subject:"\\\\\\\[Bioc\\\\\\\-devel\\\\\\\] Duplicate commit error on and off"

Re: [Bioc-devel] Duplicate commit error on and off

2017-10-06 Thread Turaga, Nitesh

This is good news!


> On Oct 5, 2017, at 7:06 PM, Thomas Girke  wrote:
> 
> Thanks. I have synced everything to the current development and was able to 
> commit back to Bioc-upstream/master.
> 
> Thomas
> 
> On Thu, Oct 5, 2017 at 10:28 AM Turaga, Nitesh 
>  wrote:
> Done. If you clone from Bioconductor again, you should get a clean copy just 
> as after the transition.
> 
> If you have questions let me know.
> 
> Best,
> 
> Nitesh
> 
> 
> > On Oct 5, 2017, at 1:05 PM, Thomas Girke  wrote:
> >
> > Yes, let's just do it this way.
> >
> > Thomas
> >
> > On Thu, Oct 5, 2017 at 9:36 AM Turaga, Nitesh 
> >  wrote:
> > It would be easier. I can do it and it would take you back to,
> >
> > commit c84c7b5fbdf1419af5030b66f8a759d29307f40b (git-svn)
> > Author: Herve Pages 
> > Date:   Mon Apr 24 19:50:57 2017 +
> >
> > bump x.y.z versions to odd y after creation of 3_5 branch
> >
> > git-svn-id: 
> > file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/systemPipeR@129129
> >  bc3139a8-67e5-0310-9ffc-ced21a209358
> >
> >
> > Give me a thumbs up and I’ll go ahead.
> >
> > > On Oct 5, 2017, at 11:03 AM, Thomas Girke  wrote:
> > >
> > > Hi Nitesh,
> > >
> > > If the reset to #c84c7b5f is the best option then let's do this.
> > >
> > > Just wondering, wouldn't it be much easier to run on your end
> > >
> > > git reset --hard <>
> > > git merge --squash HEAD@{1}
> > >
> > > This would deduplicate everything without losing any commits.
> > >
> > > Thanks,
> > >
> > > Thomas
> > >
> > > On Thu, Oct 05, 2017 at 10:56:53AM +, Turaga, Nitesh wrote:
> > >> Hi Thomas,
> > >>
> > >> Sorry for the email sent to the wrong place earlier.
> > >>
> > >> One way I can help you is, that I can take you back to the “clean” state 
> > >> on August 16th to commit (c84c7b5fbdf1419af5030b66f8a759d29307f40b).
> > >>
> > >> i.e before the commit
> > >>
> > >> commit 500a8b924b7c8bfd9b4e960b471e1e32c06f
> > >> Merge: e6ff3f8 3cd5aee
> > >> Author: tgirke 
> > >> Date:   Thu Aug 17 18:55:36 2017 -0700
> > >>
> > >>Fixed conflicts in version change
> > >>
> > >> You would have to manually replay all the commits after that on top of 
> > >> that. By this, I mean, all the commits after 500a8b9, need to be 
> > >> cherry-picked and pushed to the repo. But you need to be careful here, 
> > >> because only “non-merge” commits should be cherry picked. This avoids 
> > >> the duplicates on your contaminated branch to not enter the new clean 
> > >> “master” branch.
> > >>
> > >> Non merge commits,
> > >> commit 75bca921c1e2c85e8ab36b5a2d006fb2837c1c50
> > >> commit 49fa6d434c7bc690223c2b0c88c5353386eb39ba
> > >> commit c73fb18ad737bea84b5c7bc3967c9bea8bcd4b9c
> > >>
> > >>
> > >> After doing that, your last 4 commits will look like this,
> > >>
> > >>
> > >> commit 9fc03a5719486e333bc1182b07cd6c5e15e8798d (HEAD -> master)
> > >> Author: Hervé Pagès 
> > >> Date:   Thu Aug 31 22:28:06 2017 -0700
> > >>
> > >>restore empty folder lost during svn-to-git transition
> > >>
> > >> commit 2edc489e4d3ca642a240f062c34528e0d918e11e
> > >> Author: tgirke 
> > >> Date:   Wed Aug 23 19:21:04 2017 -0700
> > >>
> > >>moduleload with serveral envir variables
> > >>
> > >> commit 1d05c70f27ca083d76bca7ef7be59f43662ba07c
> > >> Author: tgirke 
> > >> Date:   Thu Aug 17 20:29:38 2017 -0700
> > >>
> > >>Fixed gene set naming problem in GOCluster_Report
> > >>
> > >> commit c84c7b5fbdf1419af5030b66f8a759d29307f40b (git-svn)
> > >> Author: Herve Pages 
> > >> Date:   Mon Apr 24 19:50:57 2017 +
> > >>
> > >>bump x.y.z versions to odd y after creation of 3_5 branch
> > >>
> > >>git-svn-id: 
> > >> file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/systemPipeR@129129
> > >>  bc3139a8-67e5-0310-9ffc-ced21a209358
> > >>
> > >>
> > >> This has a couple of consequences,
> > >>
> > >> 1. you need to follow 
> > >> (http://master.bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-
> > >>  ) to switch you master branch to follow bioconductor exactly.
> > >>
> > >> 2. you and your collaborators, need to re-clone from your GitHub, and 
> > >> work on the new master branch abandoning the old one.
> > >>
> > >> 3. Make sure that all the file changes you’ve made have been moved over.
> > >>
> > >> Let me know if this works for you, and we can go ahead. Another option 
> > >> is, I can do this for you, with a clean “master” on the Bioconductor 
> > >> repo, and you can follow the “force bioconductor-to-github” manual on 
> > >> your end.
> > >>
> > >> Nitesh
> > >>
> > >>
> > >>> On Oct 4, 2017, at 2:38 PM, Thomas Girke  wrote:
> > >>>
> > >>> I didn't commit the duplicate fix with git merge --squash

Re: [Bioc-devel] Duplicate commit error on and off

2017-10-05 Thread Turaga, Nitesh

Done. If you clone from Bioconductor again, you should get a clean copy just as 
after the transition. 

If you have questions let me know. 

Best,

Nitesh 


> On Oct 5, 2017, at 1:05 PM, Thomas Girke  wrote:
> 
> Yes, let's just do it this way.
> 
> Thomas
> 
> On Thu, Oct 5, 2017 at 9:36 AM Turaga, Nitesh  
> wrote:
> It would be easier. I can do it and it would take you back to,
> 
> commit c84c7b5fbdf1419af5030b66f8a759d29307f40b (git-svn)
> Author: Herve Pages 
> Date:   Mon Apr 24 19:50:57 2017 +
> 
> bump x.y.z versions to odd y after creation of 3_5 branch
> 
> git-svn-id: 
> file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/systemPipeR@129129
>  bc3139a8-67e5-0310-9ffc-ced21a209358
> 
> 
> Give me a thumbs up and I’ll go ahead.
> 
> > On Oct 5, 2017, at 11:03 AM, Thomas Girke  wrote:
> >
> > Hi Nitesh,
> >
> > If the reset to #c84c7b5f is the best option then let's do this.
> >
> > Just wondering, wouldn't it be much easier to run on your end
> >
> > git reset --hard <>
> > git merge --squash HEAD@{1}
> >
> > This would deduplicate everything without losing any commits.
> >
> > Thanks,
> >
> > Thomas
> >
> > On Thu, Oct 05, 2017 at 10:56:53AM +, Turaga, Nitesh wrote:
> >> Hi Thomas,
> >>
> >> Sorry for the email sent to the wrong place earlier.
> >>
> >> One way I can help you is, that I can take you back to the “clean” state 
> >> on August 16th to commit (c84c7b5fbdf1419af5030b66f8a759d29307f40b).
> >>
> >> i.e before the commit
> >>
> >> commit 500a8b924b7c8bfd9b4e960b471e1e32c06f
> >> Merge: e6ff3f8 3cd5aee
> >> Author: tgirke 
> >> Date:   Thu Aug 17 18:55:36 2017 -0700
> >>
> >>Fixed conflicts in version change
> >>
> >> You would have to manually replay all the commits after that on top of 
> >> that. By this, I mean, all the commits after 500a8b9, need to be 
> >> cherry-picked and pushed to the repo. But you need to be careful here, 
> >> because only “non-merge” commits should be cherry picked. This avoids the 
> >> duplicates on your contaminated branch to not enter the new clean “master” 
> >> branch.
> >>
> >> Non merge commits,
> >> commit 75bca921c1e2c85e8ab36b5a2d006fb2837c1c50
> >> commit 49fa6d434c7bc690223c2b0c88c5353386eb39ba
> >> commit c73fb18ad737bea84b5c7bc3967c9bea8bcd4b9c
> >>
> >>
> >> After doing that, your last 4 commits will look like this,
> >>
> >>
> >> commit 9fc03a5719486e333bc1182b07cd6c5e15e8798d (HEAD -> master)
> >> Author: Hervé Pagès 
> >> Date:   Thu Aug 31 22:28:06 2017 -0700
> >>
> >>restore empty folder lost during svn-to-git transition
> >>
> >> commit 2edc489e4d3ca642a240f062c34528e0d918e11e
> >> Author: tgirke 
> >> Date:   Wed Aug 23 19:21:04 2017 -0700
> >>
> >>moduleload with serveral envir variables
> >>
> >> commit 1d05c70f27ca083d76bca7ef7be59f43662ba07c
> >> Author: tgirke 
> >> Date:   Thu Aug 17 20:29:38 2017 -0700
> >>
> >>Fixed gene set naming problem in GOCluster_Report
> >>
> >> commit c84c7b5fbdf1419af5030b66f8a759d29307f40b (git-svn)
> >> Author: Herve Pages 
> >> Date:   Mon Apr 24 19:50:57 2017 +
> >>
> >>bump x.y.z versions to odd y after creation of 3_5 branch
> >>
> >>git-svn-id: 
> >> file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/systemPipeR@129129
> >>  bc3139a8-67e5-0310-9ffc-ced21a209358
> >>
> >>
> >> This has a couple of consequences,
> >>
> >> 1. you need to follow 
> >> (http://master.bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-
> >>  ) to switch you master branch to follow bioconductor exactly.
> >>
> >> 2. you and your collaborators, need to re-clone from your GitHub, and work 
> >> on the new master branch abandoning the old one.
> >>
> >> 3. Make sure that all the file changes you’ve made have been moved over.
> >>
> >> Let me know if this works for you, and we can go ahead. Another option is, 
> >> I can do this for you, with a clean “master” on the Bioconductor repo, and 
> >> you can follow the “force bioconductor-to-github” manual on your end.
> >>
> >> Nitesh
> >>
> >>
> >>> On Oct 4, 2017, at 2:38 PM, Thomas Girke  wrote:
> >>>
> >>> I didn't commit the duplicate fix with git merge --squash since I wanted 
> >>> to do the branch swap as I did with ChemmineR, but now this is not 
> >>> working anymore or there are other problems?
> >>>
> >>> One possible solution could be to allow me a one time push with the -f 
> >>> flag with the deduplicated master branch. According to the instructions 
> >>> here (https://goo.gl/xnr9j8) this should be possible but I think it has 
> >>> been disabled. Some of the Bioc/FAQs related to this topic indicate this 
> >>> too.
> >>>
> >>> Thomas
> >>>
> >>> On Wed, Oct 4, 2017 at 11:27 AM Turaga, Nitesh 
> >>>

