Re: [Bioc-devel] Difficulty obtaining access to BioC git repository

[Turaga, Nitesh]

No problem. 

As a heads up for the future, the mailing list might get a quicker response vs 
the support site as far as GIT goes.

Best,

Nitesh 

> On Oct 5, 2017, at 12:12 PM, Raborn, R. Taylor  wrote:
> 
> Hi Nitesh;
> 
> I see- this makes sense. I apologize for my error and appreciate you 
> providing me with access.
> 
> Thank you for your assistance with this.
> 
> Best regards,
> 
> Taylor
> 
>> On Oct 5, 2017, at 12:04 PM, Turaga, Nitesh  
>> wrote:
>> 
>> Hi,
>> 
>> You have submitted multiple times with bad ID’s. This has not gone too well 
>> with our application and fails add your key. You first submitted “rtraborn” 
>> with a set of keys, and then with the same set of keys with you valid SVN 
>> ID. The system does not add the same key twice with two separate usernames. 
>> 
>> I will manually make changes to give you access. 
>> 
>> Best
>> 
>> 
>>> On Oct 5, 2017, at 11:49 AM, Raborn, R. Taylor  wrote:
>>> 
>>> Hello:
>>> 
>>> I’m a co-developer and package maintainer for 
>>> TSRchitect<https://bioconductor.org/packages/release/bioc/html/TSRchitect.html>,
>>>  a relatively new Bioconductor package.
>>> 
>>> We wish to push package updates to the Bioconductor git repo, but as of yet 
>>> I have been unable to do so. This post 
>>> (link<https://support.bioconductor.org/p/100990/#101170>) on the BioC 
>>> support page describes the current situation.
>>> 
>>> Given the previous, is there anything I could be overlooking in my 
>>> attempts, or is my credential still in the process of being created?
>>> 
>>> Also, I would like to know if it would be possible to add the co-creater of 
>>> this package, Dr. Volker Brendel (cc’d on this email), as (another) 
>>> maintainer of TSRchitect. His GitHub page is here: 
>>> https://github.com/vpbrendel.
>>> 
>>> Thank you in advance for your help.
>>> 
>>> Best regards,
>>> 
>>> Taylor
>>> 
>>> 
>>> R. Taylor Raborn, PhD
>>> Postdoctoral Fellow, Brendel Group
>>> Computational Genome Science Laboratory
>>> Indiana University, Simon Hall 205B
>>> P:  812.856.9572
>>> rtrab...@indiana.edu<mailto:rtrab...@indiana.edu> | 
>>> brendelgroup.org<http://brendelgroup.org>
>>> 
>>> 
>>> 
>>> 
>>> [[alternative HTML version deleted]]
>>> 
>>> ___
>>> 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 
>> 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, 
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Re: [Bioc-devel] Duplicate commit error on and off

[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

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

[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

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

[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,
> > >>
>

Re: [Bioc-devel] Enabling SSH keys

[Turaga, Nitesh]

You have to submit your SSH keys. 

Please read the bioconductor.org/developers/how-to/git/

Best,


> On Oct 8, 2017, at 3:35 PM, mohammed Elsiddieg  wrote:
> 
> Hi All
> 
> I am maintaining the cellbaseR package, I am very glad that Bioconductor
> has finally moved to Github, However, I am still waiting for my ssh keys to
> be enabled so I can get to maintaining my package I tried twice through the
> supplied google form and never heard back, How can I get this done quickly?
> N.B I already have a GitHub account and a public ssh key
> 
> Best regards
> 
>   [[alternative HTML version deleted]]
> 
> ___
> 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 
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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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Re: [Bioc-devel] Difficulty obtaining access to BioC git repository

[Turaga, Nitesh]

Please send me the list of commands you tried, and the output.

Your key is in the system. Either you are not using the correct key, or are 
issuing the wrong command on git. 

Nitesh

> On Oct 9, 2017, at 11:45 AM, Raborn, R. Taylor  wrote:
> 
> Hi Nitesh:
> 
> Sounds great.
> 
> This morning I attempted to sync my GitHub repository with Bioconductor 
> (following the instructions here), but I still wasn’t able to login.
> 
> Is there anything further that I need to do to obtain access? I’d be happy to 
> resubmit my information in the google docs form if necessary.
> 
> Best regards,
> 
> Taylor
> 
>> On Oct 5, 2017, at 12:17 PM, Turaga, Nitesh  
>> wrote:
>> 
>> No problem. 
>> 
>> As a heads up for the future, the mailing list might get a quicker response 
>> vs the support site as far as GIT goes.
>> 
>> Best,
>> 
>> Nitesh 
>> 
>>> On Oct 5, 2017, at 12:12 PM, Raborn, R. Taylor  wrote:
>>> 
>>> Hi Nitesh;
>>> 
>>> I see- this makes sense. I apologize for my error and appreciate you 
>>> providing me with access.
>>> 
>>> Thank you for your assistance with this.
>>> 
>>> Best regards,
>>> 
>>> Taylor
>>> 
>>>> On Oct 5, 2017, at 12:04 PM, Turaga, Nitesh 
>>>>  wrote:
>>>> 
>>>> Hi,
>>>> 
>>>> You have submitted multiple times with bad ID’s. This has not gone too 
>>>> well with our application and fails add your key. You first submitted 
>>>> “rtraborn” with a set of keys, and then with the same set of keys with you 
>>>> valid SVN ID. The system does not add the same key twice with two separate 
>>>> usernames. 
>>>> 
>>>> I will manually make changes to give you access. 
>>>> 
>>>> Best
>>>> 
>>>> 
>>>>> On Oct 5, 2017, at 11:49 AM, Raborn, R. Taylor  
>>>>> wrote:
>>>>> 
>>>>> Hello:
>>>>> 
>>>>> I’m a co-developer and package maintainer for 
>>>>> TSRchitect<https://bioconductor.org/packages/release/bioc/html/TSRchitect.html>,
>>>>>  a relatively new Bioconductor package.
>>>>> 
>>>>> We wish to push package updates to the Bioconductor git repo, but as of 
>>>>> yet I have been unable to do so. This post 
>>>>> (link<https://support.bioconductor.org/p/100990/#101170>) on the BioC 
>>>>> support page describes the current situation.
>>>>> 
>>>>> Given the previous, is there anything I could be overlooking in my 
>>>>> attempts, or is my credential still in the process of being created?
>>>>> 
>>>>> Also, I would like to know if it would be possible to add the co-creater 
>>>>> of this package, Dr. Volker Brendel (cc’d on this email), as (another) 
>>>>> maintainer of TSRchitect. His GitHub page is here: 
>>>>> https://github.com/vpbrendel.
>>>>> 
>>>>> Thank you in advance for your help.
>>>>> 
>>>>> Best regards,
>>>>> 
>>>>> Taylor
>>>>> 
>>>>> 
>>>>> R. Taylor Raborn, PhD
>>>>> Postdoctoral Fellow, Brendel Group
>>>>> Computational Genome Science Laboratory
>>>>> Indiana University, Simon Hall 205B
>>>>> P:  812.856.9572
>>>>> rtrab...@indiana.edu<mailto:rtrab...@indiana.edu> | 
>>>>> brendelgroup.org<http://brendelgroup.org>
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> [[alternative HTML version deleted]]
>>>>> 
>>>>> ___
>>>>> 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 
>>>> 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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Re: [Bioc-devel] Git permission denied (publickey)

[Turaga, Nitesh]

Your key is in the system. 

Please send a list of commands you are trying along with the result.

Also send the output for 

`git remove -v`

Best,

Nitesh

> On Oct 9, 2017, at 4:22 PM, Andrea Rau  wrote:
> 
> Hello,
> A few days ago I submitted my GitHub id andreamrau (since GitHub knows my SSH 
> key) and my SVN id (a.rau) using the Git/SVN transition form, and I still 
> seem to be having difficulty accessing my packages coseq and HTSFilter. I see 
> the following message when I try to git clone one of my packages:
>  
> Permission denied (publickey).
> fatal: Could not read from remote repository
>  
> Could you let me know if there’s something I have done incorrectly with the 
> transition form?
>  
> Thanks very much for the help,
> Andrea



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Re: [Bioc-devel] Bad SSH key submissions

[Turaga, Nitesh]

Please send a list of commands you are trying along with response. 


Also send the output of 

`git remote -v`

Best,

Nitesh 

> On Oct 6, 2017, at 6:45 PM, Juan David Henao Sanchez  
> wrote:
> 
> Hi.
> 
> Thanks for taking the time to resolve my problems with the ssh connection.
> 
> I'm writing to you because in the past days my ssh public key was recognized 
> and I could clone my package from the git repository. But now I can't-do 
> that, What is the possible reason? Should I do something else with the public 
> key?
> 
> Regards.
> 
> 2017-10-05 11:12 GMT-05:00 Turaga, Nitesh :
> Hi Maintainer,
> 
> Your SVN ID is j.henao. If you want to submit SSH keys to access your 
> package, you may ONLY submit with that SVN ID in the form. Please do not 
> resubmit multiple times with the wrong key.
> 
> You already have a key under “j.henao"
> 
> Best,
> 
> Nitesh
> 
> 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.
> 
> 
> 
> -- 
> Juan David Henao
> Maestría en Bioinformática
> Universidad Nacional de Colombia



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Re: [Bioc-devel] Bad SSH key submissions

[Turaga, Nitesh]

Please resubmit your key if you have lost private key.

Nitesh


> On Oct 9, 2017, at 5:30 PM, Juan David Henao Sanchez  
> wrote:
> 
> Dear Nitesh
> 
> The command is:
> 
> git clone g...@git.bioconductor.org:packages/coexnet.git
> 
> and the message of error is:
> 
> Clonar en «coexnet»...
> Permission denied (publickey).
> fatal: Could not read from remote repository.
> 
> Please make sure you have the correct access rights
> and the repository exists.
> 
> But I already have a public key as "j.henao". The result of git remote -v is:
> 
> fatal: Not a git repository (or any of the parent directories): .git
> 
> Regards.
> 
> 
> 2017-10-09 16:13 GMT-05:00 Turaga, Nitesh :
> Please send a list of commands you are trying along with response.
> 
> 
> Also send the output of
> 
> `git remote -v`
> 
> Best,
> 
> Nitesh
> 
> > On Oct 6, 2017, at 6:45 PM, Juan David Henao Sanchez 
> >  wrote:
> >
> > Hi.
> >
> > Thanks for taking the time to resolve my problems with the ssh connection.
> >
> > I'm writing to you because in the past days my ssh public key was 
> > recognized and I could clone my package from the git repository. But now I 
> > can't-do that, What is the possible reason? Should I do something else with 
> > the public key?
> >
> > Regards.
> >
> > 2017-10-05 11:12 GMT-05:00 Turaga, Nitesh :
> > Hi Maintainer,
> >
> > Your SVN ID is j.henao. If you want to submit SSH keys to access your 
> > package, you may ONLY submit with that SVN ID in the form. Please do not 
> > resubmit multiple times with the wrong key.
> >
> > You already have a key under “j.henao"
> >
> > Best,
> >
> > Nitesh
> >
> > 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.
> >
> >
> >
> > --
> > Juan David Henao
> > Maestría en Bioinformática
> > Universidad Nacional de Colombia
> 
> 
> 
> 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.
> 
> 
> 
> -- 
> Juan David Henao
> Maestría en Bioinformática
> Universidad Nacional de Colombia



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Re: [Bioc-devel] Difficulty obtaining access to BioC git repository

[Turaga, Nitesh]

You have the following public key’s in the Bioconductor system, are you sure 
you are using the correct private keys.


ssh-rsa 
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

ssh-rsa 
B3NzaC1yc2EDAQABAAACAQDOFeUW3VXKFzoqlI/pnVvsV7PSMbaQ5qgkXx6fJpx2BNCVOuwLs2KpOzBNu6aSuqnYEYMlyRvhSfEFaYMVXkqqYlnpcorlb2prxSBcIG2RhhPmw7i0yk9tofTm6LUlAGmsH+LWs+Q5OZz6L1Yypt9MHm3+I/tlPqc5IOA+VIl7b337eHJeoX3uRp06xThwVH+75VX4XTZ0YKAoHTN4gTjZJFnd0QGX/IMOFGcJrD3lBFtSdddmCZITjSWEaMtZnS6tX4yOFEKNl06hojl6mIasMj6Node2jMl0l9DnXgwQL2zpYtQ3uS7HahTfmcY/mD0ERSz6R9EbxamHsaVcPrUUjWmb5RJxySscfJ3D4o5eii8TfhVnJz28r3+dUW3+EOdAN1ThYNlqvqFUuMoXJ9LVtxMT/Ad8pkdLbHGmDXZoCyEs5pAfcFBCpBHDUADFyeYpqULnQs0ogMUGD60ChVdEY22c/yVcalLBSRygz3owvwfSg/ZJ/oWx8pj88duU3FVKlSfLM9QnBBbuOiptir4Eco5qmbJbCYBKCVcDj0VzUJubypTyq9A3QENcw/yNsZmlCsFGAbCQDvvrx8pWcNMtMVjgMJ5vV30dcRaNc+vvgwLW3aUfWy8yVlOkOke9f2D35BIGHOD2WtjoFS8AwAVjS+/UPNJs1Kj73HSemeKpmw==

ssh-rsa 
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



> On Oct 9, 2017, at 10:24 PM, Raborn, R. Taylor  wrote:
> 
> Hi Nitesh:
> 
> Certainly. I used the following commands:
> 
>> git clone https://github.com/BrendelGroup/TSRchitect
>> cd TSRchitect/
>> git remote add upstream g...@git.bioconductor.org:packages/TSRchitect.git
>> git fetch --all
> Fetching origin
> Fetching upstream
> Permission denied (publickey).
> fatal: Could not read from remote repository.
> 
> Would you like me to provide my public key as well? I’m sorry for all the 
> trouble.
> 
> Best regards,
> 
> Taylor
> 
>> On Oct 9, 2017, at 5:01 PM, Turaga, Nitesh  
>> wrote:
>> 
>> Please send me the list of commands you tried, and the output.
>> 
>> Your key is in the system. Either you are not using the correct key, or are 
>> issuing the wrong command on git. 
>> 
>> Nitesh
>> 
>>> On Oct 9, 2017, at 11:45 AM, Raborn, R. Taylor  wrote:
>>> 
>>> Hi Nitesh:
>>> 
>>> Sounds great.
>>> 
>>> This morning I attempted to sync my GitHub repository with Bioconductor 
>>> (following the instructions here), but I still wasn’t able to login.
>>> 
>>> Is there anything further that I need to do to obtain access? I’d be happy 
>>> to resubmit my information in the google docs form if necessary.
>>> 
>>> Best regards,
>>> 
>>> Taylor
>>> 
>>>> On Oct 5, 2017, at 12:17 PM, Turaga, Nitesh 
>>>>  wrote:
>>>> 
>>>> No problem. 
>>>> 
>>>> As a heads up for the future, the mailing list might get a quicker 
>>>> response vs the support site as far as GIT goes.
>>>> 
>>>> Best,
>>>> 
>>>> Nitesh 
>>>> 
>>>>> On Oct 5, 2017, at 12:12 PM, Raborn, R. Taylor  
>>>>> wrote:
>>>>> 
>>>>> Hi Nitesh;
>>>>> 
>>>>> I see- this makes sense. I apologize for my error and appreciate you 
>>>>> providing me with access.
>>>>> 
>>>>> Thank you for your assistance with this.
>>>>> 
>>>>> Best regards,
>>>>> 
>>>>> Taylor
>>>>> 
>>>>>> On Oct 5, 2017, at 12:04 PM, Turaga, Nitesh 
>>>>>>  wrote:
>>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> You have subm

Re: [Bioc-devel] EXTERNAL: Can't push to git

[Turaga, Nitesh]

Hi

I see that you have submitted your key multiple times. But missed one key 
component to get access to your package, i.e your previous SVN-ID given to your 
by bioconductor. 

