[Bioc-devel] "Duplicate commits" after when pushing change right after doing a clean `git clone git@git.bioconductor.org:packages/chimeraviz`

On Jan 13, 2018, at 12:35 PM, Stian L?gstad <stianlagstad at gmail.com> wrote:

Hi,

Could someone help me get past the duplicate commits error? I'm not sure
what to do.

These are the steps I've taken:

1. Clone the repository. `git clone git at git.bioconductor.org:packa
ges/chimeraviz`
2. Make a small change in master + attempt to push it, and got this:
```
?  chimeraviz-bioconductor git:(master) git push

Counting objects: 4, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (4/4), done.
Writing objects: 100% (4/4), 422 bytes | 0 bytes/s, done.

Total 4 (delta 3), 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 248742bd41a1b1d862d29e612baa067c50c55e5b
remote:     git show 81ee14920be186caf4f2949e7dacfad68db64ed2
remote:
remote: to see body of commits.
remote:
To git at git.bioconductor.org:packages/chimeraviz

! [remote rejected] master -> master (pre-receive hook declined)
```

I do see what looks like duplicate commits in the git log. For
example ba964db26ac49e86a5374e0dc3040769ae799113
and 8a49e3cdd1ce5257879d752aeead83813c6a4044, which are both from Sat Apr 8
17:45:42 2017. But I've been successful in making changes after april last
year.

-- 
Stian L?gstad
+47 41 80 80 25

	[[alternative HTML version deleted]]

On Jan 13, 2018, at 8:36 PM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:

Hi Stian,

I?m looking into it. Your commit history seems to have a discontinuous history of duplicates + non-duplicates caused by merge from different sources. I?m yet to figure out how to solve this situation.

I will get back to you within a couple of days. 

Best,

Nitesh 

On Jan 13, 2018, at 12:35 PM, Stian L?gstad <stianlagstad at gmail.com> wrote:

Hi,

Could someone help me get past the duplicate commits error? I'm not sure
what to do.

These are the steps I've taken:

1. Clone the repository. `git clone git at git.bioconductor.org:packa
ges/chimeraviz`
2. Make a small change in master + attempt to push it, and got this:
```
?  chimeraviz-bioconductor git:(master) git push

Counting objects: 4, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (4/4), done.
Writing objects: 100% (4/4), 422 bytes | 0 bytes/s, done.

Total 4 (delta 3), 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 248742bd41a1b1d862d29e612baa067c50c55e5b
remote:     git show 81ee14920be186caf4f2949e7dacfad68db64ed2
remote:
remote: to see body of commits.
remote:
To git at git.bioconductor.org:packages/chimeraviz

! [remote rejected] master -> master (pre-receive hook declined)
```

I do see what looks like duplicate commits in the git log. For
example ba964db26ac49e86a5374e0dc3040769ae799113
and 8a49e3cdd1ce5257879d752aeead83813c6a4044, which are both from Sat Apr 8
17:45:42 2017. But I've been successful in making changes after april last
year.

-- 
Stian L?gstad
+47 41 80 80 25

	[[alternative HTML version deleted]]

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.

Hi Stian,

I?ve enabled you to push to your repository on Bioconductor.

Your duplicate commit history weaves in and out because of merges along
the way from your GitHub repository. At this point, there is very little I
can do to help unless I spend a lot of time on your package, manually
fixing the history.

The duplicate commits should not effect your package development, and you
should continue with it. It does not effect the build process as well.

If you feel like this is something you can fix from your end, by using
?git reset? and ?git cherry-pick? you should feel free to fix. Let me know
when you are successful, and I can help you push the updated repo.

For the future, duplicate commits are caused by ?merge? commands. You
might want to search for those if you want to know which commits are
causing these duplicates.

Best,

Nitesh

On Jan 13, 2018, at 8:36 PM, Turaga, Nitesh

<Nitesh.Turaga at RoswellPark.org> wrote:

Hi Stian,

I?m looking into it. Your commit history seems to have a discontinuous

history of duplicates + non-duplicates caused by merge from different
sources. I?m yet to figure out how to solve this situation.

I will get back to you within a couple of days.

Best,

Nitesh

On Jan 13, 2018, at 12:35 PM, Stian L?gstad <stianlagstad at gmail.com>

wrote:

Hi,

Could someone help me get past the duplicate commits error? I'm not sure
what to do.

These are the steps I've taken:

1. Clone the repository. `git clone git at git.bioconductor.org:packa
ges/chimeraviz`
2. Make a small change in master + attempt to push it, and got this:
```
?  chimeraviz-bioconductor git:(master) git push

Counting objects: 4, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (4/4), done.
Writing objects: 100% (4/4), 422 bytes | 0 bytes/s, done.

Total 4 (delta 3), 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 248742bd41a1b1d862d29e612baa067c50c55e5b
remote:     git show 81ee14920be186caf4f2949e7dacfad68db64ed2
remote:
remote: to see body of commits.
remote:
To git at git.bioconductor.org:packages/chimeraviz

! [remote rejected] master -> master (pre-receive hook declined)
```

I do see what looks like duplicate commits in the git log. For
example ba964db26ac49e86a5374e0dc3040769ae799113
and 8a49e3cdd1ce5257879d752aeead83813c6a4044, which are both from Sat

Apr 8

17:45:42 2017. But I've been successful in making changes after april

last

year.

--
Stian L?gstad
+47 41 80 80 25

     [[alternative HTML version deleted]]

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.

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.

On Jan 17, 2018, at 1:22 PM, Stian L?gstad <stianlagstad at gmail.com> wrote:

I usually create a seperate branch for work, which I merge into master when I'm happy with the result. Will that be a problem? Should I rebase instead to avoid it?