Re: [Bioc-devel] Duplicate commit error on and off

2017-10-05 Thread Thomas Girke

Yes, let's just do it this way.

Thomas

On Thu, Oct 5, 2017 at 9:36 AM Turaga, Nitesh 
wrote:

> It would be easier. I can do it and it would take you back to,
>
> commit c84c7b5fbdf1419af5030b66f8a759d29307f40b (git-svn)
> Author: Herve Pages 
> Date:   Mon Apr 24 19:50:57 2017 +
>
> bump x.y.z versions to odd y after creation of 3_5 branch
>
> git-svn-id: file:///home/git/
> hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/systemPipeR@129129
> bc3139a8-67e5-0310-9ffc-ced21a209358
>
>
> Give me a thumbs up and I’ll go ahead.
>
> > On Oct 5, 2017, at 11:03 AM, Thomas Girke  wrote:
> >
> > Hi Nitesh,
> >
> > If the reset to #c84c7b5f is the best option then let's do this.
> >
> > Just wondering, wouldn't it be much easier to run on your end
> >
> > git reset --hard <>
> > git merge --squash HEAD@{1}
> >
> > This would deduplicate everything without losing any commits.
> >
> > Thanks,
> >
> > Thomas
> >
> > On Thu, Oct 05, 2017 at 10:56:53AM +, Turaga, Nitesh wrote:
> >> Hi Thomas,
> >>
> >> Sorry for the email sent to the wrong place earlier.
> >>
> >> One way I can help you is, that I can take you back to the “clean”
> state on August 16th to commit (c84c7b5fbdf1419af5030b66f8a759d29307f40b).
> >>
> >> i.e before the commit
> >>
> >> commit 500a8b924b7c8bfd9b4e960b471e1e32c06f
> >> Merge: e6ff3f8 3cd5aee
> >> Author: tgirke 
> >> Date:   Thu Aug 17 18:55:36 2017 -0700
> >>
> >>Fixed conflicts in version change
> >>
> >> You would have to manually replay all the commits after that on top of
> that. By this, I mean, all the commits after 500a8b9, need to be
> cherry-picked and pushed to the repo. But you need to be careful here,
> because only “non-merge” commits should be cherry picked. This avoids the
> duplicates on your contaminated branch to not enter the new clean “master”
> branch.
> >>
> >> Non merge commits,
> >> commit 75bca921c1e2c85e8ab36b5a2d006fb2837c1c50
> >> commit 49fa6d434c7bc690223c2b0c88c5353386eb39ba
> >> commit c73fb18ad737bea84b5c7bc3967c9bea8bcd4b9c
> >>
> >>
> >> After doing that, your last 4 commits will look like this,
> >>
> >>
> >> commit 9fc03a5719486e333bc1182b07cd6c5e15e8798d (HEAD -> master)
> >> Author: Hervé Pagès 
> >> Date:   Thu Aug 31 22:28:06 2017 -0700
> >>
> >>restore empty folder lost during svn-to-git transition
> >>
> >> commit 2edc489e4d3ca642a240f062c34528e0d918e11e
> >> Author: tgirke 
> >> Date:   Wed Aug 23 19:21:04 2017 -0700
> >>
> >>moduleload with serveral envir variables
> >>
> >> commit 1d05c70f27ca083d76bca7ef7be59f43662ba07c
> >> Author: tgirke 
> >> Date:   Thu Aug 17 20:29:38 2017 -0700
> >>
> >>Fixed gene set naming problem in GOCluster_Report
> >>
> >> commit c84c7b5fbdf1419af5030b66f8a759d29307f40b (git-svn)
> >> Author: Herve Pages 
> >> Date:   Mon Apr 24 19:50:57 2017 +
> >>
> >>bump x.y.z versions to odd y after creation of 3_5 branch
> >>
> >>git-svn-id: file:///home/git/
> hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/systemPipeR@129129
> bc3139a8-67e5-0310-9ffc-ced21a209358
> >>
> >>
> >> This has a couple of consequences,
> >>
> >> 1. you need to follow (
> http://master.bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-
> ) to switch you master branch to follow bioconductor exactly.
> >>
> >> 2. you and your collaborators, need to re-clone from your GitHub, and
> work on the new master branch abandoning the old one.
> >>
> >> 3. Make sure that all the file changes you’ve made have been moved over.
> >>
> >> Let me know if this works for you, and we can go ahead. Another option
> is, I can do this for you, with a clean “master” on the Bioconductor repo,
> and you can follow the “force bioconductor-to-github” manual on your end.
> >>
> >> Nitesh
> >>
> >>
> >>> On Oct 4, 2017, at 2:38 PM, Thomas Girke  wrote:
> >>>
> >>> I didn't commit the duplicate fix with git merge --squash since I
> wanted to do the branch swap as I did with ChemmineR, but now this is not
> working anymore or there are other problems?
> >>>
> >>> One possible solution could be to allow me a one time push with the -f
> flag with the deduplicated master branch. According to the instructions
> here (https://goo.gl/xnr9j8) this should be possible but I think it has
> been disabled. Some of the Bioc/FAQs related to this topic indicate this
> too.
> >>>
> >>> Thomas
> >>>
> >>> On Wed, Oct 4, 2017 at 11:27 AM Turaga, Nitesh <
> nitesh.tur...@roswellpark.org> wrote:
> >>> Thanks, I’ll get back to you. I wasn’t sure because the history on
> that is not the same. It is a few commits short.
> >>>
> >>>
> >>>
>  On Oct 4, 2017, at 2:00 PM, Thomas Girke 
> wrote:
> 
>  The gitub repos is here:
>  https://github.com/tgirke/systemPipeR
>  It is also

Re: [Bioc-devel] Duplicate commit error on and off

2017-10-05 Thread Turaga, Nitesh

It would be easier. I can do it and it would take you back to,

commit c84c7b5fbdf1419af5030b66f8a759d29307f40b (git-svn)
Author: Herve Pages 
Date:   Mon Apr 24 19:50:57 2017 +

bump x.y.z versions to odd y after creation of 3_5 branch

git-svn-id: 
file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/systemPipeR@129129
 bc3139a8-67e5-0310-9ffc-ced21a209358


Give me a thumbs up and I’ll go ahead. 

