Hi all, I attempted syncing my existing GitHub repo for the mimager package with git.bioconductor.org and was left with many duplicate commits, as documented. Hoping to keep my history intact, I performed a rebase to clean-up the dupes (giving preference to commits with git-svn-ids) but can?t force push these changes upstream to Bioconductor. Would it be possible to update the Bioconductor history to match what?s on GitHub (https://github.com/aaronwolen/mimager), similar to what was done for the ASSIGN package? Thanks, Aaron
[Bioc-devel] Duplicate commits in mimager package
7 messages · Turaga, Nitesh, Rainer Johannes, Aaron Wolen
Hi Aaron, You cannot force push to the Bioconductor server as it is prevented by a pre-receive hook on our end. There are no duplicate commits on the Bioconductor version of the package right now. Can you point the commits which are duplicated on a fresh clone of the mimager package from git.bioconductor.org? Best, Nitesh
On Mar 6, 2018, at 12:23 PM, Aaron Wolen <aaron at wolen.com> wrote: Hi all, I attempted syncing my existing GitHub repo for the mimager package with git.bioconductor.org and was left with many duplicate commits, as documented. Hoping to keep my history intact, I performed a rebase to clean-up the dupes (giving preference to commits with git-svn-ids) but can?t force push these changes upstream to Bioconductor. Would it be possible to update the Bioconductor history to match what?s on GitHub (https://github.com/aaronwolen/mimager), similar to what was done for the ASSIGN package? Thanks, Aaron [[alternative HTML version deleted]]
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Thanks, Nitesh, There are about 20 dupes. Here are a few examples: -?2c01b08 and?c0f7ed1 -?77a5d90 and?464edd9 -?b952032 and?9abf5dd
On Mar 6, 2018, 1:27 PM -0500, Turaga, Nitesh <Nitesh.Turaga at roswellpark.org>, wrote:
Hi Aaron, You cannot force push to the Bioconductor server as it is prevented by a pre-receive hook on our end. There are no duplicate commits on the Bioconductor version of the package right now. Can you point the commits which are duplicated on a fresh clone of the mimager package from git.bioconductor.org? Best, Nitesh
On Mar 6, 2018, at 12:23 PM, Aaron Wolen <aaron at wolen.com> wrote: Hi all, I attempted syncing my existing GitHub repo for the mimager package with git.bioconductor.org and was left with many duplicate commits, as documented. Hoping to keep my history intact, I performed a rebase to clean-up the dupes (giving preference to commits with git-svn-ids) but can?t force push these changes upstream to Bioconductor. Would it be possible to update the Bioconductor history to match what?s on GitHub (https://github.com/aaronwolen/mimager), similar to what was done for the ASSIGN package? Thanks, Aaron [[alternative HTML version deleted]]
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I recently had a similar problem with my FamAgg and ensembldb packages. I had to remove the duplicated commits with `git rebase -i <sha from last non-duplicated commit>` (i.e. interactive rebasing). During/after that I had to fix some merge conflicts and ended overwriting my github master with the cleaned history (`git push -f origin master`) - Nithesh replaced then the Bioconductor git repos with the fixed github masters. I think the duplicated commits are leftovers from my (potentially faulty) git-svn setup. cheers, jo
On 6 Mar 2018, at 21:41, Aaron Wolen <aaron at wolen.com> wrote: Thanks, Nitesh, There are about 20 dupes. Here are a few examples: - 2c01b08 and c0f7ed1 - 77a5d90 and 464edd9 - b952032 and 9abf5dd On Mar 6, 2018, 1:27 PM -0500, Turaga, Nitesh <Nitesh.Turaga at roswellpark.org>, wrote:
Hi Aaron, You cannot force push to the Bioconductor server as it is prevented by a pre-receive hook on our end. There are no duplicate commits on the Bioconductor version of the package right now. Can you point the commits which are duplicated on a fresh clone of the mimager package from git.bioconductor.org? Best, Nitesh
On Mar 6, 2018, at 12:23 PM, Aaron Wolen <aaron at wolen.com> wrote: Hi all, I attempted syncing my existing GitHub repo for the mimager package with git.bioconductor.org and was left with many duplicate commits, as documented. Hoping to keep my history intact, I performed a rebase to clean-up the dupes (giving preference to commits with git-svn-ids) but can?t force push these changes upstream to Bioconductor. Would it be possible to update the Bioconductor history to match what?s on GitHub (https://github.com/aaronwolen/mimager), similar to what was done for the ASSIGN package? Thanks, Aaron [[alternative HTML version deleted]]
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Thanks for the information, Jo. Sounds like a very similar issue?even down to the potentially faulty git-svn setup. Glad to hear Nitesh was able to copy over your cleaned history to Bioconductor. Hopefully we can do the same for mimamger.
