[Bioc-devel] git help

Hi Kevin,

I can help you with this. I can take you back to a state before August 18th and put that repository up on our Git server.

 From that point onwards you?d have to reapply all the changes on that repository from "commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389" and onwards.

commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389
Merge: 643e470 f1785fb
Author: tgirke <tgirke at citrus.ucr.edu>
Date:   Sat Aug 19 16:32:35 2017 -0700

     resolved conflicts

I can do this tomorrow and send you an email.


Best,

Nitesh

On Jan 3, 2018, at 4:28 PM, Kevin Horan <khoran at cs.ucr.edu> wrote:

Nitesh,

    I tried to re-construct the repo starting from what is left in the SVN repository, but I couldn't get all the branches to come over and it just generally looks too different to easily replace the bioc repo.

    I was thinking though, if its easy for you to clobber the current bioc repo for ChemmineR and re-create it from the old SVN repo (ie, because you might have scripts from having done it the first time), then that might be an easier fix. Then I can check it out, apply the recent changes and push it back.

    But if you don't think that's a good idea, then I'll take your offer of help and we can try to figure out how to get rid of the duplicate commits. Thanks.


Kevin


On 01/03/2018 11:55 AM, Turaga, Nitesh wrote:

Hi Kevin,

I?ll try to help you. I?ll take a look at your package and get back to you. Please forward this message to bioc-devel so that it?s public and other maintainers/users know that there is an issue with your package.

Best,

Nitesh

On Jan 3, 2018, at 2:31 PM, Kevin Horan <khoran at globalrecordings.net> wrote:

Nitesh,

    I am one of the maintainers for the ChemmineR package on bioconductor. I have a bad duplicate commit problem I was wondering if you could help me with. Basically, it seems one string of 1000 or so commits has been duplicated twice in the repository, so that there are now 3 copies of each of these commits. This mess is already in the bioconductor repository because in order to allow me to get some last minute changes in for the last release, someone at boic disabled the duplicate commit check for me. That was before I understood the extend of the problem.

    I'm not sure if its really your job to help with this sort of thing, as I understand that it's not a bioconductor problem. So if not that is fine. I've spent 6 hours trying to fix it myself ( and I am generally good with  GIT), but I've only succeeded in make more duplicates. So I think I'd need to toss all the history up to the last release, which I image I'd need your help to reset the repo on the bioc side as well.

    If you can help, there are more specifics I can give you, just let me know.

Thanks.


Kevin Horan

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 3, 2018, at 7:10 PM, Kevin Horan <khoran at cs.ucr.edu> wrote:

Nitesh,

   That sounds great, thanks.

Kevin


On 01/03/2018 01:53 PM, Turaga, Nitesh wrote:

Hi Kevin,

I can help you with this. I can take you back to a state before August 18th and put that repository up on our Git server.

From that point onwards you?d have to reapply all the changes on that repository from "commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389" and onwards.

commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389
Merge: 643e470 f1785fb
Author: tgirke <tgirke at citrus.ucr.edu>
Date:   Sat Aug 19 16:32:35 2017 -0700

    resolved conflicts

I can do this tomorrow and send you an email.


Best,

Nitesh

On Jan 3, 2018, at 4:28 PM, Kevin Horan <khoran at cs.ucr.edu> wrote:

Nitesh,

   I tried to re-construct the repo starting from what is left in the SVN repository, but I couldn't get all the branches to come over and it just generally looks too different to easily replace the bioc repo.

   I was thinking though, if its easy for you to clobber the current bioc repo for ChemmineR and re-create it from the old SVN repo (ie, because you might have scripts from having done it the first time), then that might be an easier fix. Then I can check it out, apply the recent changes and push it back.

   But if you don't think that's a good idea, then I'll take your offer of help and we can try to figure out how to get rid of the duplicate commits. Thanks.


Kevin


On 01/03/2018 11:55 AM, Turaga, Nitesh wrote:

Hi Kevin,

I?ll try to help you. I?ll take a look at your package and get back to you. Please forward this message to bioc-devel so that it?s public and other maintainers/users know that there is an issue with your package.

Best,

Nitesh

On Jan 3, 2018, at 2:31 PM, Kevin Horan <khoran at globalrecordings.net> wrote:

Nitesh,

   I am one of the maintainers for the ChemmineR package on bioconductor. I have a bad duplicate commit problem I was wondering if you could help me with. Basically, it seems one string of 1000 or so commits has been duplicated twice in the repository, so that there are now 3 copies of each of these commits. This mess is already in the bioconductor repository because in order to allow me to get some last minute changes in for the last release, someone at boic disabled the duplicate commit check for me. That was before I understood the extend of the problem.

   I'm not sure if its really your job to help with this sort of thing, as I understand that it's not a bioconductor problem. So if not that is fine. I've spent 6 hours trying to fix it myself ( and I am generally good with  GIT), but I've only succeeded in make more duplicates. So I think I'd need to toss all the history up to the last release, which I image I'd need your help to reset the repo on the bioc side as well.

   If you can help, there are more specifics I can give you, just let me know.

Thanks.


Kevin Horan

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 4, 2018, at 10:07 AM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:

Hi Kevin,

I have your package reset to this commit e3a8d2122a65305c478276e538faace277ea9ed6. 

Please check. You will need to overlay all the commits including the new release on top of this (RELEASE_3_6).

If you have any questions further on this, please ask before pushing to Bioconductor. 

Best,

Nitesh 

On Jan 3, 2018, at 7:10 PM, Kevin Horan <khoran at cs.ucr.edu> wrote:

Nitesh,

  That sounds great, thanks.

Kevin


On 01/03/2018 01:53 PM, Turaga, Nitesh wrote:

Hi Kevin,

I can help you with this. I can take you back to a state before August 18th and put that repository up on our Git server.