You are supposed to submit your SVN ID in the google form, without with your 
keys will not get access. 

Best,

Nitesh 


> On Oct 10, 2017, at 8:40 AM, Thomas J Hardcastle  wrote:
> 
> Hi all,
> 
> I am unable to push to git with the 'tjh48' ID following the instructions on 
> https://www.bioconductor.org/developers/how-to/git/. I have submitted my 
> public key through the google form and tried to link my git account, which 
> also has my keys, but to no avail. Any solutions?
> 
> Best wishes,
> 
> Tom Hardcastle
> 
> -- 
> Dr. Thomas J. Hardcastle
> 
> Senior Research Associate
> Department of Plant Sciences
> University of Cambridge
> Downing Street
> Cambridge, CB2 3EA
> United Kingdom
> 
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel



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Re: [Bioc-devel] EXTERNAL: Re: Enabling SSH keys

[Turaga, Nitesh]

Your keys are already in our system, please make sure you are using the correct 
private key for access to the package. 

Did you try to access the system? Or are you just waiting for a response. There 
is no response provided by that google form. 


ssh-rsa 
B3NzaC1yc2EDAQABAAABAQDSTjBIKs2T0R9TMxmdbGD/NfP+XnHolRAv1bEdBXrTAuDqT0AoWc9xB1QSltatx7o0OOV/Zk9Fjm4hWVgRJQkQSTaN8IEBgQhB/d7IK97T4yT53IBu/g0jdXnRMs6UjkoLwRiTDudFaCuCQQzL2dSNbrycBfrXv/Lw0BeppflDg3w6YaRH4qa6rthZ6Pjc7I38Xdp9Y99EkSOQOTE6APrJlMgpGJtSpIN8nG2pKdC84acGqg5DQjGhuSmI6vl9bWr3DKe3vT+o4g8IQl2n7v+9VZVds37UDitKT8LjMnlYUDMZ5aCY1K+7L4XwgjhmT2PpbTqe4CIVHoD5dvVtf+a3

ssh-rsa 
B3NzaC1yc2EDAQABAAABAQCddS6hYVApawhF6fucX9U3nMYHEbTZt6p1NSFVK9lwt9TejZeT9m2VXduxU+FQ/ig5kYlSlDMUKFbFV0HetlKG6fQXPkCzG7Q1YT3eDbEZzCFI5inNd0JdeMK9hAFBW/AjDpsjeFIroPZ6dFJYAhR+H5js3H8OF0xS/OjIoK825rRzvPg2fUOy32/njM1WI2Z5NClrFR4HkrlwHWXiuG/QjmLIJobOdNg58ziQwZuh6wtmnNwLLY9Q6c1rFdC/sFK21GaGRqwOuJjmEiPoSa3ET23Kri4yuMKh+SSK5hRBIybSpXevkRdbkrDj/NUeVehkF8dRQw0x40670LwV2eKP

ssh-rsa 
B3NzaC1yc2EDAQABAAABAQCwTIx7s1XlRNzfrtdsgze8oiJb/T0EkO1Y0nDsNzjA1ZkTnIjVjIfk9lpk9uqj8NxSt3W438rseTH++2/kD7CEXi7r1BzbcNL8npVlmA1l3n0hBlprwQMswXwhbaePOE/h+svGq/xsDsjGSIAzCYBhe3cSGDlg+jxi6OqOo41Tk7nhJ8MXecaiSxgDIC4DLD2nDVYOF/d0559twyxadcm3caNv9gvTUKDKep9FHQwQAk4+wg13OjrZJbuFIFdP3kr7fQNlcxx5OXM6Hn7k6KU1ClAwRnYMy34NH0GcIjpOXhMmYgjMwpjjWUiomvawx33kz1eOMC21spOD5rL6K8bF


Best,

Nitesh 

> On Oct 10, 2017, at 7:36 AM, mohammed Elsiddieg  wrote:
> 
> Hi All
> 
> Yes, I have already done that twice, in the first time I submitted my GitHub 
> ID and in the second one I submitted my public ssh keys and did not receive 
> any response in both cases.
> I am getting a little bit nervous as there are some warnings and errors I 
> need to fix.
> Best regards 
> 
> On Tue, Oct 10, 2017 at 12:00 AM, Turaga, Nitesh 
>  wrote:
> You have to submit your SSH keys.
> 
> Please read the bioconductor.org/developers/how-to/git/
> 
> Best,
> 
> 
> > On Oct 8, 2017, at 3:35 PM, mohammed Elsiddieg  wrote:
> >
> > Hi All
> >
> > I am maintaining the cellbaseR package, I am very glad that Bioconductor
> > has finally moved to Github, However, I am still waiting for my ssh keys to
> > be enabled so I can get to maintaining my package I tried twice through the
> > supplied google form and never heard back, How can I get this done quickly?
> > N.B I already have a GitHub account and a public ssh key
> >
> > Best regards
> >
> >   [[alternative HTML version deleted]]
> >
> > ___
> > 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 
> 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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Re: [Bioc-devel] rcellminer Bioconductor package

[Turaga, Nitesh]

You should have access if you have submitted the new key.

We suggest your link your GitHub ID. And add keys to your Github, and we can 
get them from there. If you have submitted your GitHub ID once to the google 
form, you won’t have to resubmit. 

Best,

Nitesh 


> On Oct 7, 2017, at 9:04 AM, Elloumi, Fathi (NIH/NCI) [C] 
>  wrote:
> 
> Hi Nitesh,
> 
> I added a new ssh key to allow access from Laptop. Could you grant me 
> permission  for my 2 ssh keys?
> 
> Thanks.
> 
> Fathi
> 



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[Bioc-devel] Git related or ssh queries to bioc-devel

[Turaga, Nitesh]

Hi Maintainers,

I have been getting a lot of emails addressed to me directly regarding SSH or 
Git related issues. Please send these emails to bioc-devel, which gives the 
question a larger audience and potentially a faster reply from someone else.  
Another perk, other people who have the same question as you will be able to 
look at the email thread. 

If the question is sent to me directly, I will cc bioc-devel in my reply. 

Best,

Nitesh 

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Re: [Bioc-devel] EXTERNAL: error: Could not fetch upstream

[Turaga, Nitesh]

Hi 

We have a key on file for you.

Your public key is 

ssh-rsa 
B3NzaC1yc2EDAQABAAABAQCxSTknqlL1IAExkqVS4+ZpvRIq2IGWzamjcTE//PANbZ9wQg09FuB+qDDhC1/AMQUd/1YWW8s7iC1lfnLt6Qp9Jbt0v2EuY2or/RwF36efIu2P/AERsUHqlgJRZc+qW583kNXRaHo2tCfUOW0ikrjAHnFh4SeZzfDXtJ/6JipBFju6vLwW+dIz/lPYwIM50oOApPqoae00S3/khhj9WcFUWkW3HMANq5OQxHxg9MCeV6q7HYUsGcjnHFCtNMAg4WyGH64RIPhasgsTV+V/C3gVqq1yzPdk62x37xU1Fas/M8Pcw6VAK2+IufEemLUo2//8FwW4Ne23Hb0nFu7sOUnD

You should have access if you use the correct private key. 

Best,

Nitesh 


> On Oct 10, 2017, at 1:56 PM, greg gloor  wrote:
> 
> I too am having problems with this. I checked to make sure I had an ssh 
> public key on github, I submitted my svn id (gloor.g) and re-submitted the 
> form last Friday. Today I did the following, and am still not able to access 
> the upstream repository:
> 
> settings:
> originhttps://github.com/ggloor/ALDEx2.git (fetch)
> originhttps://github.com/ggloor/ALDEx2.git (push)
> upstream  g...@git.bioconductor.org:packages/ALDEx2 (fetch)
> upstream  g...@git.bioconductor.org:packages/ALDEx2 (push)
> 
> 
> git fetch --all
> Fetching origin
> Fetching upstream
> Permission denied (publickey).
> fatal: Could not read from remote repository.
> 
> Please make sure you have the correct access rights
> and the repository exists.
> error: Could not fetch upstream
> 
> I'm wondering if my form was not processed yet
> 
> Thank you
> 
> Greg
> 
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Re: [Bioc-devel] EXTERNAL: error: Could not fetch upstream

[Turaga, Nitesh]

You have to resubmit your key to the google form. 



> On Oct 10, 2017, at 2:35 PM, greg gloor  wrote:
> 
> Thanks. Could the key be changed to this, which is the output from:
> 
> more .ssh/id_rsa.pub 
> 
> 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
>  ggl...@uwo.ca
> 
> Greg
> 
> 
>> On Oct 10, 2017, at 1:59 PM, Turaga, Nitesh  
>> wrote:
>> 
>> B3NzaC1yc2EDAQABAAABAQCxSTknqlL1IAExkqVS4+ZpvRIq2IGWzamjcTE//PANbZ9wQg09FuB+qDDhC1/AMQUd/1YWW8s7iC1lfnLt6Qp9Jbt0v2EuY2or/RwF36efIu2P/AERsUHqlgJRZc+qW583kNXRaHo2tCfUOW0ikrjAHnFh4SeZzfDXtJ/6JipBFju6vLwW+dIz/lPYwIM50oOApPqoae00S3/khhj9WcFUWkW3HMANq5OQxHxg9MCeV6q7HYUsGcjnHFCtNMAg4WyGH64RIPhasgsTV+V/C3gVqq1yzPdk62x37xU1Fas/M8Pcw6VAK2+IufEemLUo2//8FwW4Ne23Hb0nFu7sOUnD
> 



This email message may contain legally privileged and/or confidential 
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Bioc-devel@r-project.org mailing list
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Re: [Bioc-devel] Fw: EXTERNAL: Re: MSnID failing on release and devel

[Turaga, Nitesh]

Hi,

What is the email you submitted with? So that I can check your submission.

Nitesh 


> On Oct 10, 2017, at 3:57 PM, Van Twisk, Daniel 
>  wrote:
> 
> 
> 
> 
> 
> From: Vladislav Petyuk 
> Sent: Tuesday, October 10, 2017 2:56 PM
> To: Van Twisk, Daniel
> Subject: EXTERNAL: Re: MSnID failing on release and devel
> 
> 
> I submitted my SSH RSA key back on Friday evening.
> 
> made sure that I have upstream in .git/config
> 
> [remote "upstream"]
> 
> url = g...@git.bioconductor.org:packages/MSnID.git
> 
> fetch = +refs/heads/*:refs/remotes/upstream/*
> 
> 
> But still can't fetch "upstream". What am I missing (if anything)?
> 
> 
> WE33801:MSnID d3m629$ git fetch --all
> 
> Fetching origin
> 
> Fetching upstream
> 
> Permission denied (publickey).
> 
> fatal: Could not read from remote repository.
> 
> 
> Please make sure you have the correct access rights
> 
> and the repository exists.
> 
> error: Could not fetch upstream
> 
> WE33801:MSnID d3m629$
> 
> On Fri, Oct 6, 2017 at 7:15 AM Van Twisk, Daniel 
> mailto:daniel.vantw...@roswellpark.org>> 
> wrote:
> 
> MSnID is a package that has been on Biocondcutor for three years, so there is 
> no reason to set up a webhook as described in the "adding-a-web-hook" section 
> in contributions.  The Bioconductor Mirror that you referred to 
> (https://github.com/Bioconductor-mirror/MSnID) is deprecated and will no 
> longer reflect further changes to your package.  I can see that you've 
> recently made new commits to your package on your github repository.  To push 
> the changes on the Bioconductor git server, you must first complete this 
> Google form, if you have not already done so, so that you can have write 
> access to your package on the BIoconductor git server 
> (https://docs.google.com/forms/d/e/1FAIpQLSdYJ86-qpStdbbcPzFFXO4_XWnN8DvF2dOgNLE_iWNd0J-g8g/viewform).
>   Once this is done, you need to follow the instructions at this link to sync 
> your existing git repository to the server's 
> https://master.bioconductor.org/developers/how-to/git/sync-existing-repositories/.
> 
> [https://lh4.googleusercontent.com/aw68Dl1RAj_x7Ub4askJuRpQYDopphhllaweY9qUhJUjm2rblsz_BOrqXW1Zk_lQUcA=w1200-h630-p]
> 
> Bioconductor SSH 
> keys
> docs.google.com
> This form allows Bioconductor developers to submit SSH keys for access to 
> their Bioconductor git repository.
> 
> 
> 
> 
> From: Vladislav Petyuk mailto:pet...@gmail.com>>
> Sent: Friday, October 6, 2017 2:56:05 AM
> To: Van Twisk, Daniel
> Subject: Re: MSnID failing on release and devel
> 
> Daniel, could you help to sort out the following problem?
> I created webhook as described here
> https://github.com/Bioconductor/Contributions#adding-a-web-hook
> However, the test delivery didn't do through.
> https://github.com/vladpetyuk/MSnID/settings/hooks/16670279#delivery-response
> It says "400 Bad Request"
> 
> I'd appreciated any pointers,
> Vlad
> 
> On Thu, Oct 5, 2017 at 12:59 PM Vladislav Petyuk 
> mailto:pet...@gmail.com>> wrote:
> I believe before it was set though webhook. Now it is a bit different.  I'll 
> try to sort it out
> http://master.bioconductor.org/developers/how-to/git/maintain-github-bioc/
> 
> On Thu, Oct 5, 2017 at 12:45 PM Vladislav Petyuk 
> mailto:pet...@gmail.com>> wrote:
> The problem is fixed.
> I apologize if I lost track how Bioconductor packages are updated.  It used 
> to be that once the commit pushed to GitHub it is propagated to 
> Bioconductor's GitHub.
> The code is updated on my account, but not on Bioconductors (after 30 min 
> wait time).
> https://github.com/vladpetyuk/MSnID
> https://github.com/Bioconductor-mirror/MSnID
> Please suggest how to make sure the code fix gets into Bioconductor repo.
> Thanks,
> Vlad
> 
> 
> On Fri, Sep 29, 2017 at 1:05 PM Vladislav Petyuk 
> mailto:pet...@gmail.com>> wrote:
> Will try. Thanks for bringing this to my attention, Vlad
> 
> On Fri, Sep 29, 2017 at 1:01 PM Van Twisk, Daniel 
> mailto:daniel.vantw...@roswellpark.org>> 
> wrote:
> 
> Hello,
> 
> 
> I am a member of the Bioconductor core team and am emailing you to notify you 
> that a package you are maintaining, MSnID, is failing on our release and 
> devel single package builders: 
> https://www.bioconductor.org/checkResults/release/bioc-LATEST/MSnID/veracruz2-buildsrc.html
>  & 
> https://www.bioconductor.org/checkResults/devel/bioc-LATEST/MSnID/veracruz1-buildsrc.html.
>   Version 3.6 of Bioconductor is coming soon and we would like the release to 
> be free of errors.  In addition, If your package is failing on the release 
> branch, these failures will be cemented into version 3.5 of Bioconductor.  
> For these reasons, we ask you make the fixes to your package by mid-October.  
> If you h

Re: [Bioc-devel] Fw: EXTERNAL: Re: MSnID failing on release and devel

[Turaga, Nitesh]

We do not have a submission with that email. 