On Mar 7, 2018, 1:26 AM -0500, Rainer Johannes <Johannes.Rainer at eurac.edu>, wrote:
I recently had a similar problem with my FamAgg and ensembldb packages. I had to remove the duplicated commits with `git rebase -i <sha from last non-duplicated commit>` (i.e. interactive rebasing). During/after that I had to fix some merge conflicts and ended overwriting my github master with the cleaned history (`git push -f origin master`) - Nithesh replaced then the Bioconductor git repos with the fixed github masters. I think the duplicated commits are leftovers from my (potentially faulty) git-svn setup. cheers, jo
On 6 Mar 2018, at 21:41, Aaron Wolen <aaron at wolen.com> wrote: Thanks, Nitesh, There are about 20 dupes. Here are a few examples: - 2c01b08 and c0f7ed1 - 77a5d90 and 464edd9 - b952032 and 9abf5dd On Mar 6, 2018, 1:27 PM -0500, Turaga, Nitesh <Nitesh.Turaga at roswellpark.org>, wrote:
Hi Aaron, You cannot force push to the Bioconductor server as it is prevented by a pre-receive hook on our end. There are no duplicate commits on the Bioconductor version of the package right now. Can you point the commits which are duplicated on a fresh clone of the mimager package from git.bioconductor.org? Best, Nitesh
On Mar 6, 2018, at 12:23 PM, Aaron Wolen <aaron at wolen.com> wrote: Hi all, I attempted syncing my existing GitHub repo for the mimager package with git.bioconductor.org and was left with many duplicate commits, as documented. Hoping to keep my history intact, I performed a rebase to clean-up the dupes (giving preference to commits with git-svn-ids) but can?t force push these changes upstream to Bioconductor. Would it be possible to update the Bioconductor history to match what?s on GitHub (https://github.com/aaronwolen/mimager), similar to what was done for the ASSIGN package? Thanks, Aaron [[alternative HTML version deleted]]
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Hi Aaron, As Johannes said, your have to fix the repo yourself. Your duplicate commits are non-contiguous which is surprising. It?s almost as if the commit dates were changed somehow. Once you fix the repo on Github, please send me the link and I can force push to Bioconductor. Best, Nitesh
On Mar 7, 2018, at 1:24 PM, Aaron Wolen <aaron at wolen.com> wrote: Thanks for the information, Jo. Sounds like a very similar issue?even down to the potentially faulty git-svn setup. Glad to hear Nitesh was able to copy over your cleaned history to Bioconductor. Hopefully we can do the same for mimamger. On Mar 7, 2018, 1:26 AM -0500, Rainer Johannes <Johannes.Rainer at eurac.edu>, wrote:
I recently had a similar problem with my FamAgg and ensembldb packages. I had to remove the duplicated commits with `git rebase -i <sha from last non-duplicated commit>` (i.e. interactive rebasing). During/after that I had to fix some merge conflicts and ended overwriting my github master with the cleaned history (`git push -f origin master`) - Nithesh replaced then the Bioconductor git repos with the fixed github masters. I think the duplicated commits are leftovers from my (potentially faulty) git-svn setup. cheers, jo
On 6 Mar 2018, at 21:41, Aaron Wolen <aaron at wolen.com> wrote: Thanks, Nitesh, There are about 20 dupes. Here are a few examples: - 2c01b08 and c0f7ed1 - 77a5d90 and 464edd9 - b952032 and 9abf5dd On Mar 6, 2018, 1:27 PM -0500, Turaga, Nitesh <Nitesh.Turaga at roswellpark.org>, wrote:
Hi Aaron, You cannot force push to the Bioconductor server as it is prevented by a pre-receive hook on our end. There are no duplicate commits on the Bioconductor version of the package right now. Can you point the commits which are duplicated on a fresh clone of the mimager package from git.bioconductor.org? Best, Nitesh