From that point onwards you?d have to reapply all the changes on that repository from "commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389" and onwards.

commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389
Merge: 643e470 f1785fb
Author: tgirke <tgirke at citrus.ucr.edu>
Date:   Sat Aug 19 16:32:35 2017 -0700

   resolved conflicts

I can do this tomorrow and send you an email.


Best,

Nitesh

On Jan 3, 2018, at 4:28 PM, Kevin Horan <khoran at cs.ucr.edu> wrote:

Nitesh,

  I tried to re-construct the repo starting from what is left in the SVN repository, but I couldn't get all the branches to come over and it just generally looks too different to easily replace the bioc repo.

  I was thinking though, if its easy for you to clobber the current bioc repo for ChemmineR and re-create it from the old SVN repo (ie, because you might have scripts from having done it the first time), then that might be an easier fix. Then I can check it out, apply the recent changes and push it back.

  But if you don't think that's a good idea, then I'll take your offer of help and we can try to figure out how to get rid of the duplicate commits. Thanks.


Kevin


On 01/03/2018 11:55 AM, Turaga, Nitesh wrote:

Hi Kevin,

I?ll try to help you. I?ll take a look at your package and get back to you. Please forward this message to bioc-devel so that it?s public and other maintainers/users know that there is an issue with your package.

Best,

Nitesh

On Jan 3, 2018, at 2:31 PM, Kevin Horan <khoran at globalrecordings.net> wrote:

Nitesh,

  I am one of the maintainers for the ChemmineR package on bioconductor. I have a bad duplicate commit problem I was wondering if you could help me with. Basically, it seems one string of 1000 or so commits has been duplicated twice in the repository, so that there are now 3 copies of each of these commits. This mess is already in the bioconductor repository because in order to allow me to get some last minute changes in for the last release, someone at boic disabled the duplicate commit check for me. That was before I understood the extend of the problem.

  I'm not sure if its really your job to help with this sort of thing, as I understand that it's not a bioconductor problem. So if not that is fine. I've spent 6 hours trying to fix it myself ( and I am generally good with  GIT), but I've only succeeded in make more duplicates. So I think I'd need to toss all the history up to the last release, which I image I'd need your help to reset the repo on the bioc side as well.

  If you can help, there are more specifics I can give you, just let me know.

Thanks.


Kevin Horan

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.

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 Kevin,

Please overlay the commits so that we can get your package building on our build machines.

Please do this soon. You also have to make RELEASE_3_6 branch now.

We have skipped your package for now, and it won?t show up in the release report.
  
Thanks

Nitesh

On Jan 4, 2018, at 10:07 AM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:

Hi Kevin,

I have your package reset to this commit e3a8d2122a65305c478276e538faace277ea9ed6.

Please check. You will need to overlay all the commits including the new release on top of this (RELEASE_3_6).

If you have any questions further on this, please ask before pushing to Bioconductor.

Best,

Nitesh

On Jan 3, 2018, at 7:10 PM, Kevin Horan <khoran at cs.ucr.edu> wrote:

Nitesh,

   That sounds great, thanks.

Kevin


On 01/03/2018 01:53 PM, Turaga, Nitesh wrote:

Hi Kevin,

I can help you with this. I can take you back to a state before August 18th and put that repository up on our Git server.

 From that point onwards you?d have to reapply all the changes on that repository from "commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389" and onwards.

commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389
Merge: 643e470 f1785fb
Author: tgirke <tgirke at citrus.ucr.edu>
Date:   Sat Aug 19 16:32:35 2017 -0700

    resolved conflicts

I can do this tomorrow and send you an email.


Best,

Nitesh

On Jan 3, 2018, at 4:28 PM, Kevin Horan <khoran at cs.ucr.edu> wrote:

Nitesh,

   I tried to re-construct the repo starting from what is left in the SVN repository, but I couldn't get all the branches to come over and it just generally looks too different to easily replace the bioc repo.

   I was thinking though, if its easy for you to clobber the current bioc repo for ChemmineR and re-create it from the old SVN repo (ie, because you might have scripts from having done it the first time), then that might be an easier fix. Then I can check it out, apply the recent changes and push it back.

   But if you don't think that's a good idea, then I'll take your offer of help and we can try to figure out how to get rid of the duplicate commits. Thanks.


Kevin


On 01/03/2018 11:55 AM, Turaga, Nitesh wrote:

Hi Kevin,

I?ll try to help you. I?ll take a look at your package and get back to you. Please forward this message to bioc-devel so that it?s public and other maintainers/users know that there is an issue with your package.

Best,

Nitesh

On Jan 3, 2018, at 2:31 PM, Kevin Horan <khoran at globalrecordings.net> wrote:

Nitesh,

   I am one of the maintainers for the ChemmineR package on bioconductor. I have a bad duplicate commit problem I was wondering if you could help me with. Basically, it seems one string of 1000 or so commits has been duplicated twice in the repository, so that there are now 3 copies of each of these commits. This mess is already in the bioconductor repository because in order to allow me to get some last minute changes in for the last release, someone at boic disabled the duplicate commit check for me. That was before I understood the extend of the problem.

   I'm not sure if its really your job to help with this sort of thing, as I understand that it's not a bioconductor problem. So if not that is fine. I've spent 6 hours trying to fix it myself ( and I am generally good with  GIT), but I've only succeeded in make more duplicates. So I think I'd need to toss all the history up to the last release, which I image I'd need your help to reset the repo on the bioc side as well.

   If you can help, there are more specifics I can give you, just let me know.

Thanks.


Kevin Horan

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.

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 7, 2018, at 1:20 PM, Kevin Horan <khoran at cs.ucr.edu> wrote:

Nitesh,

   I have pushed changes to both the master and RELEASE_3_6 branches now.

Kevin


On 01/05/2018 11:14 AM, Turaga, Nitesh wrote:

Hi Kevin,

Please overlay the commits so that we can get your package building on our build machines.