Nitesh

> On Oct 10, 2017, at 4:10 PM, Vladislav Petyuk  wrote:
> 
> pet...@gmail.com
> 
> On Tue, Oct 10, 2017 at 1:08 PM Turaga, Nitesh 
>  wrote:
> Hi,
> 
> What is the email you submitted with? So that I can check your submission.
> 
> Nitesh
> 
> 
> > On Oct 10, 2017, at 3:57 PM, Van Twisk, Daniel 
> >  wrote:
> >
> >
> >
> >
> > 
> > From: Vladislav Petyuk 
> > Sent: Tuesday, October 10, 2017 2:56 PM
> > To: Van Twisk, Daniel
> > Subject: EXTERNAL: Re: MSnID failing on release and devel
> >
> >
> > I submitted my SSH RSA key back on Friday evening.
> >
> > made sure that I have upstream in .git/config
> >
> > [remote "upstream"]
> >
> > url = g...@git.bioconductor.org:packages/MSnID.git
> >
> > fetch = +refs/heads/*:refs/remotes/upstream/*
> >
> >
> > But still can't fetch "upstream". What am I missing (if anything)?
> >
> >
> > WE33801:MSnID d3m629$ git fetch --all
> >
> > Fetching origin
> >
> > Fetching upstream
> >
> > Permission denied (publickey).
> >
> > fatal: Could not read from remote repository.
> >
> >
> > Please make sure you have the correct access rights
> >
> > and the repository exists.
> >
> > error: Could not fetch upstream
> >
> > WE33801:MSnID d3m629$
> >
> > On Fri, Oct 6, 2017 at 7:15 AM Van Twisk, Daniel 
> > mailto:daniel.vantw...@roswellpark.org>> 
> > wrote:
> >
> > MSnID is a package that has been on Biocondcutor for three years, so there 
> > is no reason to set up a webhook as described in the "adding-a-web-hook" 
> > section in contributions.  The Bioconductor Mirror that you referred to 
> > (https://github.com/Bioconductor-mirror/MSnID) is deprecated and will no 
> > longer reflect further changes to your package.  I can see that you've 
> > recently made new commits to your package on your github repository.  To 
> > push the changes on the Bioconductor git server, you must first complete 
> > this Google form, if you have not already done so, so that you can have 
> > write access to your package on the BIoconductor git server 
> > (https://docs.google.com/forms/d/e/1FAIpQLSdYJ86-qpStdbbcPzFFXO4_XWnN8DvF2dOgNLE_iWNd0J-g8g/viewform).
> >   Once this is done, you need to follow the instructions at this link to 
> > sync your existing git repository to the server's 
> > https://master.bioconductor.org/developers/how-to/git/sync-existing-repositories/.
> >
> > [https://lh4.googleusercontent.com/aw68Dl1RAj_x7Ub4askJuRpQYDopphhllaweY9qUhJUjm2rblsz_BOrqXW1Zk_lQUcA=w1200-h630-p]<https://docs.google.com/forms/d/e/1FAIpQLSdYJ86-qpStdbbcPzFFXO4_XWnN8DvF2dOgNLE_iWNd0J-g8g/viewform>
> >
> > Bioconductor SSH 
> > keys<https://docs.google.com/forms/d/e/1FAIpQLSdYJ86-qpStdbbcPzFFXO4_XWnN8DvF2dOgNLE_iWNd0J-g8g/viewform>
> > docs.google.com<http://docs.google.com>
> > This form allows Bioconductor developers to submit SSH keys for access to 
> > their Bioconductor git repository.
> >
> >
> >
> > 
> > From: Vladislav Petyuk mailto:pet...@gmail.com>>
> > Sent: Friday, October 6, 2017 2:56:05 AM
> > To: Van Twisk, Daniel
> > Subject: Re: MSnID failing on release and devel
> >
> > Daniel, could you help to sort out the following problem?
> > I created webhook as described here
> > https://github.com/Bioconductor/Contributions#adding-a-web-hook
> > However, the test delivery didn't do through.
> > https://github.com/vladpetyuk/MSnID/settings/hooks/16670279#delivery-response
> > It says "400 Bad Request"
> >
> > I'd appreciated any pointers,
> > Vlad
> >
> > On Thu, Oct 5, 2017 at 12:59 PM Vladislav Petyuk 
> > mailto:pet...@gmail.com>> wrote:
> > I believe before it was set though webhook. Now it is a bit different.  
> > I'll try to sort it out
> > http://master.bioconductor.org/developers/how-to/git/maintain-github-bioc/
> >
> > On Thu, Oct 5, 2017 at 12:45 PM Vladislav Petyuk 
> > mailto:pet...@gmail.com>> wrote:
> > The problem is fixed.
> > I apologize if I lost track how Bioconductor packages are updated.  It used 
> > to be that once the commit pushed to GitHub it is propagated to 
> > Bioconductor's GitHub.
> > The code is updated on my account, but not on Bioconductors (after 30 min 
> > wait time).

Re: [Bioc-devel] Fw: EXTERNAL: Re: MSnID failing on release and devel

[Turaga, Nitesh]

Please resubmit. 


> On Oct 10, 2017, at 4:24 PM, Turaga, Nitesh  
> wrote:
> 
> We do not have a submission with that email. 
> 
> Nitesh
> 
>> On Oct 10, 2017, at 4:10 PM, Vladislav Petyuk  wrote:
>> 
>> pet...@gmail.com
>> 
>> On Tue, Oct 10, 2017 at 1:08 PM Turaga, Nitesh 
>>  wrote:
>> Hi,
>> 
>> What is the email you submitted with? So that I can check your submission.
>> 
>> Nitesh
>> 
>> 
>>> On Oct 10, 2017, at 3:57 PM, Van Twisk, Daniel 
>>>  wrote:
>>> 
>>> 
>>> 
>>> 
>>> 
>>> From: Vladislav Petyuk 
>>> Sent: Tuesday, October 10, 2017 2:56 PM
>>> To: Van Twisk, Daniel
>>> Subject: EXTERNAL: Re: MSnID failing on release and devel
>>> 
>>> 
>>> I submitted my SSH RSA key back on Friday evening.
>>> 
>>> made sure that I have upstream in .git/config
>>> 
>>> [remote "upstream"]
>>> 
>>> url = g...@git.bioconductor.org:packages/MSnID.git
>>> 
>>> fetch = +refs/heads/*:refs/remotes/upstream/*
>>> 
>>> 
>>> But still can't fetch "upstream". What am I missing (if anything)?
>>> 
>>> 
>>> WE33801:MSnID d3m629$ git fetch --all
>>> 
>>> Fetching origin
>>> 
>>> Fetching upstream
>>> 
>>> Permission denied (publickey).
>>> 
>>> fatal: Could not read from remote repository.
>>> 
>>> 
>>> Please make sure you have the correct access rights
>>> 
>>> and the repository exists.
>>> 
>>> error: Could not fetch upstream
>>> 
>>> WE33801:MSnID d3m629$
>>> 
>>> On Fri, Oct 6, 2017 at 7:15 AM Van Twisk, Daniel 
>>> mailto:daniel.vantw...@roswellpark.org>> 
>>> wrote:
>>> 
>>> MSnID is a package that has been on Biocondcutor for three years, so there 
>>> is no reason to set up a webhook as described in the "adding-a-web-hook" 
>>> section in contributions.  The Bioconductor Mirror that you referred to 
>>> (https://github.com/Bioconductor-mirror/MSnID) is deprecated and will no 
>>> longer reflect further changes to your package.  I can see that you've 
>>> recently made new commits to your package on your github repository.  To 
>>> push the changes on the Bioconductor git server, you must first complete 
>>> this Google form, if you have not already done so, so that you can have 
>>> write access to your package on the BIoconductor git server 
>>> (https://docs.google.com/forms/d/e/1FAIpQLSdYJ86-qpStdbbcPzFFXO4_XWnN8DvF2dOgNLE_iWNd0J-g8g/viewform).
>>>   Once this is done, you need to follow the instructions at this link to 
>>> sync your existing git repository to the server's 
>>> https://master.bioconductor.org/developers/how-to/git/sync-existing-repositories/.
>>> 
>>> [https://lh4.googleusercontent.com/aw68Dl1RAj_x7Ub4askJuRpQYDopphhllaweY9qUhJUjm2rblsz_BOrqXW1Zk_lQUcA=w1200-h630-p]<https://docs.google.com/forms/d/e/1FAIpQLSdYJ86-qpStdbbcPzFFXO4_XWnN8DvF2dOgNLE_iWNd0J-g8g/viewform>
>>> 
>>> Bioconductor SSH 
>>> keys<https://docs.google.com/forms/d/e/1FAIpQLSdYJ86-qpStdbbcPzFFXO4_XWnN8DvF2dOgNLE_iWNd0J-g8g/viewform>
>>> docs.google.com<http://docs.google.com>
>>> This form allows Bioconductor developers to submit SSH keys for access to 
>>> their Bioconductor git repository.
>>> 
>>> 
>>> 
>>> 
>>> From: Vladislav Petyuk mailto:pet...@gmail.com>>
>>> Sent: Friday, October 6, 2017 2:56:05 AM
>>> To: Van Twisk, Daniel
>>> Subject: Re: MSnID failing on release and devel
>>> 
>>> Daniel, could you help to sort out the following problem?
>>> I created webhook as described here
>>> https://github.com/Bioconductor/Contributions#adding-a-web-hook
>>> However, the test delivery didn't do through.
>>> https://github.com/vladpetyuk/MSnID/settings/hooks/16670279#delivery-response
>>> It says "400 Bad Request"
>>> 
>>> I'd appreciated any pointers,
>>> Vlad
>>> 
>>> On Thu, Oct 5, 2017 at 12:59 PM Vladislav Petyuk 
>>> mailto:pet...@gmail.com>> wrote:
>>> I believe before it was set though webhook. Now it is a bit different.  
>>> I'll try to sort it out
>>> http://master.bioconductor.org/developers/how-to/git/main

Re: [Bioc-devel] Fw: EXTERNAL: Re: MSnID failing on release and devel

[Turaga, Nitesh]

I believe you have the wrong form.  
https://docs.google.com/forms/d/1CCwUhjtG82rnmcTWYqY43WcmBx5YyQm5UD4pcs1dhEs 
(this is the correct link).

http://master.bioconductor.org/developers/how-to/git/faq/ (point #3)


Best,

Nitesh 



> On Oct 10, 2017, at 4:30 PM, Vladislav Petyuk  wrote:
> 
> Here is the link I was using. 
> https://docs.google.com/forms/d/e/1FAIpQLSdYJ86-qpStdbbcPzFFXO4_XWnN8DvF2dOgNLE_iWNd0J-g8g/viewform
> 
> On Tue, Oct 10, 2017 at 1:28 PM Vladislav Petyuk  wrote:
> done
> 
> On Tue, Oct 10, 2017 at 1:24 PM Turaga, Nitesh 
>  wrote:
> Please resubmit.
> 
> 
> > On Oct 10, 2017, at 4:24 PM, Turaga, Nitesh  
> > wrote:
> >
> > We do not have a submission with that email.
> >
> > Nitesh
> >
> >> On Oct 10, 2017, at 4:10 PM, Vladislav Petyuk  wrote:
> >>
> >> pet...@gmail.com
> >>
> >> On Tue, Oct 10, 2017 at 1:08 PM Turaga, Nitesh 
> >>  wrote:
> >> Hi,
> >>
> >> What is the email you submitted with? So that I can check your submission.
> >>
> >> Nitesh
> >>
> >>
> >>> On Oct 10, 2017, at 3:57 PM, Van Twisk, Daniel 
> >>>  wrote:
> >>>
> >>>
> >>>
> >>>
> >>> 
> >>> From: Vladislav Petyuk 
> >>> Sent: Tuesday, October 10, 2017 2:56 PM
> >>> To: Van Twisk, Daniel
> >>> Subject: EXTERNAL: Re: MSnID failing on release and devel
> >>>
> >>>
> >>> I submitted my SSH RSA key back on Friday evening.
> >>>
> >>> made sure that I have upstream in .git/config
> >>>
> >>> [remote "upstream"]
> >>>
> >>> url = g...@git.bioconductor.org:packages/MSnID.git
> >>>
> >>> fetch = +refs/heads/*:refs/remotes/upstream/*
> >>>
> >>>
> >>> But still can't fetch "upstream". What am I missing (if anything)?
> >>>
> >>>
> >>> WE33801:MSnID d3m629$ git fetch --all
> >>>
> >>> Fetching origin
> >>>
> >>> Fetching upstream
> >>>
> >>> Permission denied (publickey).
> >>>
> >>> fatal: Could not read from remote repository.
> >>>
> >>>
> >>> Please make sure you have the correct access rights
> >>>
> >>> and the repository exists.
> >>>
> >>> error: Could not fetch upstream
> >>>
> >>> WE33801:MSnID d3m629$
> >>>
> >>> On Fri, Oct 6, 2017 at 7:15 AM Van Twisk, Daniel 
> >>> mailto:daniel.vantw...@roswellpark.org>> 
> >>> wrote:
> >>>
> >>> MSnID is a package that has been on Biocondcutor for three years, so 
> >>> there is no reason to set up a webhook as described in the 
> >>> "adding-a-web-hook" section in contributions.  The Bioconductor Mirror 
> >>> that you referred to (https://github.com/Bioconductor-mirror/MSnID) is 
> >>> deprecated and will no longer reflect further changes to your package.  I 
> >>> can see that you've recently made new commits to your package on your 
> >>> github repository.  To push the changes on the Bioconductor git server, 
> >>> you must first complete this Google form, if you have not already done 
> >>> so, so that you can have write access to your package on the BIoconductor 
> >>> git server 
> >>> (https://docs.google.com/forms/d/e/1FAIpQLSdYJ86-qpStdbbcPzFFXO4_XWnN8DvF2dOgNLE_iWNd0J-g8g/viewform).
> >>>   Once this is done, you need to follow the instructions at this link to 
> >>> sync your existing git repository to the server's 
> >>> https://master.bioconductor.org/developers/how-to/git/sync-existing-repositories/.
> >>>
> >>> [https://lh4.googleusercontent.com/aw68Dl1RAj_x7Ub4askJuRpQYDopphhllaweY9qUhJUjm2rblsz_BOrqXW1Zk_lQUcA=w1200-h630-p]<https://docs.google.com/forms/d/e/1FAIpQLSdYJ86-qpStdbbcPzFFXO4_XWnN8DvF2dOgNLE_iWNd0J-g8g/viewform>
> >>>
> >>> Bioconductor SSH 
> >>> keys<https://docs.google.com/forms/d/e/1FAIpQLSdYJ86-qpStdbbcPzFFXO4_XWnN8DvF2dOgNLE_iWNd0J-g8g/viewform>
> >>> docs.google.com<http://docs.google.com>
> >>> This form allows Bioconductor developers to submit SSH keys for access to 
> >>> their Bioconductor git repository.
> >>>
> >>>
> >>>
> >>> _

Re: [Bioc-devel] EXTERNAL: Re: Difficulty obtaining access to BioC git repository

[Turaga, Nitesh]

Hi Taylor,

It means that those two VM’s do not have the appropriate private keys which 
correspond to these public keys. 