> On Oct 5, 2017, at 11:03 AM, Thomas Girke  wrote:
> 
> Hi Nitesh,
> 
> If the reset to #c84c7b5f is the best option then let's do this. 
> 
> Just wondering, wouldn't it be much easier to run on your end
> 
> git reset --hard <>
> git merge --squash HEAD@{1} 
> 
> This would deduplicate everything without losing any commits.
> 
> Thanks,
> 
> Thomas
> 
> On Thu, Oct 05, 2017 at 10:56:53AM +, Turaga, Nitesh wrote:
>> Hi Thomas,
>> 
>> Sorry for the email sent to the wrong place earlier.
>> 
>> One way I can help you is, that I can take you back to the “clean” state on 
>> August 16th to commit (c84c7b5fbdf1419af5030b66f8a759d29307f40b).
>> 
>> i.e before the commit 
>> 
>> commit 500a8b924b7c8bfd9b4e960b471e1e32c06f
>> Merge: e6ff3f8 3cd5aee
>> Author: tgirke 
>> Date:   Thu Aug 17 18:55:36 2017 -0700
>> 
>>Fixed conflicts in version change
>> 
>> You would have to manually replay all the commits after that on top of that. 
>> By this, I mean, all the commits after 500a8b9, need to be cherry-picked and 
>> pushed to the repo. But you need to be careful here, because only 
>> “non-merge” commits should be cherry picked. This avoids the duplicates on 
>> your contaminated branch to not enter the new clean “master” branch.
>> 
>> Non merge commits, 
>> commit 75bca921c1e2c85e8ab36b5a2d006fb2837c1c50
>> commit 49fa6d434c7bc690223c2b0c88c5353386eb39ba
>> commit c73fb18ad737bea84b5c7bc3967c9bea8bcd4b9c
>> 
>> 
>> After doing that, your last 4 commits will look like this,
>> 
>> 
>> commit 9fc03a5719486e333bc1182b07cd6c5e15e8798d (HEAD -> master)
>> Author: Hervé Pagès 
>> Date:   Thu Aug 31 22:28:06 2017 -0700
>> 
>>restore empty folder lost during svn-to-git transition
>> 
>> commit 2edc489e4d3ca642a240f062c34528e0d918e11e
>> Author: tgirke 
>> Date:   Wed Aug 23 19:21:04 2017 -0700
>> 
>>moduleload with serveral envir variables
>> 
>> commit 1d05c70f27ca083d76bca7ef7be59f43662ba07c
>> Author: tgirke 
>> Date:   Thu Aug 17 20:29:38 2017 -0700
>> 
>>Fixed gene set naming problem in GOCluster_Report
>> 
>> commit c84c7b5fbdf1419af5030b66f8a759d29307f40b (git-svn)
>> Author: Herve Pages 
>> Date:   Mon Apr 24 19:50:57 2017 +
>> 
>>bump x.y.z versions to odd y after creation of 3_5 branch
>> 
>>git-svn-id: 
>> file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/systemPipeR@129129
>>  bc3139a8-67e5-0310-9ffc-ced21a209358
>> 
>> 
>> This has a couple of consequences,
>> 
>> 1. you need to follow 
>> (http://master.bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-
>>  ) to switch you master branch to follow bioconductor exactly. 
>> 
>> 2. you and your collaborators, need to re-clone from your GitHub, and work 
>> on the new master branch abandoning the old one.
>> 
>> 3. Make sure that all the file changes you’ve made have been moved over.
>> 
>> Let me know if this works for you, and we can go ahead. Another option is, I 
>> can do this for you, with a clean “master” on the Bioconductor repo, and you 
>> can follow the “force bioconductor-to-github” manual on your end.
>> 
>> Nitesh 
>> 
>> 
>>> On Oct 4, 2017, at 2:38 PM, Thomas Girke  wrote:
>>> 
>>> I didn't commit the duplicate fix with git merge --squash since I wanted to 
>>> do the branch swap as I did with ChemmineR, but now this is not working 
>>> anymore or there are other problems?
>>> 
>>> One possible solution could be to allow me a one time push with the -f flag 
>>> with the deduplicated master branch. According to the instructions here 
>>> (https://goo.gl/xnr9j8) this should be possible but I think it has been 
>>> disabled. Some of the Bioc/FAQs related to this topic indicate this too. 
>>> 
>>> Thomas
>>> 
>>> On Wed, Oct 4, 2017 at 11:27 AM Turaga, Nitesh 
>>>  wrote:
>>> Thanks, I’ll get back to you. I wasn’t sure because the history on that is 
>>> not the same. It is a few commits short.
>>> 
>>> 
>>> 
 On Oct 4, 2017, at 2:00 PM, Thomas Girke  wrote:
 
 The gitub repos is here:
 https://github.com/tgirke/systemPipeR
 It is also linked from the Bioc page of the package here: 
 http://bioconductor.org/packages/systemPipeR/
 
 Thomas
 
 On Wed, Oct 4, 2017 at 8:11 AM Turaga, Nitesh 
  wrote:
 Where is your primary development repo on

Re: [Bioc-devel] Duplicate commit error on and off

2017-10-04 Thread Turaga, Nitesh

Where is your primary development repo on Github? Please send me link. 

Best,

Nitesh 

> On Oct 4, 2017, at 10:14 AM, Turaga, Nitesh  
> wrote:
> 
> Hi Thomas,
> 
> The following issue occurred because there was a commit on Aug 17th with all 
> the duplicates. Unfortunately, your upstream repository has been contaminated 
> with duplicate commits. 
> 
> Till I figure out a solution on how to fix this, please hold off any further 
> commits.
> 
> I’ll keep you posted. You might have to follow a few special instructions to 
> add any commits you have on your local machine now. 
> 
> Best,
> 
> Nitesh
> 
>> On Oct 3, 2017, at 10:08 PM, Thomas Girke  wrote:
>> 
>> Hi Nitesh, 
>> 
>> Sorry for bothering you again about a similar problem. The master/devel 
>> branch of 
>> my systemPipeR package also contains upstream duplicates in the Bioc repos. 
>> However, I am 
>> not able to resolve the problem entirely. When using the 'git merge 
>> --squash' approach,
>> that worked before, then the duplicates can be removed but this time I am 
>> ending up in 
>> a trap at the push step:
>> 
>> git push upstream master
>> 
>> where I am getting the following error: 
>> 
>> To g...@git.bioconductor.org:packages/systemPipeR.git
>> ! [rejected]master -> master (non-fast-forward)
>> error: failed to push some refs to 
>> 'g...@git.bioconductor.org:packages/systemPipeR.git'
>> hint: Updates were rejected because the tip of your current branch is behind
>> hint: its remote counterpart. Integrate the remote changes (e.g.
>> hint: 'git pull ...') before pushing again.
>> hint: See the 'Note about fast-forwards' in 'git push --help' for details.
>> 
>> The solution to this would normally be to run a `git pull` first but when I 
>> do this
>> then I am getting all the duplicates back which puts me back where I 
>> started.  
>> 
>> Running a git push with the -f argument also doesn't work since the usage of 
>> this option 
>> gets rejected by the remote.
>> 
>> Do you have any suggestions what else I should try?
>> 
>> Thanks,
>> 
>> Thomas
>> 
>> 
>> On Tue, Sep 12, 2017 at 02:19:44AM +, Thomas Girke wrote:
>>> 
>>> 
>>> The following allowed me to eliminate the duplicated commits in one step
>>> via git merge --squash and then successfully push back to the bioc-git
>>> server. After this I was able to switch to the swap branch approach to
>>> avoid similar problems in the future.
>>> 
>>> Example here for master branch:
>>> 
>>> git checkout master
>>> git pull upstream master # just in case
>>> git reset --hard  # Reset the current branch to the
>>> commit right before dups started
>>> git merge --squash HEAD@{1} # Squashes duplicated commits from
>>> chosen  to HEAD@{1} (state right before previous reset
>>> step)
>>> git commit -am "some_message" # Commit squashed changes
>>> git push upstream master # Push to bioc-git server
>>> 
>>> I am not sure if the above is the best solution but I thought I report it
>>> here in case others experience similar problems. BTW: in my case the
>>> duplicates were all generated in the upstream merge (step 6) of the
>>> instructions here: https://goo.gl/wWVEeT. None of the parent branches (on
>>> github or bioc) used in this merge step contained duplicated commits at
>>> least as far as I have checked so far. Perhaps some of this relates back to
>>> the git svn/rebase steps we used under the old git mirror?
>>> 
>>> Just in case, the following command is very helpful to identify duplicate
>>> commits based on patch-id. Commits with identical patch-ids are very likely
>>> to have identical content.
>>> 
>>> git rev-list master | xargs -r -L1 git diff-tree -m -p | git
>>> patch-id | sort | uniq -w40 -D | cut -c42-80  | xargs -r git log
>>> --no-walk --pretty=format:"%h %ad %an (%cn) %s" --date-order
>>> --date=iso
>>> 
>>> After duplicated commit pairs have been identified, one can check with diff
>>> or vimdiff whether their content is identical:
>>> 
>>> git --no-pager show  > zzz1
>>> git --no-pager show  > zzz2
>>> vimdiff zzz1 zzz2
>>> 
>>> Thomas
>>> 
> 
> 
> 
> 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.
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel



This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended

Re: [Bioc-devel] Duplicate commit error on and off

2017-10-04 Thread Turaga, Nitesh

Hi Thomas,

The following issue occurred because there was a commit on Aug 17th with all 
the duplicates. Unfortunately, your upstream repository has been contaminated 
with duplicate commits. 