Please do this soon. You also have to make RELEASE_3_6 branch now.

We have skipped your package for now, and it won?t show up in the release report.
 Thanks

Nitesh

On Jan 4, 2018, at 10:07 AM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:

Hi Kevin,

I have your package reset to this commit e3a8d2122a65305c478276e538faace277ea9ed6.

Please check. You will need to overlay all the commits including the new release on top of this (RELEASE_3_6).

If you have any questions further on this, please ask before pushing to Bioconductor.

Best,

Nitesh

On Jan 3, 2018, at 7:10 PM, Kevin Horan <khoran at cs.ucr.edu> wrote:

Nitesh,

  That sounds great, thanks.

Kevin


On 01/03/2018 01:53 PM, Turaga, Nitesh wrote:

Hi Kevin,

I can help you with this. I can take you back to a state before August 18th and put that repository up on our Git server.

From that point onwards you?d have to reapply all the changes on that repository from "commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389" and onwards.

commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389
Merge: 643e470 f1785fb
Author: tgirke <tgirke at citrus.ucr.edu>
Date:   Sat Aug 19 16:32:35 2017 -0700

   resolved conflicts

I can do this tomorrow and send you an email.


Best,

Nitesh

On Jan 3, 2018, at 4:28 PM, Kevin Horan <khoran at cs.ucr.edu> wrote:

Nitesh,

  I tried to re-construct the repo starting from what is left in the SVN repository, but I couldn't get all the branches to come over and it just generally looks too different to easily replace the bioc repo.

  I was thinking though, if its easy for you to clobber the current bioc repo for ChemmineR and re-create it from the old SVN repo (ie, because you might have scripts from having done it the first time), then that might be an easier fix. Then I can check it out, apply the recent changes and push it back.

  But if you don't think that's a good idea, then I'll take your offer of help and we can try to figure out how to get rid of the duplicate commits. Thanks.


Kevin


On 01/03/2018 11:55 AM, Turaga, Nitesh wrote:

Hi Kevin,

I?ll try to help you. I?ll take a look at your package and get back to you. Please forward this message to bioc-devel so that it?s public and other maintainers/users know that there is an issue with your package.

Best,

Nitesh

On Jan 3, 2018, at 2:31 PM, Kevin Horan <khoran at globalrecordings.net> wrote:

Nitesh,

  I am one of the maintainers for the ChemmineR package on bioconductor. I have a bad duplicate commit problem I was wondering if you could help me with. Basically, it seems one string of 1000 or so commits has been duplicated twice in the repository, so that there are now 3 copies of each of these commits. This mess is already in the bioconductor repository because in order to allow me to get some last minute changes in for the last release, someone at boic disabled the duplicate commit check for me. That was before I understood the extend of the problem.

  I'm not sure if its really your job to help with this sort of thing, as I understand that it's not a bioconductor problem. So if not that is fine. I've spent 6 hours trying to fix it myself ( and I am generally good with  GIT), but I've only succeeded in make more duplicates. So I think I'd need to toss all the history up to the last release, which I image I'd need your help to reset the repo on the bioc side as well.

  If you can help, there are more specifics I can give you, just let me know.

Thanks.


Kevin Horan

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.

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 7, 2018, at 1:32 PM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:

Hi Kevin,

It seems you have lost a few commits which are important in tracking RELEASE?s in Bioconductor.


commit fb5868c2fdfa607b52e467881212b3619a8b0ae9 (HEAD -> master)
Author: Herv? Pag?s <hpages at fredhutch.org>
Date:   Mon Oct 30 12:52:08 2017 -0400

   bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

commit 46e0a56d1117cca6274fea3b8430eb8d6c7a9976 (RELEASE_3_6)
Author: Herv? Pag?s <hpages at fredhutch.org>
Date:   Mon Oct 30 12:39:24 2017 -0400

   bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

These commits are important. 

Please wait for further instructions while we figure out how to resolve this issue. 

Best,

Nitesh 

On Jan 7, 2018, at 1:20 PM, Kevin Horan <khoran at cs.ucr.edu> wrote:

Nitesh,

  I have pushed changes to both the master and RELEASE_3_6 branches now.

Kevin


On 01/05/2018 11:14 AM, Turaga, Nitesh wrote:

Hi Kevin,

Please overlay the commits so that we can get your package building on our build machines.

Please do this soon. You also have to make RELEASE_3_6 branch now.

We have skipped your package for now, and it won?t show up in the release report.
Thanks

Nitesh

On Jan 4, 2018, at 10:07 AM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:

Hi Kevin,

I have your package reset to this commit e3a8d2122a65305c478276e538faace277ea9ed6.

Please check. You will need to overlay all the commits including the new release on top of this (RELEASE_3_6).

If you have any questions further on this, please ask before pushing to Bioconductor.

Best,

Nitesh

On Jan 3, 2018, at 7:10 PM, Kevin Horan <khoran at cs.ucr.edu> wrote:

Nitesh,

 That sounds great, thanks.

Kevin


On 01/03/2018 01:53 PM, Turaga, Nitesh wrote:

Hi Kevin,

I can help you with this. I can take you back to a state before August 18th and put that repository up on our Git server.

From that point onwards you?d have to reapply all the changes on that repository from "commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389" and onwards.

commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389
Merge: 643e470 f1785fb
Author: tgirke <tgirke at citrus.ucr.edu>
Date:   Sat Aug 19 16:32:35 2017 -0700

  resolved conflicts

I can do this tomorrow and send you an email.


Best,

Nitesh

On Jan 3, 2018, at 4:28 PM, Kevin Horan <khoran at cs.ucr.edu> wrote:

Nitesh,

 I tried to re-construct the repo starting from what is left in the SVN repository, but I couldn't get all the branches to come over and it just generally looks too different to easily replace the bioc repo.