Thank you.

On Wed, Jan 17, 2018 at 6:48 PM, Turaga, Nitesh <Nitesh.Turaga at roswellpark.org> wrote:
Hi Stian,

I?ve enabled you to push to your repository on Bioconductor.

Your duplicate commit history weaves in and out because of merges along the way from your GitHub repository. At this point, there is very little I can do to help unless I spend a lot of time on your package, manually fixing the history.

The duplicate commits should not effect your package development, and you should continue with it. It does not effect the build process as well.

If you feel like this is something you can fix from your end, by using ?git reset? and ?git cherry-pick? you should feel free to fix. Let me know when you are successful, and I can help you push the updated repo.

For the future, duplicate commits are caused by ?merge? commands. You might want to search for those if you want to know which commits are causing these duplicates.

Best,

Nitesh

On Jan 13, 2018, at 8:36 PM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:

Hi Stian,

I?m looking into it. Your commit history seems to have a discontinuous history of duplicates + non-duplicates caused by merge from different sources. I?m yet to figure out how to solve this situation.

I will get back to you within a couple of days.

Best,

Nitesh

On Jan 13, 2018, at 12:35 PM, Stian L?gstad <stianlagstad at gmail.com> wrote:

Hi,

Could someone help me get past the duplicate commits error? I'm not sure
what to do.

These are the steps I've taken:

1. Clone the repository. `git clone git at git.bioconductor.org:packa
ges/chimeraviz`
2. Make a small change in master + attempt to push it, and got this:
```
?  chimeraviz-bioconductor git:(master) git push

Counting objects: 4, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (4/4), done.
Writing objects: 100% (4/4), 422 bytes | 0 bytes/s, done.

Total 4 (delta 3), 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 248742bd41a1b1d862d29e612baa067c50c55e5b
remote:     git show 81ee14920be186caf4f2949e7dacfad68db64ed2
remote:
remote: to see body of commits.
remote:
To git at git.bioconductor.org:packages/chimeraviz

! [remote rejected] master -> master (pre-receive hook declined)
```

I do see what looks like duplicate commits in the git log. For
example ba964db26ac49e86a5374e0dc3040769ae799113
and 8a49e3cdd1ce5257879d752aeead83813c6a4044, which are both from Sat Apr 8
17:45:42 2017. But I've been successful in making changes after april last
year.

--
Stian L?gstad
+47 41 80 80 25

     [[alternative HTML version deleted]]

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.

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.



-- 
Stian L?gstad
+47 41 80 80 25

The problem is not a separate branch from your primary repository. Its
the branch coming from a ?remote? which is not the primary repository
(i.e Bioconductor).

?rebase" is essentially doing what you do in two separate steps, so
that does not solve this issue.

I would just ask on this forum if you have a duplicate commit issue in
the future, before ?pushing? to Bioconductor.

Your?s is a very unique case.

Best,

Nitesh 

On Jan 17, 2018, at 1:22 PM, Stian L?gstad <stianlagstad at gmail.com> wrote:

I usually create a seperate branch for work, which I merge into master when I'm happy with the result. Will that be a problem? Should I rebase instead to avoid it?

Thank you.

On Wed, Jan 17, 2018 at 6:48 PM, Turaga, Nitesh <Nitesh.Turaga at roswellpark.org> wrote:
Hi Stian,

I?ve enabled you to push to your repository on Bioconductor.

Your duplicate commit history weaves in and out because of merges along the way from your GitHub repository. At this point, there is very little I can do to help unless I spend a lot of time on your package, manually fixing the history.

The duplicate commits should not effect your package development, and you should continue with it. It does not effect the build process as well.

If you feel like this is something you can fix from your end, by using ?git reset? and ?git cherry-pick? you should feel free to fix. Let me know when you are successful, and I can help you push the updated repo.

For the future, duplicate commits are caused by ?merge? commands. You might want to search for those if you want to know which commits are causing these duplicates.

Best,

Nitesh

On Jan 13, 2018, at 8:36 PM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:

Hi Stian,

I?m looking into it. Your commit history seems to have a discontinuous history of duplicates + non-duplicates caused by merge from different sources. I?m yet to figure out how to solve this situation.

I will get back to you within a couple of days.

Best,

Nitesh

On Jan 13, 2018, at 12:35 PM, Stian L?gstad <stianlagstad at gmail.com> wrote:

Hi,

Could someone help me get past the duplicate commits error? I'm not sure
what to do.

These are the steps I've taken:

1. Clone the repository. `git clone git at git.bioconductor.org:packa
ges/chimeraviz`
2. Make a small change in master + attempt to push it, and got this:
```
?  chimeraviz-bioconductor git:(master) git push

Counting objects: 4, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (4/4), done.
Writing objects: 100% (4/4), 422 bytes | 0 bytes/s, done.

Total 4 (delta 3), 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 248742bd41a1b1d862d29e612baa067c50c55e5b
remote:     git show 81ee14920be186caf4f2949e7dacfad68db64ed2
remote:
remote: to see body of commits.
remote:
To git at git.bioconductor.org:packages/chimeraviz

! [remote rejected] master -> master (pre-receive hook declined)
```

I do see what looks like duplicate commits in the git log. For
example ba964db26ac49e86a5374e0dc3040769ae799113
and 8a49e3cdd1ce5257879d752aeead83813c6a4044, which are both from Sat Apr 8
17:45:42 2017. But I've been successful in making changes after april last
year.

--
Stian L?gstad
+47 41 80 80 25

     [[alternative HTML version deleted]]

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.

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.



-- 
Stian L?gstad
+47 41 80 80 25

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.