973), 4.73 MiB | 1.82 MiB/s, done.
Resolving deltas: 100% (614/614), done.
Checking connectivity... done.
$ cd qcmetrics
$ echo >> DESCRIPTION
$ git commit -am "just a test"                             
[master 209d6e3] just a test
1 file changed, 1 insertion(+)
$ git push
Counting objects: 23, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (3/3), done.
Writing objects: 100% (3/3), 280 bytes | 0 bytes/s, done.
Total 3 (delta 2), 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: <bioc-devel at r-project.org>. Provide the error, the package name and
remote: any other details we might need.
remote: 
remote: Use
remote: 
remote:     git show fe33ea0a9221f5dbeea0581d1d2381df965d10ce
remote:     git show 2b089e21267bccbe23416bf756bff01036623aec
remote: 
remote: to see body of commits.
remote: 
To git at git.bioconductor.org:packages/qcmetrics.git
! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to 'git at git.bioconductor.org:packages/qcmetrics.git'

If I look at the documentation suggested above, I understand that this
is relevant for duplicated commits in github and bioconductor
histories.

Any idea how to address this within Bioconductor?

Thank you in advance.

Laurent

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

This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.

Fri, Jan 19, 2018 9:47 AM #

The pre-receive hook is catching the duplicate commits on your local repository and preventing the push from contaminating the bioconductor version of the repository.

If you need help fixing your local repository, feel free to ask questions. Try to follow the link in error message and see if you can work through that.

Best regards,

Nitesh

On Jan 19, 2018, at 12:43 PM, ni41435_ca <nitesh.turaga at roswellpark.org> wrote:

Hi Laurent,

If you check the package ?hpar? with a fresh clone from git at git.bioconductor, you?ll see that it doesn?t have any duplicate commits now. 

I think only your local repository has duplicate commits. You?d have to fix this issue on your side. 

Best regards,

Nitesh

On Jan 19, 2018, at 11:37 AM, Laurent Gatto <lg390 at cam.ac.uk> wrote:


Dear Nitesh,

I have the exact same issue with hpar:

Counting objects: 454, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (167/167), done.
Writing objects: 100% (359/359), 1.87 MiB | 0 bytes/s, done.
Total 359 (delta 225), reused 314 (delta 186)
remote: Resolving deltas: 100% (225/225), completed with 26 local objects.
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: <bioc-devel at r-project.org>. Provide the error, the package name and
remote: any other details we might need.
remote: 
remote: Use
remote: 
remote:     git show c7e7f60cf62745d1ef56c6e4afa2e125583bafb2
remote:     git show dfb82cec06e8b56d4b01ab0c313c658240ad1bae
remote: 
remote: to see body of commits.
remote: 
To git at git.bioconductor.org:packages/hpar.git
! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to 'git at git.bioconductor.org:packages/hpar.git'


I believe this is due to the old git-svn bridge, that resulted in the
duplicated commits - via the git-svn bridge and then me merging into
master on github.

Could you sort this out on your end so that I can fix my package,
please.

Thank you very much in advance.

Best wishes,

Laurent

On 17 January 2018 17:40, Turaga, Nitesh wrote:

Hi Laurent,

After checking your package, it?s very hard to get rid of the duplicate commits at this stage of development. I don?t think it should effect the build process of your package. 

The only thing it might effect is, when you look back at a later time to specific commit which is duplicated there might be confusion for developers. Just as a helpful tip, duplicate commits happen when you ?merge? different sources. So, be careful while merging in the future from a remote.

I?ve enabled you to push to your repository, so this does not hold up your development. 

Best,

Nitesh

On Jan 16, 2018, at 10:15 AM, Laurent Gatto <lg390 at cam.ac.uk> wrote:


Dear all,

There are duplicated commit in the Bioconductor commit history of the
qcmetrics package, which stop me from pushing additional changes. Here
is an illustration of the problem:

$ git clone git at git.bioconductor.org:packages/qcmetrics.git
Cloning into 'qcmetrics'...
cd remote: Counting objects: 973, done.
remote: Compressing objects: 100% (429/429), done.
remote: Total 973 (delta 614), reused 800 (delta 510)
Receiving objects: 100% (973/973), 4.73 MiB | 1.82 MiB/s, done.
Resolving deltas: 100% (614/614), done.
Checking connectivity... done.
$ cd qcmetrics
$ echo >> DESCRIPTION
$ git commit -am "just a test"                             
[master 209d6e3] just a test
1 file changed, 1 insertion(+)
$ git push
Counting objects: 23, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (3/3), done.
Writing objects: 100% (3/3), 280 bytes | 0 bytes/s, done.
Total 3 (delta 2), 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: <bioc-devel at r-project.org>. Provide the error, the package name and
remote: any other details we might need.
remote: 
remote: Use
remote: 
remote:     git show fe33ea0a9221f5dbeea0581d1d2381df965d10ce
remote:     git show 2b089e21267bccbe23416bf756bff01036623aec
remote: 
remote: to see body of commits.
remote: 
To git at git.bioconductor.org:packages/qcmetrics.git
! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to 'git at git.bioconductor.org:packages/qcmetrics.git'

If I look at the documentation suggested above, I understand that this
is relevant for duplicated commits in github and bioconductor
histories.

Any idea how to address this within Bioconductor?

Thank you in advance.

Laurent

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

This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.