 I was thinking though, if its easy for you to clobber the current bioc repo for ChemmineR and re-create it from the old SVN repo (ie, because you might have scripts from having done it the first time), then that might be an easier fix. Then I can check it out, apply the recent changes and push it back.

 But if you don't think that's a good idea, then I'll take your offer of help and we can try to figure out how to get rid of the duplicate commits. Thanks.


Kevin


On 01/03/2018 11:55 AM, Turaga, Nitesh wrote:

Hi Kevin,

I?ll try to help you. I?ll take a look at your package and get back to you. Please forward this message to bioc-devel so that it?s public and other maintainers/users know that there is an issue with your package.

Best,

Nitesh

On Jan 3, 2018, at 2:31 PM, Kevin Horan <khoran at globalrecordings.net> wrote:

Nitesh,

 I am one of the maintainers for the ChemmineR package on bioconductor. I have a bad duplicate commit problem I was wondering if you could help me with. Basically, it seems one string of 1000 or so commits has been duplicated twice in the repository, so that there are now 3 copies of each of these commits. This mess is already in the bioconductor repository because in order to allow me to get some last minute changes in for the last release, someone at boic disabled the duplicate commit check for me. That was before I understood the extend of the problem.

 I'm not sure if its really your job to help with this sort of thing, as I understand that it's not a bioconductor problem. So if not that is fine. I've spent 6 hours trying to fix it myself ( and I am generally good with  GIT), but I've only succeeded in make more duplicates. So I think I'd need to toss all the history up to the last release, which I image I'd need your help to reset the repo on the bioc side as well.

 If you can help, there are more specifics I can give you, just let me know.

Thanks.


Kevin Horan

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.

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.

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 7, 2018, at 2:17 PM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:

Now your version numbers don?t match. You skip versions without those commits

Your history is supposed to look like this,

commit 5a1ad6ff08747d1380875840fe96d3633c210ee2 (HEAD -> master)
Author: khoran <khoran at cs.ucr.edu>
Date:   Sun Jan 7 09:44:16 2018 -0800

   History was rolled back 6 months to remove dup commits.
   All changes since then are being re-applied in this one commit.

commit fb7c8ed13eb09527038e1959737d556a15667771
Author: Herv? Pag?s <hpages at fredhutch.org>
Date:   Mon Oct 30 12:52:08 2017 -0400

   bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

commit 73c4cb1d48d9f14598e63a28a9b9184e096f254e
Author: Herv? Pag?s <hpages at fredhutch.org>
Date:   Mon Oct 30 12:39:24 2017 -0400

   bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

commit e3a8d2122a65305c478276e538faace277ea9ed6
Author: Kevin Horan <khoran at cs.ucr.edu>
Date:   Fri Jun 30 20:12:52 2017 +0000

   Merge branch 'master' into devel

   git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChemmineR at 130816 bc3139a8-67e5-0310-9ffc-ced21a209358

##########################
Same for the RELEASE branch. 
##########################

commit 7111f07cc9c32977f1eca63a0f2a25cb1092f7be (HEAD -> RELEASE_3_6)
Author: khoran <khoran at cs.ucr.edu>
Date:   Sun Jan 7 10:14:49 2018 -0800

   set version for release branch

commit a2615e98aff83130f6129abc02132a65d99689b9
Author: Herv? Pag?s <hpages at fredhutch.org>
Date:   Mon Oct 30 12:39:24 2017 -0400

   bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

commit e3a8d2122a65305c478276e538faace277ea9ed6
Author: Kevin Horan <khoran at cs.ucr.edu>
Date:   Fri Jun 30 20:12:52 2017 +0000

   Merge branch 'master' into devel

   git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChemmineR at 130816 bc3139a8-67e5-0310-9ffc-ced21a209358


I can make your commit history look like this, but I?m not sure if all the changes in your code are reflected accurately. You might have to make sure manually, and see if your code and package work like you expect.

Once they work as expected, please don?t do anything with the commit history. Just add the new changes on top of what exists. It becomes extremely complicated and time taking to fix the commit history manually.

Best,

Nitesh 

On Jan 7, 2018, at 1:32 PM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:

Hi Kevin,

It seems you have lost a few commits which are important in tracking RELEASE?s in Bioconductor.


commit fb5868c2fdfa607b52e467881212b3619a8b0ae9 (HEAD -> master)
Author: Herv? Pag?s <hpages at fredhutch.org>
Date:   Mon Oct 30 12:52:08 2017 -0400

  bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

commit 46e0a56d1117cca6274fea3b8430eb8d6c7a9976 (RELEASE_3_6)
Author: Herv? Pag?s <hpages at fredhutch.org>
Date:   Mon Oct 30 12:39:24 2017 -0400

  bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

These commits are important. 

Please wait for further instructions while we figure out how to resolve this issue. 

Best,

Nitesh 

On Jan 7, 2018, at 1:20 PM, Kevin Horan <khoran at cs.ucr.edu> wrote:

Nitesh,

 I have pushed changes to both the master and RELEASE_3_6 branches now.

Kevin


On 01/05/2018 11:14 AM, Turaga, Nitesh wrote:

Hi Kevin,

Please overlay the commits so that we can get your package building on our build machines.

Please do this soon. You also have to make RELEASE_3_6 branch now.

We have skipped your package for now, and it won?t show up in the release report.
Thanks

Nitesh

On Jan 4, 2018, at 10:07 AM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:

Hi Kevin,

I have your package reset to this commit e3a8d2122a65305c478276e538faace277ea9ed6.

Please check. You will need to overlay all the commits including the new release on top of this (RELEASE_3_6).

If you have any questions further on this, please ask before pushing to Bioconductor.

Best,

Nitesh

On Jan 3, 2018, at 7:10 PM, Kevin Horan <khoran at cs.ucr.edu> wrote:

Nitesh,

That sounds great, thanks.

Kevin


On 01/03/2018 01:53 PM, Turaga, Nitesh wrote:

Hi Kevin,

I can help you with this. I can take you back to a state before August 18th and put that repository up on our Git server.

