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] Duplicate commits in Bioconductor commit history
3 messages · Laurent Gatto, Turaga, Nitesh
1 day later
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.
Thank you. Best wishes, Laurent
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
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Laurent Gatto | @lgatt0 http://cpu.sysbiol.cam.ac.uk/ http://lgatto.github.io/
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
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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.