Eg: If your public key is called “id_rsa.pub” (.pub is for public key), then, 
there is another file called “id_rsa” (no extension is the private key which 
corresponds to it). Your VM needs to have “id_rsa” locally, in the “.ssh” 
folder.

Best,

Nitesh

> On Oct 10, 2017, at 6:16 PM, Raborn, R. Taylor  wrote:
> 
> Hi Nitesh:
> 
> Thank you for sending these along.
> 
> All of our public keys match the three keys you sent to me, and we were able 
> to sync from my Desktop computer; access from our two VMs failed, suggesting 
> that it’s an issue on that side of things.
> 
> Thanks again for your help. I’ll let you know if we have any more questions.
> 
> Best regards,
> 
> Taylor
> 
>> On Oct 10, 2017, at 9:54 AM, Turaga, Nitesh  
>> wrote:
>> 
>> You have the following public key’s in the Bioconductor system, are you sure 
>> you are using the correct private keys.
>> 
>> 
>> ssh-rsa 
>> 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
>> 
>> ssh-rsa 
>> 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
>> 
>> ssh-rsa 
>> 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
>> 
>> 
>> 
>>> On Oct 9, 2017, at 10:24 PM, Raborn, R. Taylor  wrote:
>>> 
>>> Hi Nitesh:
>>> 
>>> Certainly. I used the following commands:
>>> 
>>>> git clone https://github.com/BrendelGroup/TSRchitect
>>>> cd TSRchitect/
>>>> git remote add upstream g...@git.bioconductor.org:packages/TSRchitect.git
>>>> git fetch --all
>>> Fetching origin
>>> Fetching upstream
>>> Permission denied (publickey).
>>> fatal: Could not read from remote repository.
>>> 
>>> Would you like me to provide my public key as well? I’m sorry for all the 
>>> trouble.
>>> 
>>> Best regards,
>>> 
>>> Taylor
>>> 
>>>> On Oct 9, 2017, at 5:01 PM, Turaga, Nitesh  
>>>> wrote:
>>>> 
>>>> Please send me the list of commands you tried, and the output.
>>>> 
>>>> Your key is in the system. Either you are not using the correct key, or 
>>>> are issuing the wrong command on git. 
>>>> 
>>>> Nitesh
>>>> 
>>>>> On Oct 9, 2017, at 11:45 AM, Raborn, R. Taylor  
>>>>> wrote:
>>>>> 
>>>>> Hi Nitesh:
>>>>> 
>>>>> Sounds great.
>>>>> 
>>>>> This morning I attempted to sync my GitHub repository with Bioconductor 
>>>>> (following the instructions here), but I still wasn’t able to logi

Re: [Bioc-devel] EXTERNAL: Re: Difficulty obtaining access to BioC git repository

[Turaga, Nitesh]

The ownership works with `400` and `600` for keys. Which is reflected in the 
FAQ section (point 16). 

Best,

Nitesh 

> On Oct 11, 2017, at 10:59 AM, Morgan, Martin  
> wrote:
> 
> On 10/11/2017 10:54 AM, Raborn, R. Taylor wrote:
>> Hi Nitesh:
>> Thank you for the message. In my previous email I should have mentioned that 
>> I have matched each VM public key with their respective private keys, which 
>> are in both of the respective .ssh folders.
>> It’s puzzling, but it’s something we’ll have to get to the bottom of on our 
>> end. I think we’ll start with fresh new key pairs on the VMs; if so, I’ll 
>> let you know.
> 
> ssh is very particular about directory permissions and ownership -- '600' 
> which is owner read / write, no access for others.
> 
> also if there are multiple keys then you'd like an ssh config file that 
> specifies something like FAQ #15 at 
> http://master.bioconductor.org/developers/how-to/git/faq/
> 
> 
> 
> Martin
> 
>> Best regards,
>> Taylor
>>> On Oct 11, 2017, at 6:48 AM, Turaga, Nitesh  
>>> wrote:
>>> 
>>> Hi Taylor,
>>> 
>>> It means that those two VM’s do not have the appropriate private keys which 
>>> correspond to these public keys.
>>> 
>>> Eg: If your public key is called “id_rsa.pub” (.pub is for public key), 
>>> then, there is another file called “id_rsa” (no extension is the private 
>>> key which corresponds to it). Your VM needs to have “id_rsa” locally, in 
>>> the “.ssh” folder.
>>> 
>>> Best,
>>> 
>>> Nitesh
>>> 
>>>> On Oct 10, 2017, at 6:16 PM, Raborn, R. Taylor  
>>>> wrote:
>>>> 
>>>> Hi Nitesh:
>>>> 
>>>> Thank you for sending these along.
>>>> 
>>>> All of our public keys match the three keys you sent to me, and we were 
>>>> able to sync from my Desktop computer; access from our two VMs failed, 
>>>> suggesting that it’s an issue on that side of things.
>>>> 
>>>> Thanks again for your help. I’ll let you know if we have any more 
>>>> questions.
>>>> 
>>>> Best regards,
>>>> 
>>>> Taylor
>>>> 
>>>>> On Oct 10, 2017, at 9:54 AM, Turaga, Nitesh 
>>>>>  wrote:
>>>>> 
>>>>> You have the following public key’s in the Bioconductor system, are you 
>>>>> sure you are using the correct private keys.
>>>>> 
>>>>> 
>>>>> ssh-rsa 
>>>>> 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
>>>>> 
>>>>> ssh-rsa 
>>>>> 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
>>>>> 
>>>>> ssh-rsa 
>>>>> B3NzaC1yc2EDAQABAAACAQCvkQiXYaqs216fFw6kAlFh5AEjPPEM4pYzf1I8uNtYGMeRwwqRDxMMJwtaC3BlOk0BcvZx5K4UCL5Gy9X9VxMCQ8Hie2wCe9y4vxf715sQxxDGOE/A/HccSB1dMojXt4KkiS9Q0QYg111U4O5wPGZwUxPJroTfPVPR4Gi5X2fjOf/UAjiP31njJvWxZyPGofrHamnT4eYZGlhTrEs+UQEBLZdIl7NXTUdQew8OoIyxcUjIZYfFA4Z4Yc0DUR39z//BMF8LCjc6cMiu9Ll1HVe60um0ycki9DuIR4DnDxqFPk26deyjbfqgXAXX0ftToPVpliV6jtCcKXWgmrBmVo7oyllknWqDSJVbdmyllC3In55/Xy7Xm1g3q/vujdQhfAURVckxut1FUapHrk0fubIQ5oAZEOXF9JvVECfebf1JvsgksZhrwPUUZLkbuhUF8TJUwyOSI/WeGvwnf7hK4eEkyiy73OUUnzq/Nl60HJT2FsSwyvtK7pNDzHuhWrKkjWx6xVDYfr+y/CA5XiMzHDIZtL3EOxv7

Re: [Bioc-devel] EXTERNAL: Git access for PhenStat contribute

[Turaga, Nitesh]

Hi Jeremy,

Hamed does not have access to PhenStat on Bioconductor. Hamed is also not 
listed on the maintainer list of the package. Only you have access with the 
“jmason”.

We encourage having only one maintainer, and all collaborators should just send 
in pull requests to the Github repository where the package is being developed. 
I encourage you to take a look at this thread on the mailing list, where some 
other maintainer had a similar issue.

https://stat.ethz.ch/pipermail/bioc-devel/2017-October/011790.html

Best,

Nitesh



> On Oct 11, 2017, at 11:13 AM, jmason  wrote:
> 
> Hi list,
> 
> My collaborator, Hamed, is attempting to push a new version of PhenStat to 
> the bioC git repo.
> 
> He submitted his public key via the google form on Monday.  He can clone the 
> repository and commit locally, but when attempting to push gets an error:
> 
> FATAL: W any packages/PhenStat hamedm DENIED by fallthru
> (or you mis-spelled the reponame)
> fatal: Could not read from remote repository.
> 
> Please make sure you have the correct access rights
> and the repository exists.
> 
> His username is hame...@ebi.ac.uk
> 
> I can commit and push to this repository just fine.  Is there anything extra 
> that we need to do in order to have more than one person who can push to the 
> repo?
> 
> thanks for your assistance!
> Jeremy
> 
> ___
> 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 
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recipient(s), you are hereby notified that any disclosure, copying, 
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this message in error, please notify the sender immediately by e-mail and 
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Re: [Bioc-devel] EXTERNAL: Re: failing Bioconductor Package groHMM

[Turaga, Nitesh]

Hi Anusha,

I just saw that even though you are listed as the first maintainer on the 
package DESCRIPTION, you do not have a previously issued SVN ID. Is this 
correct? 

Nitesh


> On Oct 11, 2017, at 12:10 PM, Anusha Nagari 
>  wrote:
> 
> Hi Nitesh,
> 
> I submitted the form to access permissions to the new Bioconductor git 
> repository on Monday and haven’t heard back. Please let me know if I need to 
> provide any other information to get the access to Bioconductor git and also 
> to remove Venkat Malladi as a maintainer on the groHMM package.
> 
> Thanks,
> Anusha
> 
> On 10/4/17, 3:05 PM, "Venkat Malladi"  
> wrote:
> 
>HI Nitesh,
> 
>I am confirming that I am no longer a maintainer on the groHMM packaged.
> 
>Venkat
> 
>On 10/4/17, 2:40 PM, "Turaga, Nitesh"  
> wrote:
> 
>Yes, you can submit that.
> 
>I am cc-ing Venkat for a confirmation.
> 
>Best,
> 
>Nitesh 
> 
>> On Oct 4, 2017, at 3:39 PM, Anusha Nagari  
>> wrote:
>> 
>> This message was sent securely using ZixCorp.
>> 
>> Hi Nitesh,
>> 
>> I have a question about the svn.id. The developer of the groHMM package is 
>> no longer in our group and I do not have a SVN account. Can use my github id 
>> for the second section in this form:
>> https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform
>> 
>> Regarding the changes to the maintainers, we need to remove one of the 
>> persons currently listed as maintainer (Venkat Malladi, 
>> venkat.mall...@utsouthwestern.edu). I updated the DESCRIPTION file of our 
>> package and will push the changes to g...@git.bioconductor.org.
>> 
>> Thanks,
>> Anusha
>> 
>> From: "Shepherd, Lori" 
>> Date: Wednesday, October 4, 2017 at 6:25 AM
>> To: Anusha Nagari , "Turaga, Nitesh" 
>> 
>> Cc: Tulip Nandu 
>> Subject: Re: failing Bioconductor Package groHMM
>> 
>> This message was sent securely using Zix®
>> 
>> Submitting the changes to your local github account it not sufficient.  You 
>> need to push the changes to the g...@git.bioconductor.org server. 
>> 
>> http://master.bioconductor.org/developers/how-to/git/sync-existing-repositories/
>> 
>> Before you will be able to do this you need to submit your svn.id and 
>> associated ssh key to the form 
>> 
>> https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform
>> 
>> 
>> To change maintainers, we would need one of the current maintainers to 
>> authorize by name who will be transitioning to maintainer.  We can than make 
>> the necessary changes on our system to allow access (Nitesh from our group 
>> is included in this email and can assist with this).  Please also update the 
>> maintainer field in the DESCRIPTION file of your package. 
>> 
>> Cheers, 
>> 
>> Lori Shepherd
>> Bioconductor Core Team
>> Roswell Park Cancer Institute
>> Department of Biostatistics & Bioinformatics
>> Elm & Carlton Streets
>> Buffalo, New York 14263
>> From: Anusha Nagari 
>> Sent: Tuesday, October 3, 2017 4:34:06 PM
>> To: Shepherd, Lori
>> Cc: Tulip Nandu
>> Subject: Re: failing Bioconductor Package groHMM
>> 
>> This message was sent securely using ZixCorp.
>> 
>> Hello,
>> 
>> We made the necessary changes to
>> https://github.com/Kraus-Lab/groHMM/blob/master/vignettes/groHMM.Rnw
>> 
>> Please let us know if the package passes the 'R CMD build'. We also need to 
>> update the package maintainer information, please let us know how to go 
>> about it.
>> 
>> Best regards,
>> Anusha
>> 
>> From: "Shepherd, Lori" 
>> Date: Monday, October 2, 2017 at 6:54 AM
>> To: Anusha Nagari 
>> Cc: Venkat Malladi , Tulip Nandu 
>> , Lee Kraus 
>> Subject: Re: failing Bioconductor Package groHMM
>> 
>> This message was sent securely using Zix®
>> 
>> The package continues to fail. We need this fix as soon as possible and 
>> before the next release of Bioconductor. 
>> 
>> Lori Shepherd
>> Bioconductor Core Team
>> Roswell Park Cancer Institute
>> Department of Biostatistics & Bioinformatics
>> Elm & Carlton Streets
>> Buffalo, New York 14263
>> From: Anusha Nagari 
>> Sent: Thursday, September 21, 2017 9:01:58 AM
>> To: Shepherd, Lori
>> Cc: Venkat Malladi; Tulip Nandu; Lee Kraus
>> Subject: Re: failing Bi

Re: [Bioc-devel] EXTERNAL: Re: failing Bioconductor Package groHMM

[Turaga, Nitesh]

Hi Anusha,

Since changes were made, please update your DESCRIPTION file on the package to 
reflect the most current list of maintainers. 