From that point onwards you?d have to reapply all the changes on that repository from "commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389" and onwards.

commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389
Merge: 643e470 f1785fb
Author: tgirke <tgirke at citrus.ucr.edu>
Date:   Sat Aug 19 16:32:35 2017 -0700

 resolved conflicts

I can do this tomorrow and send you an email.


Best,

Nitesh

On Jan 3, 2018, at 4:28 PM, Kevin Horan <khoran at cs.ucr.edu> wrote:

Nitesh,

I tried to re-construct the repo starting from what is left in the SVN repository, but I couldn't get all the branches to come over and it just generally looks too different to easily replace the bioc repo.

I was thinking though, if its easy for you to clobber the current bioc repo for ChemmineR and re-create it from the old SVN repo (ie, because you might have scripts from having done it the first time), then that might be an easier fix. Then I can check it out, apply the recent changes and push it back.

But if you don't think that's a good idea, then I'll take your offer of help and we can try to figure out how to get rid of the duplicate commits. Thanks.


Kevin


On 01/03/2018 11:55 AM, Turaga, Nitesh wrote:

Hi Kevin,

I?ll try to help you. I?ll take a look at your package and get back to you. Please forward this message to bioc-devel so that it?s public and other maintainers/users know that there is an issue with your package.

Best,

Nitesh

On Jan 3, 2018, at 2:31 PM, Kevin Horan <khoran at globalrecordings.net> wrote:

Nitesh,

I am one of the maintainers for the ChemmineR package on bioconductor. I have a bad duplicate commit problem I was wondering if you could help me with. Basically, it seems one string of 1000 or so commits has been duplicated twice in the repository, so that there are now 3 copies of each of these commits. This mess is already in the bioconductor repository because in order to allow me to get some last minute changes in for the last release, someone at boic disabled the duplicate commit check for me. That was before I understood the extend of the problem.

I'm not sure if its really your job to help with this sort of thing, as I understand that it's not a bioconductor problem. So if not that is fine. I've spent 6 hours trying to fix it myself ( and I am generally good with  GIT), but I've only succeeded in make more duplicates. So I think I'd need to toss all the history up to the last release, which I image I'd need your help to reset the repo on the bioc side as well.

If you can help, there are more specifics I can give you, just let me know.

Thanks.


Kevin Horan

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.

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.

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 Kevin,

One last message, give me a green light to fix your repository once you have had a chance to see my emails.

Best,

Nitesh

On Jan 7, 2018, at 2:17 PM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:

Now your version numbers don?t match. You skip versions without those commits

Your history is supposed to look like this,

commit 5a1ad6ff08747d1380875840fe96d3633c210ee2 (HEAD -> master)
Author: khoran <khoran at cs.ucr.edu>
Date:   Sun Jan 7 09:44:16 2018 -0800

    History was rolled back 6 months to remove dup commits.
    All changes since then are being re-applied in this one commit.

commit fb7c8ed13eb09527038e1959737d556a15667771
Author: Herv? Pag?s <hpages at fredhutch.org>
Date:   Mon Oct 30 12:52:08 2017 -0400

    bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

commit 73c4cb1d48d9f14598e63a28a9b9184e096f254e
Author: Herv? Pag?s <hpages at fredhutch.org>
Date:   Mon Oct 30 12:39:24 2017 -0400

    bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

commit e3a8d2122a65305c478276e538faace277ea9ed6
Author: Kevin Horan <khoran at cs.ucr.edu>
Date:   Fri Jun 30 20:12:52 2017 +0000

    Merge branch 'master' into devel

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChemmineR at 130816 bc3139a8-67e5-0310-9ffc-ced21a209358

##########################
Same for the RELEASE branch.
##########################

commit 7111f07cc9c32977f1eca63a0f2a25cb1092f7be (HEAD -> RELEASE_3_6)
Author: khoran <khoran at cs.ucr.edu>
Date:   Sun Jan 7 10:14:49 2018 -0800

    set version for release branch

commit a2615e98aff83130f6129abc02132a65d99689b9
Author: Herv? Pag?s <hpages at fredhutch.org>
Date:   Mon Oct 30 12:39:24 2017 -0400

    bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

commit e3a8d2122a65305c478276e538faace277ea9ed6
Author: Kevin Horan <khoran at cs.ucr.edu>
Date:   Fri Jun 30 20:12:52 2017 +0000

    Merge branch 'master' into devel

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChemmineR at 130816 bc3139a8-67e5-0310-9ffc-ced21a209358


I can make your commit history look like this, but I?m not sure if all the changes in your code are reflected accurately. You might have to make sure manually, and see if your code and package work like you expect.

Once they work as expected, please don?t do anything with the commit history. Just add the new changes on top of what exists. It becomes extremely complicated and time taking to fix the commit history manually.

Best,

Nitesh

On Jan 7, 2018, at 1:32 PM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:

Hi Kevin,

It seems you have lost a few commits which are important in tracking RELEASE?s in Bioconductor.


commit fb5868c2fdfa607b52e467881212b3619a8b0ae9 (HEAD -> master)
Author: Herv? Pag?s <hpages at fredhutch.org>
Date:   Mon Oct 30 12:52:08 2017 -0400

   bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

commit 46e0a56d1117cca6274fea3b8430eb8d6c7a9976 (RELEASE_3_6)
Author: Herv? Pag?s <hpages at fredhutch.org>
Date:   Mon Oct 30 12:39:24 2017 -0400

   bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

These commits are important.

Please wait for further instructions while we figure out how to resolve this issue.

Best,

Nitesh

On Jan 7, 2018, at 1:20 PM, Kevin Horan <khoran at cs.ucr.edu> wrote:

Nitesh,

  I have pushed changes to both the master and RELEASE_3_6 branches now.