Till I figure out a solution on how to fix this, please hold off any further 
commits.

I’ll keep you posted. You might have to follow a few special instructions to 
add any commits you have on your local machine now. 

Best,

Nitesh

> On Oct 3, 2017, at 10:08 PM, Thomas Girke  wrote:
> 
> Hi Nitesh, 
> 
> Sorry for bothering you again about a similar problem. The master/devel 
> branch of 
> my systemPipeR package also contains upstream duplicates in the Bioc repos. 
> However, I am 
> not able to resolve the problem entirely. When using the 'git merge --squash' 
> approach,
> that worked before, then the duplicates can be removed but this time I am 
> ending up in 
> a trap at the push step:
> 
> git push upstream master
> 
> where I am getting the following error: 
> 
> To g...@git.bioconductor.org:packages/systemPipeR.git
> ! [rejected]master -> master (non-fast-forward)
> error: failed to push some refs to 
> 'g...@git.bioconductor.org:packages/systemPipeR.git'
> hint: Updates were rejected because the tip of your current branch is behind
> hint: its remote counterpart. Integrate the remote changes (e.g.
> hint: 'git pull ...') before pushing again.
> hint: See the 'Note about fast-forwards' in 'git push --help' for details.
> 
> The solution to this would normally be to run a `git pull` first but when I 
> do this
> then I am getting all the duplicates back which puts me back where I started. 
>  
> 
> Running a git push with the -f argument also doesn't work since the usage of 
> this option 
> gets rejected by the remote.
> 
> Do you have any suggestions what else I should try?
> 
> Thanks,
> 
> Thomas
> 
> 
> On Tue, Sep 12, 2017 at 02:19:44AM +, Thomas Girke wrote:
>> 
>> 
>> The following allowed me to eliminate the duplicated commits in one step
>> via git merge --squash and then successfully push back to the bioc-git
>> server. After this I was able to switch to the swap branch approach to
>> avoid similar problems in the future.
>> 
>> Example here for master branch:
>> 
>> git checkout master
>> git pull upstream master # just in case
>> git reset --hard  # Reset the current branch to the
>> commit right before dups started
>> git merge --squash HEAD@{1} # Squashes duplicated commits from
>> chosen  to HEAD@{1} (state right before previous reset
>> step)
>> git commit -am "some_message" # Commit squashed changes
>> git push upstream master # Push to bioc-git server
>> 
>> I am not sure if the above is the best solution but I thought I report it
>> here in case others experience similar problems. BTW: in my case the
>> duplicates were all generated in the upstream merge (step 6) of the
>> instructions here: https://goo.gl/wWVEeT. None of the parent branches (on
>> github or bioc) used in this merge step contained duplicated commits at
>> least as far as I have checked so far. Perhaps some of this relates back to
>> the git svn/rebase steps we used under the old git mirror?
>> 
>> Just in case, the following command is very helpful to identify duplicate
>> commits based on patch-id. Commits with identical patch-ids are very likely
>> to have identical content.
>> 
>> git rev-list master | xargs -r -L1 git diff-tree -m -p | git
>> patch-id | sort | uniq -w40 -D | cut -c42-80  | xargs -r git log
>> --no-walk --pretty=format:"%h %ad %an (%cn) %s" --date-order
>> --date=iso
>> 
>> After duplicated commit pairs have been identified, one can check with diff
>> or vimdiff whether their content is identical:
>> 
>> git --no-pager show  > zzz1
>> git --no-pager show  > zzz2
>> vimdiff zzz1 zzz2
>> 
>> Thomas
>> 



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 
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___
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Re: [Bioc-devel] Duplicate commit error on and off

2017-09-11 Thread Thomas Girke

The following allowed me to eliminate the duplicated commits in one step
via git merge --squash and then successfully push back to the bioc-git
server. After this I was able to switch to the swap branch approach to
avoid similar problems in the future.

Example here for master branch:

git checkout master
git pull upstream master # just in case
git reset --hard  # Reset the current branch to the commit
right before dups started
git merge --squash HEAD@{1} # Squashes duplicated commits from chosen
 to HEAD@{1} (state right before previous reset step)
git commit -am "some_message" # Commit squashed changes
git push upstream master # Push to bioc-git server

I am not sure if the above is the best solution but I thought I report it
here in case others experience similar problems. BTW: in my case the
duplicates were all generated in the upstream merge (step 6) of the
instructions here: https://goo.gl/wWVEeT. None of the parent branches (on
github or bioc) used in this merge step contained duplicated commits at
least as far as I have checked so far. Perhaps some of this relates back to
the git svn/rebase steps we used under the old git mirror?

Just in case, the following command is very helpful to identify duplicate
commits based on patch-id. Commits with identical patch-ids are very likely
to have identical content.

git rev-list master | xargs -r -L1 git diff-tree -m -p | git patch-id
| sort | uniq -w40 -D | cut -c42-80  | xargs -r git log --no-walk
--pretty=format:"%h %ad %an (%cn) %s" --date-order --date=iso

After duplicated commit pairs have been identified, one can check with diff
or vimdiff whether their content is identical:

git --no-pager show  > zzz1
git --no-pager show  > zzz2
vimdiff zzz1 zzz2

Thomas

On Fri, Sep 8, 2017 at 9:16 PM Thomas Girke  wrote:

Since our duplicate commits slipped through to Bioc (probably during
> pre-receive hook downtime), the only option I see, to actually get to the
> actual swap branch step, is to first fix the current duplicate problem in
> the upstream Bioc remote by resetting the affected branches back to the
> commit right before the duplicates occurred. Manual fixes seem unrealistic
> given the number of instances. However, when following (see below) the
> reset instructions here (https://goo.gl/SeNCPk) I am getting a “hook
> declined” error. Not sure how to get beyond this? Or are there alternative
> solutions I should try?
>
> Interestingly, according to the instructions on the top of the Bioc
> instructions of this very topic (https://goo.gl/SeNCPk) I am supposedly
> now someone who "went nuclear". Wasn't this term introduced (or perhaps
> just abused) by the last presidential campaign? How can it get anymore
> frustrating than being affiliated with this outcome :).
>
> Thomas
>
> git reset --hard e3a8d2122a65305c478276e538faace277ea9ed6
> git push -f origin master
> git push -f upstream master
>
> Total 0 (delta 0), reused 0 (delta 0)
> remote: FATAL: + refs/heads/master packages/ChemmineR t.girke DENIED by 
> fallthru
> remote: error: hook declined to update refs/heads/master
> To g...@git.bioconductor.org:packages/ChemmineR.git
>  ! [remote rejected] master -> master (hook declined)
> error: failed to push some refs to 
> 'g...@git.bioconductor.org:packages/ChemmineR.git'
>
> 
>
> On Fri, Sep 8, 2017 at 12:21 PM Turaga, Nitesh <
> nitesh.tur...@roswellpark.org> wrote:
>
>> Hi Thomas,
>>
>> Thanks for understanding. Swapping branches is the best solution I could
>> come up with, and would advice you to go ahead with that.
>>
>> The catching of false positives was a couple of bugs in our pre-receive
>> hooks code, which we have since fixed. I’m glad to have made the shift to
>> Git, and hope the community enjoys it.
>>
>> Best Regards,
>>
>> Nitesh
>>
>>
>> > On Sep 8, 2017, at 2:59 PM, Thomas Girke  wrote:
>> >
>> > Dear Martin and Nitesh,
>> >
>> > If swapping branches is the recommended solution then I will do so. The
>> on/off situation with the duplicate commit error misled me to believe it is
>> a temporary problem on the Bioc end. I am sorry for the extra noise my
>> message may have caused.
>> >
>> > As a group that maintains GitHub versions of all our Bioc packages, we
>> are extremely excited about the recent git transition. Thanks Nitesh (and
>> your colleagues) for doing all of this. It must have been a massive effort
>> for so many packages.
>> >
>> > Best,
>> >
>> > Thomas
>> >
>> >
>> > On Fri, Sep 8, 2017 at 7:11 AM Martin Morgan <
>> martin.mor...@roswellpark.org> wrote:
>> > On 09/08/2017 09:34 AM, Turaga, Nitesh wrote:
>> > > Hi Thomas,
>> > >
>> > > So, you do actually have a “duplicate” commit and you should NOT be
>> pushing this to the bioc-git server. Notice that the body of both those
>> commits is the same.
>> > >
>> > > If you want to check the rest of your commit history, please try `git
>> log - -oneline` . And you will see that you will have multiple duplicate
>> commits. This

Re: [Bioc-devel] Duplicate commit error on and off

2017-09-08 Thread Thomas Girke

Since our duplicate commits slipped through to Bioc (probably during
pre-receive hook downtime), the only option I see, to actually get to the
actual swap branch step, is to first fix the current duplicate problem in
the upstream Bioc remote by resetting the affected branches back to the
commit right before the duplicates occurred. Manual fixes seem unrealistic
given the number of instances. However, when following (see below) the
reset instructions here (https://goo.gl/SeNCPk) I am getting a “hook
declined” error. Not sure how to get beyond this? Or are there alternative
solutions I should try?