Nitesh


> On Oct 11, 2017, at 12:18 PM, Anusha Nagari 
>  wrote:
> 
> Hi Nitesh,
> 
> Yes, I do not have an SVN ID. The developer of the package left our group and 
> I was listed as the first maintainer on the package. This would be first time 
> I am submitting the changes to the groHMM package.
> 
> Best,
> Anusha
> 
> On 10/11/17, 11:15 AM, "Turaga, Nitesh"  wrote:
> 
>Hi Anusha,
> 
>I just saw that even though you are listed as the first maintainer on the 
> package DESCRIPTION, you do not have a previously issued SVN ID. Is this 
> correct? 
> 
>Nitesh
> 
> 
>> On Oct 11, 2017, at 12:10 PM, Anusha Nagari 
>>  wrote:
>> 
>> Hi Nitesh,
>> 
>> I submitted the form to access permissions to the new Bioconductor git 
>> repository on Monday and haven’t heard back. Please let me know if I need to 
>> provide any other information to get the access to Bioconductor git and also 
>> to remove Venkat Malladi as a maintainer on the groHMM package.
>> 
>> Thanks,
>> Anusha
>> 
>> On 10/4/17, 3:05 PM, "Venkat Malladi"  
>> wrote:
>> 
>>   HI Nitesh,
>> 
>>   I am confirming that I am no longer a maintainer on the groHMM packaged.
>> 
>>   Venkat
>> 
>>   On 10/4/17, 2:40 PM, "Turaga, Nitesh"  
>> wrote:
>> 
>>   Yes, you can submit that.
>> 
>>   I am cc-ing Venkat for a confirmation.
>> 
>>   Best,
>> 
>>   Nitesh 
>> 
>>> On Oct 4, 2017, at 3:39 PM, Anusha Nagari 
>>>  wrote:
>>> 
>>> This message was sent securely using ZixCorp.
>>> 
>>> Hi Nitesh,
>>> 
>>> I have a question about the svn.id. The developer of the groHMM package is 
>>> no longer in our group and I do not have a SVN account. Can use my github 
>>> id for the second section in this form:
>>> https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform
>>> 
>>> Regarding the changes to the maintainers, we need to remove one of the 
>>> persons currently listed as maintainer (Venkat Malladi, 
>>> venkat.mall...@utsouthwestern.edu). I updated the DESCRIPTION file of our 
>>> package and will push the changes to g...@git.bioconductor.org.
>>> 
>>> Thanks,
>>> Anusha
>>> 
>>> From: "Shepherd, Lori" 
>>> Date: Wednesday, October 4, 2017 at 6:25 AM
>>> To: Anusha Nagari , "Turaga, Nitesh" 
>>> 
>>> Cc: Tulip Nandu 
>>> Subject: Re: failing Bioconductor Package groHMM
>>> 
>>> This message was sent securely using Zix®
>>> 
>>> Submitting the changes to your local github account it not sufficient.  You 
>>> need to push the changes to the g...@git.bioconductor.org server. 
>>> 
>>> http://master.bioconductor.org/developers/how-to/git/sync-existing-repositories/
>>> 
>>> Before you will be able to do this you need to submit your svn.id and 
>>> associated ssh key to the form 
>>> 
>>> https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform
>>> 
>>> 
>>> To change maintainers, we would need one of the current maintainers to 
>>> authorize by name who will be transitioning to maintainer.  We can than 
>>> make the necessary changes on our system to allow access (Nitesh from our 
>>> group is included in this email and can assist with this).  Please also 
>>> update the maintainer field in the DESCRIPTION file of your package. 
>>> 
>>> Cheers, 
>>> 
>>> Lori Shepherd
>>> Bioconductor Core Team
>>> Roswell Park Cancer Institute
>>> Department of Biostatistics & Bioinformatics
>>> Elm & Carlton Streets
>>> Buffalo, New York 14263
>>> From: Anusha Nagari 
>>> Sent: Tuesday, October 3, 2017 4:34:06 PM
>>> To: Shepherd, Lori
>>> Cc: Tulip Nandu
>>> Subject: Re: failing Bioconductor Package groHMM
>>> 
>>> This message was sent securely using ZixCorp.
>>> 
>>> Hello,
>>> 
>>> We made the necessary changes to
>>> https://github.com/Kraus-Lab/groHMM/blob/master/vignettes/groHMM.Rnw
>>> 
>>> Please let us know if the package passes the 'R CMD build'. We also need to 
>>> update 

Re: [Bioc-devel] EXTERNAL: Permission denied (publickey)

[Turaga, Nitesh]

Hi Eugenia

Your package was accepted on August 1st, and added to the SVN list of packages 
before the SVN —> GIT transition on August 15th.  You should have received an 
email with the “e.galeota” as your SVN ID to access your package on SVN. 

 

> On Oct 12, 2017, at 9:44 AM, Eugenia Galeota  
> wrote:
> 
> Thank you Lori,
> I have a couple of small questions, how do I know that my SVN id is
> e.galeota? Because my user id on Github for Onassis is eugeniaeueu and I
> submitted the package through Github Bioconductor contributions. When
> Onassis has been accepted in Bioconductor I received a mail @eugeniaeueu
> user and this was saying that another mail would have been sent to the
> maintainer of the package (which is still me and the e-mail I'm writing
> from). Anyway, regarding the key that I generated in github, is it still

This email should have your SVN ID.

> possible to fill the form using the same key as befor and user id you just
> provided? Thanks

Since it’s pretty close to the transition, I’ll make an exception and change 
your user ID on our end to avoid further confusion.

You will not need to do anything else, and you will have access now.

Best

Nitesh 

> 
> Eugenia
> 
> 2017-10-12 13:39 GMT+02:00 Shepherd, Lori :
> 
>> Once the package moves over to the daily build system, the builds are not
>> triggered immediately on a version bump and the results will no longer post
>> to the issue tracker.  The package is considered part of the daily build
>> system and the version bump and successful push to g...@git.bioconductor.org:
>> packages/Onassis.git. triggers a build there; you will be able to view
>> the report
>> 
>> 
>> http://bioconductor.org/checkResults/
>> 
>> 
>> It can take up to 24 hours for keys to be processed as they are only
>> processed once per day.  It looks like you submitted a key this morning but
>> with a different id. The user id listed for your package is your svnid 
>> e.galeota
>> and the associated ssh key for that id would need to be submitted. The id
>> submitted to the form was eugeniaeueu.
>> 
>> 
>> 
>> Lori Shepherd
>> 
>> Bioconductor Core Team
>> 
>> Roswell Park Cancer Institute
>> 
>> Department of Biostatistics & Bioinformatics
>> 
>> Elm & Carlton Streets
>> 
>> Buffalo, New York 14263
>> --
>> *From:* Bioc-devel  on behalf of
>> Eugenia Galeota 
>> *Sent:* Thursday, October 12, 2017 7:24:35 AM
>> *To:* bioc-devel@r-project.org
>> *Subject:* EXTERNAL: [Bioc-devel] Permission denied (publickey)
>> 
>> Hi, I'm having problems in updating Onassis. I followed all the
>> instructions to add the ssh public key to the repository and also filled
>> the form to ask it to Bioconductor. A second issue is related to the build.
>> I am changing the version of the package but no build starts, is the hook
>> still working? Thanks
>> Eugenia
>> 
>> --
>> Eugenia Galeota, PhD
>> Center for Genomic Science of IIT@SEMM
>> Computational Epigenomics
>> Email: eugenia.gale...@iit.it
>> Tel: +39 02 9437 5046 <+39%2002%209437%205046>
>> Via Adamello 16, 20139 Milan, Italy
>> 
>> 
>>[[alternative HTML version deleted]]
>> 
>> ___
>> 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
>> 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.
> 
> 
> 
> 
> -- 
> Eugenia Galeota, PhD
> Center for Genomic Science of IIT@SEMM
> Computational Epigenomics
> Email: eugenia.gale...@iit.it
> Tel: +39 02 9437 5046 <+39%2002%209437%205046>
> Via Adamello 16, 20139 Milan, Italy
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] EXTERNAL: whitespace or or end of line format conflict in git merge

[Turaga, Nitesh]

Hi,

The white space (formatting) is a mistake on our end. 

But as far as the instructions go it is mostly accurate. 

Once GIT reports after the “merge” that you have conflicts, you could also, try 
this command,

`git mergetool`

which will open a GUI to help you choose which version you want i.e HEAD vs 
upstream/master. 

https://git-scm.com/docs/git-mergetool

Best,

Nitesh 


> On Oct 12, 2017, at 2:03 PM, Vladislav Petyuk  wrote:
> 
> While resolving conflicts according to this protocol
> https://master.bioconductor.org/developers/how-to/git/resolve-conflicts/
> I ran into a quite a number of seeming duplications of the file content
> between HEAD and upstream/master. It looks like either some sort of
> whitespace or end of line formatting issue.
> E.g.
> <<< HEAD
> BiocGenerics:::testPackage("MSnID")
> ===
> BiocGenerics:::testPackage("MSnID")
 upstream/master
> What is the recommended way to avoid all this trouble?
> Thanks,
> Vlad
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] EXTERNAL: Git push error and duplicate commits

[Turaga, Nitesh]

Hi Matthew,

I remember fixing this repository for you a few weeks ago. 

You cannot push branches to the Bioconductor repository, that is in the FAQ, 
and documentation.

Can you tell me what exactly are the steps you are trying that, you are getting 
duplicate commits again?

Best,

Nitesh 

> On Oct 13, 2017, at 3:39 AM, Matthew Myint  wrote:
> 
> Hi,
> 
> Recently I noticed in hindsight that my repository had duplicate
> commits, but I missed this during my normal package updating
> procedures.
> 
> It was odd that the hook didn't reject these, so I made a clean branch
> from a commit before the problem occurred and cherry-picking commits
> to the present state. However, trying to push this to bioconductor git
> returned an error
> 
>> remote: FATAL: + refs/heads/master packages/cytofkit c.hao DENIED by fallthru
>> remote: error: hook declined to update refs/heads/master
>> To git.bioconductor.org:packages/cytofkit.git
>> ! [remote rejected] master -> master (hook declined)
>> error: failed to push some refs to 
>> 'g...@git.bioconductor.org:packages/cytofkit.git'
> 
> I've kept the original backed up, and here is the clean branch and
> back up branch for reference.
> 
> Here is the link to my repo for additional reference
> https://github.com/JinmiaoChenLab/cytofkit
> https://github.com/JinmiaoChenLab/cytofkit/network (network display
> for easy visualisation)
> 
> Sorry for the hassle
> 
> Regards
> Matthew Myint
> Life Science Undergraduate, Year 4
> NUS
> 
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel



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Re: [Bioc-devel] EXTERNAL: Permission denied for ImmuneSpaceR repo

[Turaga, Nitesh]

Please send me a list of commands you have tried. I’d like to see the outputs 
as well.

e.henrich has associated keys to it coming from www.github.com/immunespace.keys 

Best,

Nitesh 

> On Oct 13, 2017, at 1:36 PM, Immune Space  wrote:
> 
> Hi Nitesh,
> 
> We resubmitted the git transition form again on Wednesday, but we still don't 
> have access to ImmuneSpaceR repository in BIoc yet. Could you look into this?
> 
> Best,
> ImmuneSpace Team



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Re: [Bioc-devel] EXTERNAL: Re: Cannot move 'xps' to GIT

[Turaga, Nitesh]

Hi,

Both your `origin` and `upstream` are set to the same location i.e 
g...@git.bioconductor.org:packages/xps.

This is wrong. You want your origin to point to `g...@github.com:cstrato/xps`

You can do this by following the commands, 

`git remote set-url origin g...@github.com:cstrato/xps.git`

`git push origin master` 

All of this documentation is given in bioconductor.org/developers/how-to/git/. 