Kevin


On 01/05/2018 11:14 AM, Turaga, Nitesh wrote:

Hi Kevin,

Please overlay the commits so that we can get your package building on our build machines.

Please do this soon. You also have to make RELEASE_3_6 branch now.

We have skipped your package for now, and it won?t show up in the release report.
Thanks

Nitesh

On Jan 4, 2018, at 10:07 AM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:

Hi Kevin,

I have your package reset to this commit e3a8d2122a65305c478276e538faace277ea9ed6.

Please check. You will need to overlay all the commits including the new release on top of this (RELEASE_3_6).

If you have any questions further on this, please ask before pushing to Bioconductor.

Best,

Nitesh

On Jan 3, 2018, at 7:10 PM, Kevin Horan <khoran at cs.ucr.edu> wrote:

Nitesh,

That sounds great, thanks.

Kevin


On 01/03/2018 01:53 PM, Turaga, Nitesh wrote:

Hi Kevin,

I can help you with this. I can take you back to a state before August 18th and put that repository up on our Git server.

 From that point onwards you?d have to reapply all the changes on that repository from "commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389" and onwards.

commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389
Merge: 643e470 f1785fb
Author: tgirke <tgirke at citrus.ucr.edu>
Date:   Sat Aug 19 16:32:35 2017 -0700

  resolved conflicts

I can do this tomorrow and send you an email.


Best,

Nitesh

On Jan 3, 2018, at 4:28 PM, Kevin Horan <khoran at cs.ucr.edu> wrote:

Nitesh,

I tried to re-construct the repo starting from what is left in the SVN repository, but I couldn't get all the branches to come over and it just generally looks too different to easily replace the bioc repo.

I was thinking though, if its easy for you to clobber the current bioc repo for ChemmineR and re-create it from the old SVN repo (ie, because you might have scripts from having done it the first time), then that might be an easier fix. Then I can check it out, apply the recent changes and push it back.

But if you don't think that's a good idea, then I'll take your offer of help and we can try to figure out how to get rid of the duplicate commits. Thanks.


Kevin


On 01/03/2018 11:55 AM, Turaga, Nitesh wrote:

Hi Kevin,

I?ll try to help you. I?ll take a look at your package and get back to you. Please forward this message to bioc-devel so that it?s public and other maintainers/users know that there is an issue with your package.

Best,

Nitesh

On Jan 3, 2018, at 2:31 PM, Kevin Horan <khoran at globalrecordings.net> wrote:

Nitesh,

I am one of the maintainers for the ChemmineR package on bioconductor. I have a bad duplicate commit problem I was wondering if you could help me with. Basically, it seems one string of 1000 or so commits has been duplicated twice in the repository, so that there are now 3 copies of each of these commits. This mess is already in the bioconductor repository because in order to allow me to get some last minute changes in for the last release, someone at boic disabled the duplicate commit check for me. That was before I understood the extend of the problem.

I'm not sure if its really your job to help with this sort of thing, as I understand that it's not a bioconductor problem. So if not that is fine. I've spent 6 hours trying to fix it myself ( and I am generally good with  GIT), but I've only succeeded in make more duplicates. So I think I'd need to toss all the history up to the last release, which I image I'd need your help to reset the repo on the bioc side as well.

If you can help, there are more specifics I can give you, just let me know.

Thanks.


Kevin Horan

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.

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.

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 8, 2018, at 8:39 PM, Kevin Horan <khoran at cs.ucr.edu> wrote:

Nitesh,

   Sorry, just saw your email now. You can go ahead and make those changes. Thanks for all your help.

Kevin


On 01/07/2018 11:22 AM, Turaga, Nitesh wrote:

Hi Kevin,

One last message, give me a green light to fix your repository once you have had a chance to see my emails.

Best,

Nitesh

On Jan 7, 2018, at 2:17 PM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:

Now your version numbers don?t match. You skip versions without those commits

Your history is supposed to look like this,

commit 5a1ad6ff08747d1380875840fe96d3633c210ee2 (HEAD -> master)
Author: khoran <khoran at cs.ucr.edu>
Date:   Sun Jan 7 09:44:16 2018 -0800

   History was rolled back 6 months to remove dup commits.
   All changes since then are being re-applied in this one commit.

commit fb7c8ed13eb09527038e1959737d556a15667771
Author: Herv? Pag?s <hpages at fredhutch.org>
Date:   Mon Oct 30 12:52:08 2017 -0400

   bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

commit 73c4cb1d48d9f14598e63a28a9b9184e096f254e
Author: Herv? Pag?s <hpages at fredhutch.org>
Date:   Mon Oct 30 12:39:24 2017 -0400

   bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

commit e3a8d2122a65305c478276e538faace277ea9ed6
Author: Kevin Horan <khoran at cs.ucr.edu>
Date:   Fri Jun 30 20:12:52 2017 +0000

   Merge branch 'master' into devel

   git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChemmineR at 130816 bc3139a8-67e5-0310-9ffc-ced21a209358

##########################
Same for the RELEASE branch.
##########################

commit 7111f07cc9c32977f1eca63a0f2a25cb1092f7be (HEAD -> RELEASE_3_6)
Author: khoran <khoran at cs.ucr.edu>
Date:   Sun Jan 7 10:14:49 2018 -0800

   set version for release branch

commit a2615e98aff83130f6129abc02132a65d99689b9
Author: Herv? Pag?s <hpages at fredhutch.org>
Date:   Mon Oct 30 12:39:24 2017 -0400

   bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

commit e3a8d2122a65305c478276e538faace277ea9ed6
Author: Kevin Horan <khoran at cs.ucr.edu>
Date:   Fri Jun 30 20:12:52 2017 +0000

   Merge branch 'master' into devel

   git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChemmineR at 130816 bc3139a8-67e5-0310-9ffc-ced21a209358


I can make your commit history look like this, but I?m not sure if all the changes in your code are reflected accurately. You might have to make sure manually, and see if your code and package work like you expect.