Interestingly, according to the instructions on the top of the Bioc
instructions of this very topic (https://goo.gl/SeNCPk) I am supposedly now
someone who "went nuclear". Wasn't this term introduced (or perhaps just
abused) by the last presidential campaign? How can it get anymore
frustrating than being affiliated with this outcome :).

Thomas

git reset --hard e3a8d2122a65305c478276e538faace277ea9ed6
git push -f origin master
git push -f upstream master

Total 0 (delta 0), reused 0 (delta 0)
remote: FATAL: + refs/heads/master packages/ChemmineR t.girke DENIED by fallthru
remote: error: hook declined to update refs/heads/master
To g...@git.bioconductor.org:packages/ChemmineR.git
 ! [remote rejected] master -> master (hook declined)
error: failed to push some refs to
'g...@git.bioconductor.org:packages/ChemmineR.git'



On Fri, Sep 8, 2017 at 12:21 PM Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:

> Hi Thomas,
>
> Thanks for understanding. Swapping branches is the best solution I could
> come up with, and would advice you to go ahead with that.
>
> The catching of false positives was a couple of bugs in our pre-receive
> hooks code, which we have since fixed. I’m glad to have made the shift to
> Git, and hope the community enjoys it.
>
> Best Regards,
>
> Nitesh
>
>
> > On Sep 8, 2017, at 2:59 PM, Thomas Girke  wrote:
> >
> > Dear Martin and Nitesh,
> >
> > If swapping branches is the recommended solution then I will do so. The
> on/off situation with the duplicate commit error misled me to believe it is
> a temporary problem on the Bioc end. I am sorry for the extra noise my
> message may have caused.
> >
> > As a group that maintains GitHub versions of all our Bioc packages, we
> are extremely excited about the recent git transition. Thanks Nitesh (and
> your colleagues) for doing all of this. It must have been a massive effort
> for so many packages.
> >
> > Best,
> >
> > Thomas
> >
> >
> > On Fri, Sep 8, 2017 at 7:11 AM Martin Morgan <
> martin.mor...@roswellpark.org> wrote:
> > On 09/08/2017 09:34 AM, Turaga, Nitesh wrote:
> > > Hi Thomas,
> > >
> > > So, you do actually have a “duplicate” commit and you should NOT be
> pushing this to the bioc-git server. Notice that the body of both those
> commits is the same.
> > >
> > > If you want to check the rest of your commit history, please try `git
> log - -oneline` . And you will see that you will have multiple duplicate
> commits. This compromises your commit history on both your Github repo, and
> on the bioc-git server.
> > >
> > > As suggested in the error message,
> > >
> > > remote: Take a look at the documentation to fix this,
> > > remote:
> https://bioconductor.org/developers/how-to/git/sync-existing-repositories/
> ,
> > >particularly, point  #8 (force Bioconductor master to
> Github master).
> > >
> > > I would advice you to take a look at that. If you have other thoughts
> on how to solve this problem, I’d be happy to listen.
> >
> > Seemed like Thomas wasn't eager to replace his current master with
> > git.bicoonductor.org's master (swap branches). Maybe one thing that
> > makes it more palatable is that the current master can be retained,
> > e.g., as a branch master_archive.
> >
> > What are the alternatives to forcing master branch to be
> > git.bioconductor.org's version?
> >
> > Selectively removing duplicate commits (how does one  do that?)
> >
> > Cherry-picking (into the official Bioconductor branch) rather than
> merging?
> >
> > I know it'll get hairy here, and maybe no easy or complete or simple
> > solution... maybe seeing the steps required for alternative solutions
> > would make the branch swap solution more palatable :)
> >
> > Martin
> >
> > >
> > > Best,
> > >
> > > Nitesh
> > >
> > >
> > >
> > >> On Sep 7, 2017, at 11:02 PM, Thomas Girke 
> wrote:
> > >>
> > >> Sure, it’s pretty long but here it is:
> > >>
> > >> git show 8210e1e04e8dc6819b84820077293d8d61914cf5
> > >> commit 8210e1e04e8dc6819b84820077293d8d61914cf5
> > >> Author: Kevin Horan <
> > >> kho...@cs.ucr.edu
> > >>>
> > >> Date:   Fri Jun
> > >> 30 21:37:15 2017 +
> > >>
> > >>
> > >>  fix
> > >> for RSQLite 2
> > >>
> > >>
> > >>  git-svn-id: file:///home/git/
> > >>
> hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ChemmineR@130824
> bc3139a8-67e5-0310
> > >>

Re: [Bioc-devel] Duplicate commit error on and off

2017-09-08 Thread Turaga, Nitesh

Hi Thomas,

Thanks for understanding. Swapping branches is the best solution I could come 
up with, and would advice you to go ahead with that. 

The catching of false positives was a couple of bugs in our pre-receive hooks 
code, which we have since fixed. I’m glad to have made the shift to Git, and 
hope the community enjoys it.

Best Regards,

Nitesh


> On Sep 8, 2017, at 2:59 PM, Thomas Girke  wrote:
> 
> Dear Martin and Nitesh,
> 
> If swapping branches is the recommended solution then I will do so. The 
> on/off situation with the duplicate commit error misled me to believe it is a 
> temporary problem on the Bioc end. I am sorry for the extra noise my message 
> may have caused.
> 
> As a group that maintains GitHub versions of all our Bioc packages, we are 
> extremely excited about the recent git transition. Thanks Nitesh (and your 
> colleagues) for doing all of this. It must have been a massive effort for so 
> many packages. 
> 
> Best,
> 
> Thomas
> 
> 
> On Fri, Sep 8, 2017 at 7:11 AM Martin Morgan  
> wrote:
> On 09/08/2017 09:34 AM, Turaga, Nitesh wrote:
> > Hi Thomas,
> >
> > So, you do actually have a “duplicate” commit and you should NOT be pushing 
> > this to the bioc-git server. Notice that the body of both those commits is 
> > the same.
> >
> > If you want to check the rest of your commit history, please try `git log - 
> > -oneline` . And you will see that you will have multiple duplicate commits. 
> > This compromises your commit history on both your Github repo, and on the 
> > bioc-git server.
> >
> > As suggested in the error message,
> >
> > remote: Take a look at the documentation to fix this,
> > remote: 
> > https://bioconductor.org/developers/how-to/git/sync-existing-repositories/,
> >particularly, point  #8 (force Bioconductor master to Github 
> > master).
> >
> > I would advice you to take a look at that. If you have other thoughts on 
> > how to solve this problem, I’d be happy to listen.
> 
> Seemed like Thomas wasn't eager to replace his current master with
> git.bicoonductor.org's master (swap branches). Maybe one thing that
> makes it more palatable is that the current master can be retained,
> e.g., as a branch master_archive.
> 
> What are the alternatives to forcing master branch to be
> git.bioconductor.org's version?
> 
> Selectively removing duplicate commits (how does one  do that?)
> 
> Cherry-picking (into the official Bioconductor branch) rather than merging?
> 
> I know it'll get hairy here, and maybe no easy or complete or simple
> solution... maybe seeing the steps required for alternative solutions
> would make the branch swap solution more palatable :)
> 
> Martin
> 
> >
> > Best,
> >
> > Nitesh
> >
> >
> >
> >> On Sep 7, 2017, at 11:02 PM, Thomas Girke  wrote:
> >>
> >> Sure, it’s pretty long but here it is:
> >>
> >> git show 8210e1e04e8dc6819b84820077293d8d61914cf5
> >> commit 8210e1e04e8dc6819b84820077293d8d61914cf5
> >> Author: Kevin Horan <
> >> kho...@cs.ucr.edu
> >>>
> >> Date:   Fri Jun
> >> 30 21:37:15 2017 +
> >>
> >>
> >>  fix
> >> for RSQLite 2
> >>
> >>
> >>  git-svn-id: file:///home/git/
> >> hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ChemmineR@130824
> >>  bc3139a8-67e5-0310
> >> -9ffc-ced21a209358
> >>
> >> diff --git a/DESCRIPTION b/DESCRIPTION
> >> index 4b4d514..c96da6e
> >> 100644
> >>
> >> --- a/DESCRIPTION
> >> +++ b/DESCRIPTION
> >> @@ -
> >> 1,8 +1,8
> >>   @@
> >>   Package: ChemmineR
> >>   Type: Package
> >>   Title: Cheminformatics Toolkit
> >> for
> >>   R
> >> -Version:
> >> 2.28.0
> >>
> >> -Date:
> >> 2016-11-30
> >>
> >> +Version:
> >> 2.28.1
> >>
> >> +Date:
> >> 2017-6-30
> >>
> >>   Author: Y. Eddie Cao, Kevin Horan, Tyler Backman, Thomas Girke
> >>   Maintainer: Thomas Girke <
> >> thomas.gi...@ucr.edu
> >>>
> >>   Description: ChemmineR is a cheminformatics package
> >> for analyzing drug-like small molecule data in R. Its latest version 
> >> contains functions for
> >>   efficient processing of large numbers of molecules, physicochemical
> >> diff --git a/R/compound_db.R b/R/compound_db.R
> >> index 76d1f6c..970c4a2
> >> 100644
> >>
> >> --- a/R/compound_db.R
> >> +++ b/R/compound_db.R
> >> @@ -
> >> 38,7 +38,7 @@ initDb <- function
> >> (handle){
> >>collapse=
> >> ""),";",fixed=TRUE
> >> ))
> >>
> >> #print(statements)
> >>
> >>
> >> -   Map(
> >> function
> >> (sql) dbOp(dbGetQuery(conn,sql)),statements)
> >> +   Map(
> >> function
> >> (sql) dbOp(dbExecute(conn,sql)),statements)
> >>  }
> >>  conn
> >>   }
> >> @@ -
> >> 54,7 +54,7 @@ dbTransaction <- function
> >> (conn,expr){
> >>
> >> # be paranoid about setting this as bad things will happen if its not set
> >>
> >>  enableForeignKeys(conn)
> >>
> >> -   dbGetQuery(conn,
> >> "BEGIN TRANSACTION"
> >> )
>