Best,

Nitesh 


> On Oct 13, 2017, at 2:07 PM, cstrato  wrote:
> 
> Dear Martin,
> 
> Following your advice
> 
>   https://bioconductor.org/developers/how-to/git/maintain-github-bioc/
> 
> I did the following:
> 
> $ cd xps
> $ git remote add upstream g...@git.bioconductor.org:packages/xps.git
> $ git fetch upstream
> Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa':
> From git.bioconductor.org:packages/xps
> * [new branch]  RELEASE_2_10 -> upstream/RELEASE_2_10
> * [new branch]  RELEASE_2_11 -> upstream/RELEASE_2_11
> * [new branch]  RELEASE_2_12 -> upstream/RELEASE_2_12
> * [new branch]  RELEASE_2_13 -> upstream/RELEASE_2_13
> * [new branch]  RELEASE_2_14 -> upstream/RELEASE_2_14
> * [new branch]  RELEASE_2_2 -> upstream/RELEASE_2_2
> * [new branch]  RELEASE_2_3 -> upstream/RELEASE_2_3
> * [new branch]  RELEASE_2_4 -> upstream/RELEASE_2_4
> * [new branch]  RELEASE_2_5 -> upstream/RELEASE_2_5
> * [new branch]  RELEASE_2_6 -> upstream/RELEASE_2_6
> * [new branch]  RELEASE_2_7 -> upstream/RELEASE_2_7
> * [new branch]  RELEASE_2_8 -> upstream/RELEASE_2_8
> * [new branch]  RELEASE_2_9 -> upstream/RELEASE_2_9
> * [new branch]  RELEASE_3_0 -> upstream/RELEASE_3_0
> * [new branch]  RELEASE_3_1 -> upstream/RELEASE_3_1
> * [new branch]  RELEASE_3_2 -> upstream/RELEASE_3_2
> * [new branch]  RELEASE_3_3 -> upstream/RELEASE_3_3
> * [new branch]  RELEASE_3_4 -> upstream/RELEASE_3_4
> * [new branch]  RELEASE_3_5 -> upstream/RELEASE_3_5
> * [new branch]  master -> upstream/master
> $ git fetch upstream
> Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa':
> $ git merge upstream/master
> Already up-to-date.
> $ git push origin master
> Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa':
> Everything up-to-date
> $ git remote -v
> origin  g...@git.bioconductor.org:packages/xps (fetch)
> origin  g...@git.bioconductor.org:packages/xps (push)
> upstreamg...@git.bioconductor.org:packages/xps.git (fetch)
> upstreamg...@git.bioconductor.org:packages/xps.git (push)
> $ git checkout master
> M   DESCRIPTION
> M   NEWS
> M   configure.in
> Already on 'master'
> Your branch is up-to-date with 'origin/master'.
> $ git add -v DESCRIPTION
> add 'DESCRIPTION'
> $ git add -v NEWS
> add 'NEWS'
> $ git add -v configure.in
> add 'configure.in'
> $ git push origin master
> Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa':
> Everything up-to-date
> $ git push upstream master
> Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa':
> Everything up-to-date
> 
> 
> I hope that I could commit my changes and my development version on
> 
>   https://github.com/cstrato/xps
> 
> will be updated to 'xps_1.37.2'
> 
> 
> (PS: my repository https://github.com/cstrato/xps is still empty)
> 
> Thank you very much for your help.
> Best regards,
> Christian
> 
> 
> On 10/12/17 23:21, Martin Morgan wrote:
>> On 10/12/2017 04:13 PM, cstrato wrote:
>>> Dear Martin,
>>> 
>>> Thank you for your informative reply.
>>> 
>>> 1, My SSH public key that you mentioned is the correct one.
>>> 
>>> 
>>> 
>>> 2, After following your advice and running
>>> 
>>>ssh -v g...@git.bioconductor.org
>>> 
>>> I got:
>>> 
>>> OpenSSH_7.4p1, LibreSSL 2.5.0
>>> debug1: Reading configuration data /etc/ssh/ssh_config
>>> debug1: Connecting to git.bioconductor.org [34.192.48.227] port 22.
>>> debug1: Connection established.
>>> debug1: identity file /Users/rabbitus/.ssh/id_rsa type 1
>>> debug1: key_load_public: No such file or directory
>>> ...
>>> debug1: Remote: PTY allocation disabled.
>>> PTY allocation request failed on channel 0
>>> hello c.stratowa, this is git@ip-172-30-0-33 running gitolite3 
>>> v3.6.6-6-g7c8f0ab on git 2.13.0
>>> ...
>>> bash: debug1:: command not found
>>> 
>>> 
>>> 
>>> 3, Nevertheless, I could run:
>>> 
>>>git clone g...@git.bioconductor.org:packages/xps
>>> 
>>> I got:
>>> Cloning into 'xps'...
>>> Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa':
>>> remote: Counting objects: 2757, done.
>>> remote: Compressing objects: 100% (2741/2741), done.
>>> remote: Total 2757 (delta 2077), reused 0 (delta 0)
>>> Receiving objects: 100% (2757/2757), 5.62 MiB | 945.00 KiB/s, done.
>>> Resolving deltas: 100% (2077/2077), done.
>>> Checking connectivity... done.
>> From the Bioconductor perspective, I think you are 'good to go', and you 
>> could follow, e.g.,
>> http://bioconductor.org/developers/how-to/git/maintain-bioc-only/
>> to commit and push changes to the Bioconductor git repository. These chan

Re: [Bioc-devel] EXTERNAL: Git push error and duplicate commits

[Turaga, Nitesh]

Hi Matthew,

I’ll have to fix your branch again, for this I need some time. Do not push any 
more changes. 

*When you pull from the upstream (g...@git.bioconductor.org), you are not 
supposed to get any duplicate commits.* 

If a merge is giving you duplicate commits, it means that you didn’t switch 
your master branch out. Or forgot to checkout the non-duplicate master.

Best,

Nitesh 



> On Oct 13, 2017, at 2:13 PM, Matthew Myint  wrote:
> 
> Hi,
> 
> After you helped me fix my repository, whenever I had updates I would use the 
> steps from 
> https://master.bioconductor.org/developers/how-to/git/push-to-github-bioc/
> 
>  1) note down what files needed to be updated in the repository
> 
> 2) pull from upstream and merge to local branch 
> https://master.bioconductor.org/developers/how-to/git/pull-upstream-changes/
> 
> 3) update the needed files in the repository and commit
> 
> 4) push to both origin and upstream
> 
> Also, just to clarify, the branch pushing I was referring to was the 
> “switcheroo” in the link 
> https://github.com/Bioconductor/bioc_git_transition/blob/master/doc/scenario-6-abandon-changes.md
> 
> Thanks and regards
> Matthew 
> Sent from my iPhone
> 
> On 13 Oct 2017, at 22:35, Turaga, Nitesh  
> wrote:
> 
>> Hi Matthew,
>> 
>> I remember fixing this repository for you a few weeks ago. 
>> 
>> You cannot push branches to the Bioconductor repository, that is in the FAQ, 
>> and documentation.
>> 
>> Can you tell me what exactly are the steps you are trying that, you are 
>> getting duplicate commits again?
>> 
>> Best,
>> 
>> Nitesh 
>> 
>>> On Oct 13, 2017, at 3:39 AM, Matthew Myint  
>>> wrote:
>>> 
>>> Hi,
>>> 
>>> Recently I noticed in hindsight that my repository had duplicate
>>> commits, but I missed this during my normal package updating
>>> procedures.
>>> 
>>> It was odd that the hook didn't reject these, so I made a clean branch
>>> from a commit before the problem occurred and cherry-picking commits
>>> to the present state. However, trying to push this to bioconductor git
>>> returned an error
>>> 
>>>> remote: FATAL: + refs/heads/master packages/cytofkit c.hao DENIED by 
>>>> fallthru
>>>> remote: error: hook declined to update refs/heads/master
>>>> To git.bioconductor.org:packages/cytofkit.git
>>>> ! [remote rejected] master -> master (hook declined)
>>>> error: failed to push some refs to 
>>>> 'g...@git.bioconductor.org:packages/cytofkit.git'
>>> 
>>> I've kept the original backed up, and here is the clean branch and
>>> back up branch for reference.
>>> 
>>> Here is the link to my repo for additional reference
>>> https://github.com/JinmiaoChenLab/cytofkit
>>> https://github.com/JinmiaoChenLab/cytofkit/network (network display
>>> for easy visualisation)
>>> 
>>> Sorry for the hassle
>>> 
>>> Regards
>>> Matthew Myint
>>> Life Science Undergraduate, Year 4
>>> NUS
>>> 
>>> ___
>>> 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 
>> 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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Re: [Bioc-devel] EXTERNAL: Git push error and duplicate commits

[Turaga, Nitesh]

Hi Matthew,

After closer inspection of “cytofkit”, it was this commit which caused the 
duplicates. 

commit 4050c245d04af30705245f48931e677a6b4ae159
Merge: 467f659 e6cef6c
Author: Hervé Pagès 
Date:   Wed Sep 20 13:19:45 2017 -0700

Merge branch 'master' of git.bioconductor.org:packages/cytofkit


It was a fetch and merge. So, it means that the GitHub repository hosted 
(https://github.com/JinmiaoChenLab/cytofkit) did not deprecate the “master” 
with duplicate commits by Sept 20th. This was not done till Sept 27th, based on 
your GitHub 
logs(https://github.com/JinmiaoChenLab/cytofkit/commits/master_deprecated). 


Best,

Nitesh 


> On Oct 13, 2017, at 2:18 PM, Turaga, Nitesh  
> wrote:
> 
> Hi Matthew,
> 
> I’ll have to fix your branch again, for this I need some time. Do not push 
> any more changes. 
> 
> *When you pull from the upstream (g...@git.bioconductor.org), you are not 
> supposed to get any duplicate commits.* 
> 
> If a merge is giving you duplicate commits, it means that you didn’t switch 
> your master branch out. Or forgot to checkout the non-duplicate master.
> 
> Best,
> 
> Nitesh 
> 
> 
> 
>> On Oct 13, 2017, at 2:13 PM, Matthew Myint  
>> wrote:
>> 
>> Hi,
>> 
>> After you helped me fix my repository, whenever I had updates I would use 
>> the steps from 
>> https://master.bioconductor.org/developers/how-to/git/push-to-github-bioc/
>> 
>> 1) note down what files needed to be updated in the repository
>> 
>> 2) pull from upstream and merge to local branch 
>> https://master.bioconductor.org/developers/how-to/git/pull-upstream-changes/
>> 
>> 3) update the needed files in the repository and commit
>> 
>> 4) push to both origin and upstream
>> 
>> Also, just to clarify, the branch pushing I was referring to was the 
>> “switcheroo” in the link 
>> https://github.com/Bioconductor/bioc_git_transition/blob/master/doc/scenario-6-abandon-changes.md
>> 
>> Thanks and regards
>> Matthew 
>> Sent from my iPhone
>> 
>> On 13 Oct 2017, at 22:35, Turaga, Nitesh  
>> wrote:
>> 
>>> Hi Matthew,
>>> 
>>> I remember fixing this repository for you a few weeks ago. 
>>> 
>>> You cannot push branches to the Bioconductor repository, that is in the 
>>> FAQ, and documentation.
>>> 
>>> Can you tell me what exactly are the steps you are trying that, you are 
>>> getting duplicate commits again?
>>> 
>>> Best,
>>> 
>>> Nitesh 
>>> 
>>>> On Oct 13, 2017, at 3:39 AM, Matthew Myint  
>>>> wrote:
>>>> 
>>>> Hi,
>>>> 
>>>> Recently I noticed in hindsight that my repository had duplicate
>>>> commits, but I missed this during my normal package updating
>>>> procedures.
>>>> 
>>>> It was odd that the hook didn't reject these, so I made a clean branch
>>>> from a commit before the problem occurred and cherry-picking commits
>>>> to the present state. However, trying to push this to bioconductor git
>>>> returned an error
>>>> 
>>>>> remote: FATAL: + refs/heads/master packages/cytofkit c.hao DENIED by 
>>>>> fallthru
>>>>> remote: error: hook declined to update refs/heads/master
>>>>> To git.bioconductor.org:packages/cytofkit.git
>>>>> ! [remote rejected] master -> master (hook declined)
>>>>> error: failed to push some refs to 
>>>>> 'g...@git.bioconductor.org:packages/cytofkit.git'
>>>> 
>>>> I've kept the original backed up, and here is the clean branch and
>>>> back up branch for reference.
>>>> 
>>>> Here is the link to my repo for additional reference
>>>> https://github.com/JinmiaoChenLab/cytofkit
>>>> https://github.com/JinmiaoChenLab/cytofkit/network (network display
>>>> for easy visualisation)
>>>> 
>>>> Sorry for the hassle
>>>> 
>>>> Regards
>>>> Matthew Myint
>>>> Life Science Undergraduate, Year 4
>>>> NUS
>>>> 
>>>> ___
>>>> 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 

Re: [Bioc-devel] EXTERNAL: Git push error and duplicate commits

[Turaga, Nitesh]

Yes. That is correct. 


> On Oct 13, 2017, at 2:59 PM, Matthew Myint  wrote:
> 
> Hi,
> 
> Thanks for the explanation! To clarify, the proper step after the
> first time you helped restore my repository was to change the Github
> branch (with duplicates) to master_deprecated, and switch in the
> restored one as master? id="DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2">
> 
>   
> href="https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail";
> target="_blank"> src="https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-animated-no-repeat-v1.gif";
> alt="" width="46" height="29" style="width: 46px; height: 29px;"
> />
>   Virus-free.  href="https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail";
> target="_blank" style="color: #4453ea;">www.avast.com
>   
>   
>  height="1">
> Regards
> Matthew Myint
> Life Science Undergraduate, Year 4
> NUS
> 
> 
> On Sat, Oct 14, 2017 at 2:49 AM, Turaga, Nitesh
>  wrote:
>> Hi Matthew,
>> 
>> After closer inspection of “cytofkit”, it was this commit which caused the 
>> duplicates.
>> 
>> commit 4050c245d04af30705245f48931e677a6b4ae159
>> Merge: 467f659 e6cef6c
>> Author: Hervé Pagès 
>> Date:   Wed Sep 20 13:19:45 2017 -0700
>> 
>>Merge branch 'master' of git.bioconductor.org:packages/cytofkit
>> 
>> 
>> It was a fetch and merge. So, it means that the GitHub repository hosted 
>> (https://github.com/JinmiaoChenLab/cytofkit) did not deprecate the “master” 
>> with duplicate commits by Sept 20th. This was not done till Sept 27th, based 
>> on your GitHub 
>> logs(https://github.com/JinmiaoChenLab/cytofkit/commits/master_deprecated).
>> 
>> 
>> Best,
>> 
>> Nitesh
>> 
>> 
>>> On Oct 13, 2017, at 2:18 PM, Turaga, Nitesh  
>>> wrote:
>>> 
>>> Hi Matthew,
>>> 
>>> I’ll have to fix your branch again, for this I need some time. Do not push 
>>> any more changes.
>>> 
>>> *When you pull from the upstream (g...@git.bioconductor.org), you are not 
>>> supposed to get any duplicate commits.*
>>> 
>>> If a merge is giving you duplicate commits, it means that you didn’t switch 
>>> your master branch out. Or forgot to checkout the non-duplicate master.
>>> 
>>> Best,
>>> 
>>> Nitesh
>>> 
>>> 
>>> 
>>>> On Oct 13, 2017, at 2:13 PM, Matthew Myint  
>>>> wrote:
>>>> 
>>>> Hi,
>>>> 
>>>> After you helped me fix my repository, whenever I had updates I would use 
>>>> the steps from 
>>>> https://master.bioconductor.org/developers/how-to/git/push-to-github-bioc/
>>>> 
>>>> 1) note down what files needed to be updated in the repository
>>>> 
>>>> 2) pull from upstream and merge to local branch 
>>>> https://master.bioconductor.org/developers/how-to/git/pull-upstream-changes/
>>>> 
>>>> 3) update the needed files in the repository and commit
>>>> 
>>>> 4) push to both origin and upstream
>>>> 
>>>> Also, just to clarify, the branch pushing I was referring to was the 
>>>> “switcheroo” in the link 
>>>> https://github.com/Bioconductor/bioc_git_transition/blob/master/doc/scenario-6-abandon-changes.md
>>>> 
>>>> Thanks and regards
>>>> Matthew
>>>> Sent from my iPhone
>>>> 
>>>> On 13 Oct 2017, at 22:35, Turaga, Nitesh  
>>>> wrote:
>>>> 
>>>>> Hi Matthew,
>>>>> 
>>>>> I remember fixing this repository for you a few weeks ago.
>>>>> 
>>>>> You cannot push branches to the Bioconductor repository, that is in the 
>>>>> FAQ, and documentation.
>>>>> 
>>>>> Can you tell me what exactly are the steps you are trying that, you are 
>>>>> getting duplicate commits again?
>>>>> 
>>>>> Best,
>>>>> 
>>>>> Nitesh
>>>>> 
>>>>>> On Oct 13, 2017, at 3:39 AM, Matthew Myint  
>>>>>> wrote:
>>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>>

Re: [Bioc-devel] EXTERNAL: Permission Denied when pushing to bioc repo

[Turaga, Nitesh]

Hi,

Your SVN ID is t.sherman, you did not submit that in the google form. That is 
why you did not get access to your package, till now. 