Once they work as expected, please don?t do anything with the commit history. Just add the new changes on top of what exists. It becomes extremely complicated and time taking to fix the commit history manually.

Best,

Nitesh

On Jan 7, 2018, at 1:32 PM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:

Hi Kevin,

It seems you have lost a few commits which are important in tracking RELEASE?s in Bioconductor.


commit fb5868c2fdfa607b52e467881212b3619a8b0ae9 (HEAD -> master)
Author: Herv? Pag?s <hpages at fredhutch.org>
Date:   Mon Oct 30 12:52:08 2017 -0400

  bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

commit 46e0a56d1117cca6274fea3b8430eb8d6c7a9976 (RELEASE_3_6)
Author: Herv? Pag?s <hpages at fredhutch.org>
Date:   Mon Oct 30 12:39:24 2017 -0400

  bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

These commits are important.

Please wait for further instructions while we figure out how to resolve this issue.

Best,

Nitesh

On Jan 7, 2018, at 1:20 PM, Kevin Horan <khoran at cs.ucr.edu> wrote:

Nitesh,

 I have pushed changes to both the master and RELEASE_3_6 branches now.

Kevin


On 01/05/2018 11:14 AM, Turaga, Nitesh wrote:

Hi Kevin,

Please overlay the commits so that we can get your package building on our build machines.

Please do this soon. You also have to make RELEASE_3_6 branch now.

We have skipped your package for now, and it won?t show up in the release report.
Thanks

Nitesh

On Jan 4, 2018, at 10:07 AM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:

Hi Kevin,

I have your package reset to this commit e3a8d2122a65305c478276e538faace277ea9ed6.

Please check. You will need to overlay all the commits including the new release on top of this (RELEASE_3_6).

If you have any questions further on this, please ask before pushing to Bioconductor.

Best,

Nitesh

On Jan 3, 2018, at 7:10 PM, Kevin Horan <khoran at cs.ucr.edu> wrote:

Nitesh,

That sounds great, thanks.

Kevin


On 01/03/2018 01:53 PM, Turaga, Nitesh wrote:

Hi Kevin,

I can help you with this. I can take you back to a state before August 18th and put that repository up on our Git server.

From that point onwards you?d have to reapply all the changes on that repository from "commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389" and onwards.

commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389
Merge: 643e470 f1785fb
Author: tgirke <tgirke at citrus.ucr.edu>
Date:   Sat Aug 19 16:32:35 2017 -0700

 resolved conflicts

I can do this tomorrow and send you an email.


Best,

Nitesh

On Jan 3, 2018, at 4:28 PM, Kevin Horan <khoran at cs.ucr.edu> wrote:

Nitesh,

I tried to re-construct the repo starting from what is left in the SVN repository, but I couldn't get all the branches to come over and it just generally looks too different to easily replace the bioc repo.

I was thinking though, if its easy for you to clobber the current bioc repo for ChemmineR and re-create it from the old SVN repo (ie, because you might have scripts from having done it the first time), then that might be an easier fix. Then I can check it out, apply the recent changes and push it back.

But if you don't think that's a good idea, then I'll take your offer of help and we can try to figure out how to get rid of the duplicate commits. Thanks.


Kevin


On 01/03/2018 11:55 AM, Turaga, Nitesh wrote:

Hi Kevin,

I?ll try to help you. I?ll take a look at your package and get back to you. Please forward this message to bioc-devel so that it?s public and other maintainers/users know that there is an issue with your package.

Best,

Nitesh

On Jan 3, 2018, at 2:31 PM, Kevin Horan <khoran at globalrecordings.net> wrote:

Nitesh,

I am one of the maintainers for the ChemmineR package on bioconductor. I have a bad duplicate commit problem I was wondering if you could help me with. Basically, it seems one string of 1000 or so commits has been duplicated twice in the repository, so that there are now 3 copies of each of these commits. This mess is already in the bioconductor repository because in order to allow me to get some last minute changes in for the last release, someone at boic disabled the duplicate commit check for me. That was before I understood the extend of the problem.

I'm not sure if its really your job to help with this sort of thing, as I understand that it's not a bioconductor problem. So if not that is fine. I've spent 6 hours trying to fix it myself ( and I am generally good with  GIT), but I've only succeeded in make more duplicates. So I think I'd need to toss all the history up to the last release, which I image I'd need your help to reset the repo on the bioc side as well.

If you can help, there are more specifics I can give you, just let me know.

Thanks.


Kevin Horan

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Hi Kevin,

Your repository should now be fixed.  Please re-clone your repository.

Best,

Nitesh

On Jan 8, 2018, at 8:39 PM, Kevin Horan <khoran at cs.ucr.edu> wrote:

Nitesh,

    Sorry, just saw your email now. You can go ahead and make those changes. Thanks for all your help.

Kevin


On 01/07/2018 11:22 AM, Turaga, Nitesh wrote:

Hi Kevin,

One last message, give me a green light to fix your repository once you have had a chance to see my emails.