Re: [Bioc-devel] Duplicate commit error on and off

2017-09-08 Thread Thomas Girke

Dear Martin and Nitesh,

If swapping branches is the recommended solution then I will do so. The
on/off situation with the duplicate commit error misled me to believe it is
a temporary problem on the Bioc end. I am sorry for the extra noise my
message may have caused.

As a group that maintains GitHub versions of all our Bioc packages, we are
extremely excited about the recent git transition. Thanks Nitesh (and your
colleagues) for doing all of this. It must have been a massive effort for
so many packages.

Best,

Thomas


On Fri, Sep 8, 2017 at 7:11 AM Martin Morgan 
wrote:

> On 09/08/2017 09:34 AM, Turaga, Nitesh wrote:
> > Hi Thomas,
> >
> > So, you do actually have a “duplicate” commit and you should NOT be
> pushing this to the bioc-git server. Notice that the body of both those
> commits is the same.
> >
> > If you want to check the rest of your commit history, please try `git
> log - -oneline` . And you will see that you will have multiple duplicate
> commits. This compromises your commit history on both your Github repo, and
> on the bioc-git server.
> >
> > As suggested in the error message,
> >
> > remote: Take a look at the documentation to fix this,
> > remote:
> https://bioconductor.org/developers/how-to/git/sync-existing-repositories/
> ,
> >particularly, point  #8 (force Bioconductor master to Github
> master).
> >
> > I would advice you to take a look at that. If you have other thoughts on
> how to solve this problem, I’d be happy to listen.
>
> Seemed like Thomas wasn't eager to replace his current master with
> git.bicoonductor.org's master (swap branches). Maybe one thing that
> makes it more palatable is that the current master can be retained,
> e.g., as a branch master_archive.
>
> What are the alternatives to forcing master branch to be
> git.bioconductor.org's version?
>
> Selectively removing duplicate commits (how does one  do that?)
>
> Cherry-picking (into the official Bioconductor branch) rather than merging?
>
> I know it'll get hairy here, and maybe no easy or complete or simple
> solution... maybe seeing the steps required for alternative solutions
> would make the branch swap solution more palatable :)
>
> Martin
>
> >
> > Best,
> >
> > Nitesh
> >
> >
> >
> >> On Sep 7, 2017, at 11:02 PM, Thomas Girke  wrote:
> >>
> >> Sure, it’s pretty long but here it is:
> >>
> >> git show 8210e1e04e8dc6819b84820077293d8d61914cf5
> >> commit 8210e1e04e8dc6819b84820077293d8d61914cf5
> >> Author: Kevin Horan <
> >> kho...@cs.ucr.edu
> >>>
> >> Date:   Fri Jun
> >> 30 21:37:15 2017 +
> >>
> >>
> >>  fix
> >> for RSQLite 2
> >>
> >>
> >>  git-svn-id: file:///home/git/
> >>
> hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ChemmineR@130824
> bc3139a8-67e5-0310
> >> -9ffc-ced21a209358
> >>
> >> diff --git a/DESCRIPTION b/DESCRIPTION
> >> index 4b4d514..c96da6e
> >> 100644
> >>
> >> --- a/DESCRIPTION
> >> +++ b/DESCRIPTION
> >> @@ -
> >> 1,8 +1,8
> >>   @@
> >>   Package: ChemmineR
> >>   Type: Package
> >>   Title: Cheminformatics Toolkit
> >> for
> >>   R
> >> -Version:
> >> 2.28.0
> >>
> >> -Date:
> >> 2016-11-30
> >>
> >> +Version:
> >> 2.28.1
> >>
> >> +Date:
> >> 2017-6-30
> >>
> >>   Author: Y. Eddie Cao, Kevin Horan, Tyler Backman, Thomas Girke
> >>   Maintainer: Thomas Girke <
> >> thomas.gi...@ucr.edu
> >>>
> >>   Description: ChemmineR is a cheminformatics package
> >> for analyzing drug-like small molecule data in R. Its latest version
> contains functions for
> >>   efficient processing of large numbers of molecules, physicochemical
> >> diff --git a/R/compound_db.R b/R/compound_db.R
> >> index 76d1f6c..970c4a2
> >> 100644
> >>
> >> --- a/R/compound_db.R
> >> +++ b/R/compound_db.R
> >> @@ -
> >> 38,7 +38,7 @@ initDb <- function
> >> (handle){
> >>collapse=
> >> ""),";",fixed=TRUE
> >> ))
> >>
> >> #print(statements)
> >>
> >>
> >> -   Map(
> >> function
> >> (sql) dbOp(dbGetQuery(conn,sql)),statements)
> >> +   Map(
> >> function
> >> (sql) dbOp(dbExecute(conn,sql)),statements)
> >>  }
> >>  conn
> >>   }
> >> @@ -
> >> 54,7 +54,7 @@ dbTransaction <- function
> >> (conn,expr){
> >>
> >> # be paranoid about setting this as bad things will happen if its not
> set
> >>
> >>  enableForeignKeys(conn)
> >>
> >> -   dbGetQuery(conn,
> >> "BEGIN TRANSACTION"
> >> )
> >> +   dbExecute(conn,
> >> "BEGIN TRANSACTION"
> >> )
> >>  ret=expr
> >>  dbCommit(conn)
> >>  ret
> >> @@ -
> >> 64,8 +64,11 @@ dbTransaction <- function
> >> (conn,expr){
> >>
> >> stop(paste("db error inside transaction: "
> >> ,e$message))
> >>  })
> >>   }
> >>
> >> -dbGetQueryChecked <-
> >> function(conn,statement,...
> >> ){
> >> -   ret=dbGetQuery(conn,statement)
> >> +dbGetQueryChecked <-
> >>

Re: [Bioc-devel] Duplicate commit error on and off

2017-09-08 Thread Martin Morgan


On 09/08/2017 09:34 AM, Turaga, Nitesh wrote:

Hi Thomas,

So, you do actually have a “duplicate” commit and you should NOT be pushing 
this to the bioc-git server. Notice that the body of both those commits is the 
same.

If you want to check the rest of your commit history, please try `git log - 
-oneline` . And you will see that you will have multiple duplicate commits. 
This compromises your commit history on both your Github repo, and on the 
bioc-git server.

As suggested in the error message,

remote: Take a look at the documentation to fix this,
remote: 
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/,
 particularly, point  #8 (force Bioconductor master to Github 
master).

I would advice you to take a look at that. If you have other thoughts on how to 
solve this problem, I’d be happy to listen.


Seemed like Thomas wasn't eager to replace his current master with 
git.bicoonductor.org's master (swap branches). Maybe one thing that 
makes it more palatable is that the current master can be retained, 
e.g., as a branch master_archive.


What are the alternatives to forcing master branch to be 
git.bioconductor.org's version?


Selectively removing duplicate commits (how does one  do that?)

Cherry-picking (into the official Bioconductor branch) rather than merging?