On Mar 6, 2018, at 12:23 PM, Aaron Wolen <aaron at wolen.com> wrote: Hi all, I attempted syncing my existing GitHub repo for the mimager package with git.bioconductor.org and was left with many duplicate commits, as documented. Hoping to keep my history intact, I performed a rebase to clean-up the dupes (giving preference to commits with git-svn-ids) but can?t force push these changes upstream to Bioconductor. Would it be possible to update the Bioconductor history to match what?s on GitHub (https://github.com/aaronwolen/mimager), similar to what was done for the ASSIGN package? Thanks, Aaron [[alternative HTML version deleted]]
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[[alternative HTML version deleted]]
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Thanks, Nitesh. I?ve already gone through the process of fixing the duplicate commits and force pushed the cleaned history to GitHub (https://github.com/aaronwolen/mimager). No idea why the duplicates appeared out of order but I did verify the dates/times were unchanged by comparing to a backup.
On Mar 7, 2018, 1:33 PM -0500, Turaga, Nitesh <Nitesh.Turaga at roswellpark.org>, wrote:
Hi Aaron, As Johannes said, your have to fix the repo yourself. Your duplicate commits are non-contiguous which is surprising. It?s almost as if the commit dates were changed somehow. Once you fix the repo on Github, please send me the link and I can force push to Bioconductor. Best, Nitesh
On Mar 7, 2018, at 1:24 PM, Aaron Wolen <aaron at wolen.com> wrote: Thanks for the information, Jo. Sounds like a very similar issue?even down to the potentially faulty git-svn setup. Glad to hear Nitesh was able to copy over your cleaned history to Bioconductor. Hopefully we can do the same for mimamger. On Mar 7, 2018, 1:26 AM -0500, Rainer Johannes <Johannes.Rainer at eurac.edu>, wrote:
I recently had a similar problem with my FamAgg and ensembldb packages. I had to remove the duplicated commits with `git rebase -i <sha from last non-duplicated commit>` (i.e. interactive rebasing). During/after that I had to fix some merge conflicts and ended overwriting my github master with the cleaned history (`git push -f origin master`) - Nithesh replaced then the Bioconductor git repos with the fixed github masters. I think the duplicated commits are leftovers from my (potentially faulty) git-svn setup. cheers, jo
On 6 Mar 2018, at 21:41, Aaron Wolen <aaron at wolen.com> wrote: Thanks, Nitesh, There are about 20 dupes. Here are a few examples: - 2c01b08 and c0f7ed1 - 77a5d90 and 464edd9 - b952032 and 9abf5dd On Mar 6, 2018, 1:27 PM -0500, Turaga, Nitesh <Nitesh.Turaga at roswellpark.org>, wrote:
Hi Aaron, You cannot force push to the Bioconductor server as it is prevented by a pre-receive hook on our end. There are no duplicate commits on the Bioconductor version of the package right now. Can you point the commits which are duplicated on a fresh clone of the mimager package from git.bioconductor.org? Best, Nitesh
On Mar 6, 2018, at 12:23 PM, Aaron Wolen <aaron at wolen.com> wrote: Hi all, I attempted syncing my existing GitHub repo for the mimager package with git.bioconductor.org and was left with many duplicate commits, as documented. Hoping to keep my history intact, I performed a rebase to clean-up the dupes (giving preference to commits with git-svn-ids) but can?t force push these changes upstream to Bioconductor. Would it be possible to update the Bioconductor history to match what?s on GitHub (https://github.com/aaronwolen/mimager), similar to what was done for the ASSIGN package? Thanks, Aaron [[alternative HTML version deleted]]
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[[alternative HTML version deleted]]
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