Best,

Nitesh

On Jan 7, 2018, at 2:17 PM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:

Now your version numbers don?t match. You skip versions without those commits

Your history is supposed to look like this,

commit 5a1ad6ff08747d1380875840fe96d3633c210ee2 (HEAD -> master)
Author: khoran <khoran at cs.ucr.edu>
Date:   Sun Jan 7 09:44:16 2018 -0800

    History was rolled back 6 months to remove dup commits.
    All changes since then are being re-applied in this one commit.

commit fb7c8ed13eb09527038e1959737d556a15667771
Author: Herv? Pag?s <hpages at fredhutch.org>
Date:   Mon Oct 30 12:52:08 2017 -0400

    bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

commit 73c4cb1d48d9f14598e63a28a9b9184e096f254e
Author: Herv? Pag?s <hpages at fredhutch.org>
Date:   Mon Oct 30 12:39:24 2017 -0400

    bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

commit e3a8d2122a65305c478276e538faace277ea9ed6
Author: Kevin Horan <khoran at cs.ucr.edu>
Date:   Fri Jun 30 20:12:52 2017 +0000

    Merge branch 'master' into devel

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChemmineR at 130816 bc3139a8-67e5-0310-9ffc-ced21a209358

##########################
Same for the RELEASE branch.
##########################

commit 7111f07cc9c32977f1eca63a0f2a25cb1092f7be (HEAD -> RELEASE_3_6)
Author: khoran <khoran at cs.ucr.edu>
Date:   Sun Jan 7 10:14:49 2018 -0800

    set version for release branch

commit a2615e98aff83130f6129abc02132a65d99689b9
Author: Herv? Pag?s <hpages at fredhutch.org>
Date:   Mon Oct 30 12:39:24 2017 -0400

    bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

commit e3a8d2122a65305c478276e538faace277ea9ed6
Author: Kevin Horan <khoran at cs.ucr.edu>
Date:   Fri Jun 30 20:12:52 2017 +0000

    Merge branch 'master' into devel

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChemmineR at 130816 bc3139a8-67e5-0310-9ffc-ced21a209358


I can make your commit history look like this, but I?m not sure if all the changes in your code are reflected accurately. You might have to make sure manually, and see if your code and package work like you expect.

Once they work as expected, please don?t do anything with the commit history. Just add the new changes on top of what exists. It becomes extremely complicated and time taking to fix the commit history manually.

Best,

Nitesh

On Jan 7, 2018, at 1:32 PM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:

Hi Kevin,

It seems you have lost a few commits which are important in tracking RELEASE?s in Bioconductor.


commit fb5868c2fdfa607b52e467881212b3619a8b0ae9 (HEAD -> master)
Author: Herv? Pag?s <hpages at fredhutch.org>
Date:   Mon Oct 30 12:52:08 2017 -0400

   bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

commit 46e0a56d1117cca6274fea3b8430eb8d6c7a9976 (RELEASE_3_6)
Author: Herv? Pag?s <hpages at fredhutch.org>
Date:   Mon Oct 30 12:39:24 2017 -0400

   bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

These commits are important.

Please wait for further instructions while we figure out how to resolve this issue.

Best,

Nitesh

On Jan 7, 2018, at 1:20 PM, Kevin Horan <khoran at cs.ucr.edu> wrote:

Nitesh,

  I have pushed changes to both the master and RELEASE_3_6 branches now.

Kevin


On 01/05/2018 11:14 AM, Turaga, Nitesh wrote:

Hi Kevin,

Please overlay the commits so that we can get your package building on our build machines.

Please do this soon. You also have to make RELEASE_3_6 branch now.

We have skipped your package for now, and it won?t show up in the release report.
Thanks

Nitesh

On Jan 4, 2018, at 10:07 AM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:

Hi Kevin,

I have your package reset to this commit e3a8d2122a65305c478276e538faace277ea9ed6.

Please check. You will need to overlay all the commits including the new release on top of this (RELEASE_3_6).

If you have any questions further on this, please ask before pushing to Bioconductor.

Best,

Nitesh

On Jan 3, 2018, at 7:10 PM, Kevin Horan <khoran at cs.ucr.edu> wrote:

Nitesh,

That sounds great, thanks.

Kevin


On 01/03/2018 01:53 PM, Turaga, Nitesh wrote:

Hi Kevin,

I can help you with this. I can take you back to a state before August 18th and put that repository up on our Git server.

 From that point onwards you?d have to reapply all the changes on that repository from "commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389" and onwards.

commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389
Merge: 643e470 f1785fb
Author: tgirke <tgirke at citrus.ucr.edu>
Date:   Sat Aug 19 16:32:35 2017 -0700

  resolved conflicts

I can do this tomorrow and send you an email.


Best,

Nitesh

On Jan 3, 2018, at 4:28 PM, Kevin Horan <khoran at cs.ucr.edu> wrote:

Nitesh,

I tried to re-construct the repo starting from what is left in the SVN repository, but I couldn't get all the branches to come over and it just generally looks too different to easily replace the bioc repo.

I was thinking though, if its easy for you to clobber the current bioc repo for ChemmineR and re-create it from the old SVN repo (ie, because you might have scripts from having done it the first time), then that might be an easier fix. Then I can check it out, apply the recent changes and push it back.

But if you don't think that's a good idea, then I'll take your offer of help and we can try to figure out how to get rid of the duplicate commits. Thanks.


Kevin


On 01/03/2018 11:55 AM, Turaga, Nitesh wrote:

Hi Kevin,

I?ll try to help you. I?ll take a look at your package and get back to you. Please forward this message to bioc-devel so that it?s public and other maintainers/users know that there is an issue with your package.

Best,

Nitesh

On Jan 3, 2018, at 2:31 PM, Kevin Horan <khoran at globalrecordings.net> wrote:

Nitesh,

I am one of the maintainers for the ChemmineR package on bioconductor. I have a bad duplicate commit problem I was wondering if you could help me with. Basically, it seems one string of 1000 or so commits has been duplicated twice in the repository, so that there are now 3 copies of each of these commits. This mess is already in the bioconductor repository because in order to allow me to get some last minute changes in for the last release, someone at boic disabled the duplicate commit check for me. That was before I understood the extend of the problem.

I'm not sure if its really your job to help with this sort of thing, as I understand that it's not a bioconductor problem. So if not that is fine. I've spent 6 hours trying to fix it myself ( and I am generally good with  GIT), but I've only succeeded in make more duplicates. So I think I'd need to toss all the history up to the last release, which I image I'd need your help to reset the repo on the bioc side as well.

If you can help, there are more specifics I can give you, just let me know.

Thanks.


Kevin Horan

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.

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.

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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.