I know it'll get hairy here, and maybe no easy or complete or simple 
solution... maybe seeing the steps required for alternative solutions 
would make the branch swap solution more palatable :)


Martin



Best,

Nitesh




On Sep 7, 2017, at 11:02 PM, Thomas Girke  wrote:

Sure, it’s pretty long but here it is:

git show 8210e1e04e8dc6819b84820077293d8d61914cf5
commit 8210e1e04e8dc6819b84820077293d8d61914cf5
Author: Kevin Horan <
kho...@cs.ucr.edu



Date:   Fri Jun
30 21:37:15 2017 +


 fix
for RSQLite 2


 git-svn-id: file:///home/git/
hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ChemmineR@130824
 bc3139a8-67e5-0310
-9ffc-ced21a209358

diff --git a/DESCRIPTION b/DESCRIPTION
index 4b4d514..c96da6e
100644

--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -
1,8 +1,8
  @@
  Package: ChemmineR
  Type: Package
  Title: Cheminformatics Toolkit
for
  R
-Version:
2.28.0

-Date:
2016-11-30

+Version:
2.28.1

+Date:
2017-6-30

  Author: Y. Eddie Cao, Kevin Horan, Tyler Backman, Thomas Girke
  Maintainer: Thomas Girke <
thomas.gi...@ucr.edu



  Description: ChemmineR is a cheminformatics package
for analyzing drug-like small molecule data in R. Its latest version contains 
functions for
  efficient processing of large numbers of molecules, physicochemical
diff --git a/R/compound_db.R b/R/compound_db.R
index 76d1f6c..970c4a2
100644

--- a/R/compound_db.R
+++ b/R/compound_db.R
@@ -
38,7 +38,7 @@ initDb <- function
(handle){
   collapse=
""),";",fixed=TRUE
))
 
#print(statements)



-   Map(
function
(sql) dbOp(dbGetQuery(conn,sql)),statements)
+   Map(
function
(sql) dbOp(dbExecute(conn,sql)),statements)
 }
 conn
  }
@@ -
54,7 +54,7 @@ dbTransaction <- function
(conn,expr){
 
# be paranoid about setting this as bad things will happen if its not set


 enableForeignKeys(conn)

-   dbGetQuery(conn,
"BEGIN TRANSACTION"
)
+   dbExecute(conn,
"BEGIN TRANSACTION"
)
 ret=expr
 dbCommit(conn)
 ret
@@ -
64,8 +64,11 @@ dbTransaction <- function
(conn,expr){
 
stop(paste("db error inside transaction: "

,e$message))
 })
  }

-dbGetQueryChecked <-
function(conn,statement,...
){
-   ret=dbGetQuery(conn,statement)
+dbGetQueryChecked <-
function(conn,statement,execute=FALSE,...
){
+
if(execute == TRUE
)
+   ret=dbExecute(conn,statement)
+
else


+   ret=dbGetQuery(conn,statement)
 err=dbGetException(conn)
 
if(err$errorMsg[1] != "OK"

)
 
stop("error in dbGetQuery: ",err$errorMsg,"  "

,traceback())
@@ -
895,10 +898,10 @@ createFeature <- function
(conn,name, isNumeric){
 dbGetQueryChecked(conn,
 paste(
"CREATE TABLE feature_",name,
" (
 compound_id INTEGER PRIMARY KEY REFERENCES 
compounds(compound_id) ON DELETE CASCADE ON UPDATE CASCADE, "
,
-
"",name," ",sqlType," )",sep=""
))
+
"",name," ",sqlType," )",sep=""),execute=TRUE
)

 
#print("made table")


-   dbGetQuery(conn,paste(
"CREATE INDEX feature_",name,
"_index ON
+   dbExecute(conn,paste("
CREATE INDEX feature_",name,"
_index ON
  feature_
",name,"(\"",name,"\")",sep=""
))
 
#print("made index")



@@ -
913,7 +916,7 @@ insertDef <- function
(conn,data)  {
  
"VALUES(:definition,:definition_checksum,:format)",sep=""

),

Re: [Bioc-devel] Duplicate commit error on and off

2017-09-08 Thread Turaga, Nitesh

Hi Thomas,

So, you do actually have a “duplicate” commit and you should NOT be pushing 
this to the bioc-git server. Notice that the body of both those commits is the 
same. 

If you want to check the rest of your commit history, please try `git log - 
-oneline` . And you will see that you will have multiple duplicate commits. 
This compromises your commit history on both your Github repo, and on the 
bioc-git server.

As suggested in the error message,

remote: Take a look at the documentation to fix this,
remote: 
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/,
 particularly, point  #8 (force Bioconductor master to Github 
master).

I would advice you to take a look at that. If you have other thoughts on how to 
solve this problem, I’d be happy to listen.

Best,

Nitesh



> On Sep 7, 2017, at 11:02 PM, Thomas Girke  wrote:
> 
> Sure, it’s pretty long but here it is:
> 
> git show 8210e1e04e8dc6819b84820077293d8d61914cf5
> commit 8210e1e04e8dc6819b84820077293d8d61914cf5
> Author: Kevin Horan <
> kho...@cs.ucr.edu
> >
> Date:   Fri Jun 
> 30 21:37:15 2017 +
> 
> 
> fix 
> for RSQLite 2
> 
> 
> git-svn-id: file:///home/git/
> hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ChemmineR@130824
>  bc3139a8-67e5-0310
> -9ffc-ced21a209358
> 
> diff --git a/DESCRIPTION b/DESCRIPTION
> index 4b4d514..c96da6e 
> 100644
> 
> --- a/DESCRIPTION
> +++ b/DESCRIPTION
> @@ -
> 1,8 +1,8
>  @@
>  Package: ChemmineR
>  Type: Package
>  Title: Cheminformatics Toolkit 
> for
>  R
> -Version: 
> 2.28.0
> 
> -Date: 
> 2016-11-30
> 
> +Version: 
> 2.28.1
> 
> +Date: 
> 2017-6-30
> 
>  Author: Y. Eddie Cao, Kevin Horan, Tyler Backman, Thomas Girke
>  Maintainer: Thomas Girke <
> thomas.gi...@ucr.edu
> >
>  Description: ChemmineR is a cheminformatics package 
> for analyzing drug-like small molecule data in R. Its latest version contains 
> functions for
>  efficient processing of large numbers of molecules, physicochemical
> diff --git a/R/compound_db.R b/R/compound_db.R
> index 76d1f6c..970c4a2 
> 100644
> 
> --- a/R/compound_db.R
> +++ b/R/compound_db.R
> @@ -
> 38,7 +38,7 @@ initDb <- function
> (handle){
>   collapse=
> ""),";",fixed=TRUE
> ))
> 
> #print(statements)
> 
> 
> -   Map(
> function
> (sql) dbOp(dbGetQuery(conn,sql)),statements)
> +   Map(
> function
> (sql) dbOp(dbExecute(conn,sql)),statements)
> }
> conn
>  }
> @@ -
> 54,7 +54,7 @@ dbTransaction <- function
> (conn,expr){
> 
> # be paranoid about setting this as bad things will happen if its not set
> 
> enableForeignKeys(conn)
> 
> -   dbGetQuery(conn,
> "BEGIN TRANSACTION"
> )
> +   dbExecute(conn,
> "BEGIN TRANSACTION"
> )
> ret=expr
> dbCommit(conn)
> ret
> @@ -
> 64,8 +64,11 @@ dbTransaction <- function
> (conn,expr){
> 
> stop(paste("db error inside transaction: "
> ,e$message))
> })
>  }
> 
> -dbGetQueryChecked <- 
> function(conn,statement,...
> ){
> -   ret=dbGetQuery(conn,statement)
> +dbGetQueryChecked <- 
> function(conn,statement,execute=FALSE,...
> ){
> +   
> if(execute == TRUE
> )
> +   ret=dbExecute(conn,statement)
> +   
> else
> 
> 
> +   ret=dbGetQuery(conn,statement)
> err=dbGetException(conn)
> 
> if(err$errorMsg[1] != "OK"
> )
> 
> stop("error in dbGetQuery: ",err$errorMsg,"  "
> ,traceback())
> @@ -
> 895,10 +898,10 @@ createFeature <- function
> (conn,name, isNumeric){
> dbGetQueryChecked(conn,
> paste(
> "CREATE TABLE feature_",name,
> " (
> compound_id INTEGER PRIMARY KEY REFERENCES 
> compounds(compound_id) ON DELETE CASCADE ON UPDATE CASCADE, "
> ,
> -   
> "",name," ",sqlType," )",sep=""
> ))
> +   
> "",name," ",sqlType," )",sep=""),execute=TRUE
> )
> 
> 
> #print("made table")
> 
> -   dbGetQuery(conn,paste(
> "CREATE INDEX feature_",name,
> "_index ON
> +   dbExecute(conn,paste("
> CREATE INDEX feature_",name,"
> _index ON
>  feature_
> ",name,"(\"",name,"\")",sep=""
> ))
> 
> #print("made index")
> 
> 
> @@ -
> 913,7 +916,7 @@ insertDef <- function
> (conn,data)  {
>  
> "VALUES(:definition,:definition_checksum,:format)",sep=""
> ), bind.data=data[fields])
> }
> else if(inherits(conn,"PostgreSQLConnection"
> )){
> 
> if(debug) print(data[,"definition_checksum"
> ])
> -   apply(data[,fields],
> 1,function
> (row) dbOp(dbGetQuery(conn, 
> +   apply(data[,fields],
> 1,function
> (row) dbOp(dbExecute(conn, 
>