For now, I’ve changed it to accept your current key. You should have access 
now. Please try again.

Nitesh 

> On Oct 16, 2017, at 2:17 PM, Thomas Sherman  wrote:
> 
> Hello,
> 
> 
> I am a developer of the RVS package 
> (https://bioconductor.org/packages/devel/bioc/html/RVS.html).
> 
> 
> I am having trouble pushing my changes to the Bioconductor repository. I 
> submitted my github account (sherman5) which has the ssh key I'm trying to 
> use. I've also submitted this key explicitly.
> 
> 
> These are the urls I'm using
> 
> 
>origin  g...@github.com:sherman5/RVS.git (fetch)
>origin  g...@github.com:sherman5/RVS.git (push)
>upstreamg...@git.bioconductor.org:packages/RVS (fetch)
>upstreamg...@git.bioconductor.org:packages/RVS (push)
> ?
> I can push to origin using my github key, but when I try to do the same with 
> upstream I receive the error message:
> 
>FATAL: W any packages/RVS sherman5 DENIED by fallthru
>(or you mis-spelled the reponame)
>fatal: Could not read from remote repository.
> 
>Please make sure you have the correct access rights
>and the repository exists.
> 
> I'm not really sure at this point what I'm doing wrong, any help would be 
> much appreciated.
> 
> Thanks,
> 
> Tom
> 
> 
> 
> 
>   [[alternative HTML version deleted]]
> 
> ___
> 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 
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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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Re: [Bioc-devel] EXTERNAL: Permission Denied when pushing to bioc repo

[Turaga, Nitesh]

Yes, you should have received an email with that ID.


> On Oct 16, 2017, at 2:37 PM, Thomas Sherman  wrote:
> 
> Thank you so much for the help, everything works now.
> 
> I was not aware of my SVN ID, was that assigned when I submitted the package?
> ________
> From: Turaga, Nitesh 
> Sent: Monday, October 16, 2017 2:23 PM
> To: Thomas Sherman
> Cc: bioc-devel@r-project.org
> Subject: Re: EXTERNAL: [Bioc-devel] Permission Denied when pushing to bioc 
> repo
> 
> Hi,
> 
> Your SVN ID is t.sherman, you did not submit that in the google form. That is 
> why you did not get access to your package, till now.
> 
> For now, I’ve changed it to accept your current key. You should have access 
> now. Please try again.
> 
> Nitesh
> 
>> On Oct 16, 2017, at 2:17 PM, Thomas Sherman  wrote:
>> 
>> Hello,
>> 
>> 
>> I am a developer of the RVS package 
>> (https://bioconductor.org/packages/devel/bioc/html/RVS.html).
>> 
>> 
>> I am having trouble pushing my changes to the Bioconductor repository. I 
>> submitted my github account (sherman5) which has the ssh key I'm trying to 
>> use. I've also submitted this key explicitly.
>> 
>> 
>> These are the urls I'm using
>> 
>> 
>>   origin  g...@github.com:sherman5/RVS.git (fetch)
>>   origin  g...@github.com:sherman5/RVS.git (push)
>>   upstreamg...@git.bioconductor.org:packages/RVS (fetch)
>>   upstreamg...@git.bioconductor.org:packages/RVS (push)
>> ?
>> I can push to origin using my github key, but when I try to do the same with 
>> upstream I receive the error message:
>> 
>>   FATAL: W any packages/RVS sherman5 DENIED by fallthru
>>   (or you mis-spelled the reponame)
>>   fatal: Could not read from remote repository.
>> 
>>   Please make sure you have the correct access rights
>>   and the repository exists.
>> 
>> I'm not really sure at this point what I'm doing wrong, any help would be 
>> much appreciated.
>> 
>> Thanks,
>> 
>> Tom
>> 
>> 
>> 
>> 
>>  [[alternative HTML version deleted]]
>> 
>> ___
>> 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 
> 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 
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Re: [Bioc-devel] EXTERNAL: Unexpected message when using 'git commit'

[Turaga, Nitesh]

Hi 

Your email and username, need to be the same as your Github ID. 

I’m not sure why you are trying to add  "rabbitus@lumimacs-iMac.local” as your 
email and username. 

Could you please explain that? 


> On Oct 16, 2017, at 4:07 PM, cstrato  wrote:
> 
> Dear All,
> 
> When I first  did:
> 
> $ git commit -m "update for configure.in"
> 
> everything seemed to be ok.
> 
> 
> 
> However, the next day when I tried once again to run 'git commit'
> I got the following message:
> 
> $ git commit -m "update for configure.in"
> [master 7a9855f] update for configure.in
> Committer: rabbitus 
> Your name and email address were configured automatically based
> on your username and hostname. Please check that they are accurate.
> You can suppress this message by setting them explicitly. Run the
> following command and follow the instructions in your editor to edit
> your configuration file:
> 
>git config --global --edit
> 
> After doing this, you may fix the identity used for this commit with:
> 
>git commit --amend --reset-author
> 
> 3 files changed, 62 insertions(+), 58 deletions(-)
> 
> 
> 
> Searching for an answer I found the following link:
> 
> https://stackoverflow.com/questions/10946893/git-name-and-email-address-configuration
> 
> and did:
> 
> $ git config --global user.name "cstrato"
> $ git config --global user.email cstr...@aon.at
> 
> Now the file '~/.gitconfig' does contain the corrected name and email.
> 
> 
> 
> Afterwards, I tried:
> 
> $ git commit --amend --reset-author
> 
> and got the following text file, 'COMMIT_EDITMSG':
> 
> update for configure.in
> 
> # Please enter the commit message for your changes. Lines starting
> # with '#' will be ignored, and an empty message aborts the commit.
> # On branch master
> # Your branch is up-to-date with 'origin/master'.
> #
> # Changes to be committed:
> #   modified:   DESCRIPTION
> #   modified:   NEWS
> #   modified:   configure.in
> #
> 
> The file 'COMMIT_EDITMSG' can be found in my 'CRAN/GIT/xps/.git' directory.
> 
> 
> 
> My questions now are:
> 
> 1, Why did I receive this message after a did 'git commit' the second time?
> 
> 
> 2, Is it correct that I have changed my user.name and user.email to above 
> values?
> 
> 
> 3, Why do I need to reset the commit information?
> 
> 
> 4, Do I have to edit the file 'COMMIT_EDITMSG'?
> 
> 
> 
> Thank you.
> Best regards,
> Christian
> _._._._._._._._._._._._._._._._._._
> C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
> V.i.e.n.n.a   A.u.s.t.r.i.a
> e.m.a.i.l:cstrato at aon.at
> _._._._._._._._._._._._._._._._._._
> 
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel



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agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
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this message in error, please notify the sender immediately by e-mail and 
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Re: [Bioc-devel] EXTERNAL: Unexpected message when using 'git commit'

[Turaga, Nitesh]

Hi Christian,

Please see my inline comments for all your questions. 


> On Oct 16, 2017, at 5:46 PM, cstrato  wrote:
> 
> Dear Turaga,
> 
> Thank you for your reply.
> 
> This is exactly the problem which I do not understand.
> 
> I did NOT add  "rabbitus@lumimacs-iMac.local” as my email.
> 


This was probably done because you did not set a default email address, and 
this is the “address” of your local machine. 
You don’t need to do anything fancy to change the emails, 
https://help.github.com/articles/setting-your-commit-email-address-in-git/.


> This was done automatically when I called 'git commit'.
> 
> The message says:
> Your name and email address were configured automatically based
> on your username and hostname.
> 
> 
> I did get the following message:
> $ git config --global --edit
> # This is Git's per-user configuration file.
> [user]
> # Please adapt and uncomment the following lines:
> #   name = rabbitus
> #   email = rabbitus@lumimacs-iMac.local
> 
> 
> I must admit that I was astonished since I did not expect this (and I did not 
> want this!)
> 
> So I changed it to:
> # This is Git's per-user configuration file.
> [user]
> # Please adapt and uncomment the following lines:
>   name = cstrato
>   email = cstr...@aon.at
> 
> 
> My other question was:
> 
> Do I have to edit the file 'COMMIT_EDITMSG'?

Why do you want to edit the commit message? You are not committing anything 
here. Please don’t edit. When you do commit to a git repo from your local 
machine, you should write out a informative commit message about the changes 
made, these are commit specific. 


> Best regards,
> Christian
> 
> 
> 
> On 10/16/17 22:09, Turaga, Nitesh wrote:
>> Hi
>> Your email and username, need to be the same as your Github ID.
>> I’m not sure why you are trying to add  "rabbitus@lumimacs-iMac.local” as 
>> your email and username.
>> Could you please explain that?
>>> On Oct 16, 2017, at 4:07 PM, cstrato  wrote:
>>> 
>>> Dear All,
>>> 
>>> When I first  did:
>>> 
>>> $ git commit -m "update for configure.in"
>>> 
>>> everything seemed to be ok.
>>> 
>>> 
>>> 
>>> However, the next day when I tried once again to run 'git commit'
>>> I got the following message:
>>> 
>>> $ git commit -m "update for configure.in"
>>> [master 7a9855f] update for configure.in
>>> Committer: rabbitus 
>>> Your name and email address were configured automatically based
>>> on your username and hostname. Please check that they are accurate.
>>> You can suppress this message by setting them explicitly. Run the
>>> following command and follow the instructions in your editor to edit
>>> your configuration file:
>>> 
>>>git config --global --edit
>>> 
>>> After doing this, you may fix the identity used for this commit with:
>>> 
>>>git commit --amend --reset-author
>>> 
>>> 3 files changed, 62 insertions(+), 58 deletions(-)
>>> 
>>> 
>>> 
>>> Searching for an answer I found the following link:
>>> 
>>> https://stackoverflow.com/questions/10946893/git-name-and-email-address-configuration
>>> 
>>> and did:
>>> 
>>> $ git config --global user.name "cstrato"
>>> $ git config --global user.email cstr...@aon.at
>>> 
>>> Now the file '~/.gitconfig' does contain the corrected name and email.
>>> 
>>> 
>>> 
>>> Afterwards, I tried:
>>> 
>>> $ git commit --amend --reset-author
>>> 
>>> and got the following text file, 'COMMIT_EDITMSG':
>>> 
>>> update for configure.in
>>> 
>>> # Please enter the commit message for your changes. Lines starting
>>> # with '#' will be ignored, and an empty message aborts the commit.
>>> # On branch master
>>> # Your branch is up-to-date with 'origin/master'.
>>> #
>>> # Changes to be committed:
>>> #   modified:   DESCRIPTION
>>> #   modified:   NEWS
>>> #   modified:   configure.in
>>> #
>>> 
>>> The file 'COMMIT_EDITMSG' can be found in my 'CRAN/GIT/xps/.git' directory.
>>> 
>>> 
>>> 
>>> My questions now are:
>>> 
>>> 1, Why did I receive this message after a did 'git commit' the second time?
>>&g

Re: [Bioc-devel] EXTERNAL: RE: Failing bioconductor package KEGGprofile

[Turaga, Nitesh]

If you have further trouble, I think you should submit your key again to the 
google form. And wait for the new key to be added. 

It might also help to read the instructions here again, 
bioconductor.org/developers/how-to/git/.