Re: [Bioc-devel] Duplicate commit error on and off

2017-09-07 Thread Thomas Girke

Sure, it’s pretty long but here it is:

git show 8210e1e04e8dc6819b84820077293d8d61914cf5
commit 8210e1e04e8dc6819b84820077293d8d61914cf5
Author: Kevin Horan 
Date:   Fri Jun 30 21:37:15 2017 +

fix for RSQLite 2

git-svn-id:
file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ChemmineR@130824
bc3139a8-67e5-0310-9ffc-ced21a209358

diff --git a/DESCRIPTION b/DESCRIPTION
index 4b4d514..c96da6e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: ChemmineR
 Type: Package
 Title: Cheminformatics Toolkit for R
-Version: 2.28.0
-Date: 2016-11-30
+Version: 2.28.1
+Date: 2017-6-30
 Author: Y. Eddie Cao, Kevin Horan, Tyler Backman, Thomas Girke
 Maintainer: Thomas Girke 
 Description: ChemmineR is a cheminformatics package for analyzing
drug-like small molecule data in R. Its latest version contains
functions for efficient processing of large numbers of molecules,
physicochemical
diff --git a/R/compound_db.R b/R/compound_db.R
index 76d1f6c..970c4a2 100644
--- a/R/compound_db.R
+++ b/R/compound_db.R
@@ -38,7 +38,7 @@ initDb <- function(handle){

collapse=""),";",fixed=TRUE))
#print(statements)

-   Map(function(sql) dbOp(dbGetQuery(conn,sql)),statements)
+   Map(function(sql) dbOp(dbExecute(conn,sql)),statements)
}
conn
 }
@@ -54,7 +54,7 @@ dbTransaction <- function(conn,expr){
# be paranoid about setting this as bad things will
happen if its not set
enableForeignKeys(conn)

-   dbGetQuery(conn,"BEGIN TRANSACTION")
+   dbExecute(conn,"BEGIN TRANSACTION")
ret=expr
dbCommit(conn)
ret
@@ -64,8 +64,11 @@ dbTransaction <- function(conn,expr){
stop(paste("db error inside transaction: ",e$message))
})
 }

-dbGetQueryChecked <- function(conn,statement,...){
-   ret=dbGetQuery(conn,statement)
+dbGetQueryChecked <- function(conn,statement,execute=FALSE,...){
+   if(execute == TRUE)
+   ret=dbExecute(conn,statement)
+   else

+   ret=dbGetQuery(conn,statement)
err=dbGetException(conn)
if(err$errorMsg[1] != "OK")
stop("error in dbGetQuery: ",err$errorMsg,"  ",traceback())
@@ -895,10 +898,10 @@ createFeature <- function(conn,name, isNumeric){
dbGetQueryChecked(conn,
paste("CREATE TABLE feature_",name," (
compound_id INTEGER PRIMARY KEY REFERENCES
compounds(compound_id) ON DELETE CASCADE ON UPDATE CASCADE, ",
-   "",name," ",sqlType," )",sep=""))
+   "",name," ",sqlType," )",sep=""),execute=TRUE)

#print("made table")
-   dbGetQuery(conn,paste("CREATE INDEX feature_",name,"_index ON
+   dbExecute(conn,paste("CREATE INDEX feature_",name,"_index ON

feature_",name,"(\"",name,"\")",sep=""))
#print("made index")

@@ -913,7 +916,7 @@ insertDef <- function(conn,data)  {

"VALUES(:definition,:definition_checksum,:format)",sep=""),
bind.data=data[fields])
}else if(inherits(conn,"PostgreSQLConnection")){
if(debug) print(data[,"definition_checksum"])
-   apply(data[,fields],1,function(row) dbOp(dbGetQuery(conn,
+   apply(data[,fields],1,function(row) dbOp(dbExecute(conn,
 "INSERT INTO
compounds(definition,definition_checksum,format) VALUES($1,$2,$3)",
 row)))
}else{
@@ -990,7 +993,7 @@ insertDescriptor <- function(conn,data){
})
apply(data[,fields2],1,function(row) {
row[2] = descTypes[row[2]] #translate
descriptor_type to descriptor_type_id
-   dbTransaction(conn,dbGetQuery(conn,
paste("INSERT INTO compound_descriptors(compound_id,
+   dbTransaction(conn,dbExecute(conn,
paste("INSERT INTO compound_descriptors(compound_id,

   descriptor_id) ",
"VALUES( (SELECT compound_id
FROM compounds WHERE definition_checksum = $1),

(SELECT descriptor_id FROM descriptors
@@ -1006,7 +1009,7 @@ insertDescriptorType <- function(conn,data){
 bind.data=data)
}else if(inherits(conn,"PostgreSQLConnection")){
apply(data,1,function(row)
-   dbGetQuery(conn,paste("INSERT INTO
descriptor_types(descriptor_type) VALUES($1)"),row))
+   dbExecute(conn,paste("INSERT INTO
descriptor_types(descriptor_type) VALUES($1)"),row))
}else{
stop("database ",class(conn)," unsupported")
}
@@ -1019,7 +1022,7 @@ updatePriorities <- function(conn,data){

descriptor_id=:descriptor_id", bind.data=data)
}else

Re: [Bioc-devel] Duplicate commit error on and off

2017-09-07 Thread Turaga, Nitesh

Dear Thomas,

Can you please send me the output of the two `git show` commands?

> git show 8210e1e04e8dc6819b84820077293d8d61914cf5
> git show f514d35b793e1d9462b899bf3c76cc06ab4dcc91


I’ll need to take a look at those to advice accordingly.


Best,

Nitesh


> On Sep 7, 2017, at 7:04 PM, Thomas Girke  wrote:
> 
> Dear Nitesh,
> 
> In the release branch of our ChemmineR package I am getting a duplicate 
> commit error. Last week we had a similar error across several of our packages 
> but then you made some changes in response to a similar problem reported on 
> the bioc-developer site which eliminated the problem by itself. Now the 
> problem is back again and it is not clear to me how to resolve it. The 
> suggestions given here https://goo.gl/5mk8vV sound a bit harsh.
> 
> tgirke@tgirke-XPS-13-9343
> :~/Dropbox/Software/ChemmineR/ChemmineR$ git push upstream RELEASE_3_5
> Counting objects: 
> 26
> , done.
> Delta compression using up to 
> 4
>  threads.
> Compressing objects: 
> 100% (4/4
> ), done.
> Writing objects: 
> 100% (4/4), 387 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@r-project.org
> >. Provide the error, the package name and
> remote: any other details we might need.
> remote:
> remote: Use
> remote:
> remote: git show 8210e1e04e8dc6819b84820077293d8d61914cf5
> remote: git show f514d35b793e1d9462b899bf3c76cc06ab4dcc91
> remote:
> remote: to see body of commits.
> remote:
> To g...@git.bioconductor.org:packages/ChemmineR.git
>  ! [remote rejected] RELEASE_3_5 -> RELEASE_3_5 (pre-receive hook declined)
> error: failed to push some refs to 
> 'g...@git.bioconductor.org:packages/ChemmineR.git'
> Thanks,
> 
> Thomas
> 
> --
> 
> Thomas Girke, Ph.D.
> 
> Professor of Bioinformatics
> 
> Director of HPC Center
> 
> 1207F Genomics Building
> 
> University of California
> 
> Riverside, CA 92521
> 
> 
> 
> 
> E-mail: thomas.gi...@ucr.edu
> 
> Phone/Cell/Text: 951-732-7072



This email message may contain legally privileged and/or confidential 
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this message in error, please notify the sender immediately by e-mail and 
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Re: [Bioc-devel] Duplicate commit error on and off

Re: [Bioc-devel] Duplicate commit error on and off

Re: [Bioc-devel] Duplicate commit error on and off

Re: [Bioc-devel] Duplicate commit error on and off

Re: [Bioc-devel] Duplicate commit error on and off

Re: [Bioc-devel] Duplicate commit error on and off

Re: [Bioc-devel] Duplicate commit error on and off

Re: [Bioc-devel] Duplicate commit error on and off

Re: [Bioc-devel] Duplicate commit error on and off

Re: [Bioc-devel] Duplicate commit error on and off

Re: [Bioc-devel] Duplicate commit error on and off

Re: [Bioc-devel] Duplicate commit error on and off

Re: [Bioc-devel] Duplicate commit error on and off

Re: [Bioc-devel] Duplicate commit error on and off

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