> On Oct 17, 2017, at 11:39 AM, Zhao, Shilin  
> wrote:
> 
> See below. Thanks!
>  
> ssh -v g...@git.bioconductor.org
> OpenSSH_5.3p1, OpenSSL 1.0.1e-fips 11 Feb 2013
> debug1: Reading configuration data /etc/ssh/ssh_config
> debug1: Applying options for *
> debug1: Connecting to git.bioconductor.org [34.192.48.227] port 22.
> debug1: Connection established.
> debug1: identity file /home/zhaos/.ssh/identity type -1
> debug1: identity file /home/zhaos/.ssh/identity-cert type -1
> debug1: identity file /home/zhaos/.ssh/id_rsa type 1
> debug1: identity file /home/zhaos/.ssh/id_rsa-cert type -1
> debug1: identity file /home/zhaos/.ssh/id_dsa type -1
> debug1: identity file /home/zhaos/.ssh/id_dsa-cert type -1
> debug1: identity file /home/zhaos/.ssh/id_ecdsa type -1
> debug1: identity file /home/zhaos/.ssh/id_ecdsa-cert type -1
> debug1: Remote protocol version 2.0, remote software version OpenSSH_7.2p2 
> Ubuntu-4ubuntu2.2
> debug1: match: OpenSSH_7.2p2 Ubuntu-4ubuntu2.2 pat OpenSSH*
> debug1: Enabling compatibility mode for protocol 2.0
> debug1: Local version string SSH-2.0-OpenSSH_5.3
> debug1: SSH2_MSG_KEXINIT sent
> debug1: SSH2_MSG_KEXINIT received
> debug1: kex: server->client aes128-ctr hmac-sha1 none
> debug1: kex: client->server aes128-ctr hmac-sha1 none
> debug1: SSH2_MSG_KEX_DH_GEX_REQUEST(1024<2048<8192) sent
> debug1: expecting SSH2_MSG_KEX_DH_GEX_GROUP
> debug1: SSH2_MSG_KEX_DH_GEX_INIT sent
> debug1: expecting SSH2_MSG_KEX_DH_GEX_REPLY
> debug1: Host 'git.bioconductor.org' is known and matches the RSA host key.
> debug1: Found key in /home/zhaos/.ssh/known_hosts:12
> debug1: ssh_rsa_verify: signature correct
> debug1: SSH2_MSG_NEWKEYS sent
> debug1: expecting SSH2_MSG_NEWKEYS
> debug1: SSH2_MSG_NEWKEYS received
> debug1: SSH2_MSG_SERVICE_REQUEST sent
> debug1: SSH2_MSG_SERVICE_ACCEPT received
> debug1: Authentications that can continue: publickey
> debug1: Next authentication method: publickey
> debug1: Trying private key: /home/zhaos/.ssh/identity
> debug1: Offering public key: /home/zhaos/.ssh/id_rsa
> debug1: Authentications that can continue: publickey
> debug1: Trying private key: /home/zhaos/.ssh/id_dsa
> debug1: Trying private key: /home/zhaos/.ssh/id_ecdsa
> debug1: No more authentication methods to try.
> Permission denied (publickey).
>  
>  
> more /home/zhaos/.ssh/id_rsa.pub
> ssh-rsa 
> B3NzaC1yc2EBIwAAAgEAnTHeitBs6pakp2KmWdsAcqE7XJ3EAHZUsVP9t5AsN0FWG0gJg5V7I5jCckzfW2aYL4HdbKO39fpVzixNpa3Tqi6QPNoBBo7SKkpBhxQrsh8xRvFlGmV27qXJUbRhOEOkvWhJFuSXZ1Di+xvwFpvjUFOYWafItOjHTuI5TTkVQRTydu9sw3n15PN1BWhvA
> pnLmKJzQNWJvskQINMgMpO0L+cswF9dtDcStkK7hVuow0Gz7Z3/kKxgTNd9becUHEteK0RpXKm0SLgAphvQfvYe7FLDEQ1JlSwaZ42lS74f+5uFFUPNtzc1IuvdWPKxsNxODhOLFCX8Xao6fO3X7KpcLEc5o0SX8SxSLFI4U8l/1V3xYcDFklp786zfb0BsnSilIErcbtTeMJOG6FdlHO3gjzScwkS9u1
> mw8ZIu3CvOFV1/IarMuuTTrYLI8b22ho4TTo/aiQOm1zYayxVsp65tMwNbjwSBLjOvR9A9a+sGbVk9xZRvGeH8DYYaPQoJHLJwMXEiULLAjaL4HJaV9pEuaWD6cLnRxqkoSILIsSboele5H4A2EKZXztfdq8rzS4pgw0tv9fap+Y0+DiDk5P98Wf8Cm5dzrpMty7xBvMDFBAWJTnRlakFv5kA5pLWJtc5
> +o6pXv4QK5+VuHrHGrj3V/ViYMoYGqZYck2lAm2WNMSk= zhaoshi...@gmail.com
>  
>  
> -Original Message-
> From: Turaga, Nitesh [mailto:nitesh.tur...@roswellpark.org] 
> Sent: Tuesday, October 17, 2017 6:05 AM
> To: Zhao, Shilin 
> Cc: Shepherd, Lori 
> Subject: Re: EXTERNAL: RE: Failing bioconductor package KEGGprofile
>  
> Try this command and send the output, it is likely you are not using the 
> correct key on your machine. Your key is in our system already.
>  
> ssh -v g...@git.bioconductor.org
>  
> See, if the public key you submitted is being used.
>  
> ssh-rsa 
> B3NzaC1yc2EBIwAAAgEAnTHeitBs6pakp2KmWdsAcqE7XJ3EAHZUsVP9t5AsN0FWG0gJg5V7I5jCckzfW2aYL4HdbKO39fpVzixNpa3Tqi6QPNoBBo7SKkpBhxQrsh8xRvFlGmV27qXJUbRhOEOkvWhJFuSXZ1Di+xvwFpvjUFOYWafItOjHTuI5TTkVQRTydu9sw3n15PN1BWh
>  
> vApnLmKJzQNWJvskQINMgMpO0L+cswF9dtDcStkK7hVuow0Gz7Z3/kKxgTNd9becUHEteK0RpXKm0SLgAphvQfvYe7FLDEQ1JlSwaZ42lS74f+5uFFUPNtzc1IuvdWPKxsNxODhOLFCX8Xao6fO3X7KpcLEc5o0SX8SxSLFI4U8l/1V3xYcDFklp786zfb0BsnSilIErcbtTeMJOG6FdlHO3gjzScwk
>  
> S9u1mw8ZIu3CvOFV1/IarMuuTTrYLI8b22ho4TTo/aiQOm1zYayxVsp65tMwNbjwSBLjOvR9A9a+sGbVk9xZRvGeH8DYYaPQoJHLJwMXEiULLAjaL4HJaV9pEuaWD6cLnRxqkoSILIsSboele5H4A2EKZXztfdq8rzS4pgw0tv9fap+Y0+DiDk5P98Wf8Cm5dzrpMty7xBvMDFBAWJTnRlakFv5kA5p
>  LWJtc5+o6pXv4QK5+VuHrHGrj3V/ViYMoYGqZYck2lAm2WNMSk= zhaoshi...@gmail.com
>  
> > On Oct 17, 2017, at 12:34 AM, Zhao, Shilin  
> > wrote:
> >
> > Hi Nitesh,
> >  
> > 

Re: [Bioc-devel] EXTERNAL: Cardinal duplicate commits

[Turaga, Nitesh]

Hi Kylie,

I will take a look at your package and get back to you. Avoid making any 
changes till I give you further notice. 

Best,

Nitesh 

> On Oct 17, 2017, at 1:13 PM, Bemis, Kylie  wrote:
> 
> Hi all,
> 
> I have a problem with duplicate commits in my package “Cardinal”. So far I 
> have avoided making more commits to my other package “matter” until I am sure 
> how to avoid this again.
> 
> Soon after the git transition, I made a few small commits to the Bioconductor 
> git repo, which I notice now included duplicate commits in the history. They 
> were not rejected at the time. New commits now are rejected for me.
> 
> Locally and on my own Github repo (https://github.com/kuwisdelu/Cardinal) I 
> have reverted to a commit from before I merged the Bioconductor master, to 
> get a clean history without duplicate commits.
> 
> I have been trying to push this with
> 
> 
> git push -f upstream
> 
> from the “Abandon changes” help page.
> 
> This is being rejected with:
> 
> kuwisdelu$ git push --force upstream master
> Total 0 (delta 0), reused 0 (delta 0)
> remote: FATAL: + refs/heads/master packages/Cardinal k.bemis DENIED by 
> fallthru
> remote: error: hook declined to update refs/heads/master
> To git.bioconductor.org:packages/Cardinal.git
> ! [remote rejected] master -> master (hook declined)
> error: failed to push some refs to 
> 'g...@git.bioconductor.org:packages/Cardinal.git'
> 
> What is the best way to get a clean history and avoid this happening again?
> 
> Thank you,
> Kylie
> 
> ~~~
> Kylie Ariel Bemis
> Future Faculty Fellow
> College of Computer and Information Science
> Northeastern University
> kuwisdelu.github.io
> 
> 
> 
> 
> 
>   [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel



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Re: [Bioc-devel] EXTERNAL: Needs access to devel Git Repository

[Turaga, Nitesh]

We process the keys manually at noon EST every business day.

You submitted at 17/10/2017 21:54:46 . Please wait.

Best,

Nitesh 

> On Oct 17, 2017, at 11:33 PM, Yang Liao  wrote:
> 
> Dear Bioconductor maintainers,
> 
> 
> I'm the co-maintainer of the Rsubread package. When we're preparing Rsubread 
> for the new release, I found that I don't have the access to the "devel" Git 
> Repository (g...@git.bioconductor.org:packages/Rsubread).
> 
> 
> My SVN account is "y.liao", and my GitHub account is "dbpz". The SSH keys 
> have been set up on GitHub. Can anyone please change my settings so I can 
> clone and submit the changes to our Rsubread package?
> 
> 
> Cheers,
> 
> 
> Yang
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] EXTERNAL: Git push error and duplicate commits

[Turaga, Nitesh]

Hi Matthew,

I’ve reset your package to the original clean state. Same place we were last 
time when this happened. 

I encourage you to ask questions on bioc-devel if you are not sure about a 
certain command, or are facing problems.

Best,

Nitesh 

> On Oct 13, 2017, at 3:31 PM, Turaga, Nitesh  
> wrote:
> 
> Yes. That is correct. 
> 
> 
>> On Oct 13, 2017, at 2:59 PM, Matthew Myint  
>> wrote:
>> 
>> Hi,
>> 
>> Thanks for the explanation! To clarify, the proper step after the
>> first time you helped restore my repository was to change the Github
>> branch (with duplicates) to master_deprecated, and switch in the
>> restored one as master?> id="DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2">
>> 
>>  
>>   > href="https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail";
>> target="_blank">> src="https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-animated-no-repeat-v1.gif";
>> alt="" width="46" height="29" style="width: 46px; height: 29px;"
>> />
>>  Virus-free. > href="https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail";
>> target="_blank" style="color: #4453ea;">www.avast.com
>>  
>>  
>> > height="1">
>> Regards
>> Matthew Myint
>> Life Science Undergraduate, Year 4
>> NUS
>> 
>> 
>> On Sat, Oct 14, 2017 at 2:49 AM, Turaga, Nitesh
>>  wrote:
>>> Hi Matthew,
>>> 
>>> After closer inspection of “cytofkit”, it was this commit which caused the 
>>> duplicates.
>>> 
>>> commit 4050c245d04af30705245f48931e677a6b4ae159
>>> Merge: 467f659 e6cef6c
>>> Author: Hervé Pagès 
>>> Date:   Wed Sep 20 13:19:45 2017 -0700
>>> 
>>>   Merge branch 'master' of git.bioconductor.org:packages/cytofkit
>>> 
>>> 
>>> It was a fetch and merge. So, it means that the GitHub repository hosted 
>>> (https://github.com/JinmiaoChenLab/cytofkit) did not deprecate the “master” 
>>> with duplicate commits by Sept 20th. This was not done till Sept 27th, 
>>> based on your GitHub 
>>> logs(https://github.com/JinmiaoChenLab/cytofkit/commits/master_deprecated).
>>> 
>>> 
>>> Best,
>>> 
>>> Nitesh
>>> 
>>> 
>>>> On Oct 13, 2017, at 2:18 PM, Turaga, Nitesh 
>>>>  wrote:
>>>> 
>>>> Hi Matthew,
>>>> 
>>>> I’ll have to fix your branch again, for this I need some time. Do not push 
>>>> any more changes.
>>>> 
>>>> *When you pull from the upstream (g...@git.bioconductor.org), you are not 
>>>> supposed to get any duplicate commits.*
>>>> 
>>>> If a merge is giving you duplicate commits, it means that you didn’t 
>>>> switch your master branch out. Or forgot to checkout the non-duplicate 
>>>> master.
>>>> 
>>>> Best,
>>>> 
>>>> Nitesh
>>>> 
>>>> 
>>>> 
>>>>> On Oct 13, 2017, at 2:13 PM, Matthew Myint  
>>>>> wrote:
>>>>> 
>>>>> Hi,
>>>>> 
>>>>> After you helped me fix my repository, whenever I had updates I would use 
>>>>> the steps from 
>>>>> https://master.bioconductor.org/developers/how-to/git/push-to-github-bioc/
>>>>> 
>>>>> 1) note down what files needed to be updated in the repository
>>>>> 
>>>>> 2) pull from upstream and merge to local branch 
>>>>> https://master.bioconductor.org/developers/how-to/git/pull-upstream-changes/
>>>>> 
>>>>> 3) update the needed files in the repository and commit
>>>>> 
>>>>> 4) push to both origin and upstream
>>>>> 
>>>>> Also, just to clarify, the branch pushing I was referring to was the 
>>>>> “switcheroo” in the link 
>>>>> https://github.com/Bioconductor/bioc_git_transition/blob/master/doc/scenario-6-abandon-changes.md
>>>>> 
>>>>> Thanks and regards
>>>>> Matthew
>>>>> Sent from my iPhone
>>>>> 
>>>>> On 13 Oct 2017, at 22:35, Turaga, Nitesh  
>>>>> wrote:
>>>>> 
>>>>&

Re: [Bioc-devel] EXTERNAL: Cardinal duplicate commits

[Turaga, Nitesh]

Hi Kylie,

I have reset your package to its original state. The best way to proceed is 
with this documentation, 
http://master.bioconductor.org/developers/how-to/git/sync-existing-repositories/

You specifically want to take a look at point#8 
(http://master.bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-).

It is the process of switching your master branch, on your Github. Feel free to 
ask questions on bioc-devel. 

Best,

Nitesh 

> On Oct 17, 2017, at 5:14 PM, Turaga, Nitesh  
> wrote:
> 
> Hi Kylie,
> 
> I will take a look at your package and get back to you. Avoid making any 
> changes till I give you further notice. 
> 
> Best,
> 
> Nitesh 
> 
>> On Oct 17, 2017, at 1:13 PM, Bemis, Kylie  wrote:
>> 
>> Hi all,
>> 
>> I have a problem with duplicate commits in my package “Cardinal”. So far I 
>> have avoided making more commits to my other package “matter” until I am 
>> sure how to avoid this again.
>> 
>> Soon after the git transition, I made a few small commits to the 
>> Bioconductor git repo, which I notice now included duplicate commits in the 
>> history. They were not rejected at the time. New commits now are rejected 
>> for me.
>> 
>> Locally and on my own Github repo (https://github.com/kuwisdelu/Cardinal) I 
>> have reverted to a commit from before I merged the Bioconductor master, to 
>> get a clean history without duplicate commits.
>> 
>> I have been trying to push this with
>> 
>> 
>> git push -f upstream
>> 
>> from the “Abandon changes” help page.
>> 
>> This is being rejected with:
>> 
>> kuwisdelu$ git push --force upstream master
>> Total 0 (delta 0), reused 0 (delta 0)
>> remote: FATAL: + refs/heads/master packages/Cardinal k.bemis DENIED by 
>> fallthru
>> remote: error: hook declined to update refs/heads/master
>> To git.bioconductor.org<http://git.bioconductor.org>:packages/Cardinal.git
>> ! [remote rejected] master -> master (hook declined)
>> error: failed to push some refs to 
>> 'g...@git.bioconductor.org<mailto:g...@git.bioconductor.org>:packages/Cardinal.git'
>> 
>> What is the best way to get a clean history and avoid this happening again?
>> 
>> Thank you,
>> Kylie
>> 
>> ~~~
>> Kylie Ariel Bemis
>> Future Faculty Fellow
>> College of Computer and Information Science
>> Northeastern University
>> kuwisdelu.github.io<https://kuwisdelu.github.io>
>> 
>> 
>> 
>> 
>> 
>>  [[alternative HTML version deleted]]
>> 
>> ___
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>> 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 
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> recipient(s), you are hereby notified that any disclosure, copying, 
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[Bioc-devel] Fwd: EXTERNAL: Re: name of git repo for brgedata/BRGEdata package

[Turaga, Nitesh]

Get Outlook for Android<https://aka.ms/ghei36>


From: Carles Hern�ndez 
Sent: Tuesday, October 24, 2017 9:11:30 AM
To: Turaga, Nitesh
Cc: Juan Ram�n Gonzalez; Carlos Ruiz; Ramos Perez, Marcel; Morgan, Martin; Van 
Twisk, Daniel; Herv� Pag�s
Subject: EXTERNAL: Re: name of git repo for brgedata/BRGEdata package

Dear Nitesh,


I checked again if I can fetch the repo in order to push the properly changes 
to "brgedata" (and to "omicRexposome"). As you can see:

chernandez@workstation01 MINGW64 ~/Projects/BRGEdata (master)
$ git fetch --all
Fetching origin
Fetching upstream
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
error: Could not fetch upstream


Kind regards,

Carles Hernandez-Ferrer
Bioinformatic Analyst / PhD Student
ISGlobal
Barcelona Institute for Global Health - Campus Mar
Barcelona Biomedical Research Park (PRBB) (office 183.01 A)
Doctor Aiguader, 88
08003 Barcelona, Spain
Tel. +34 93 214 73 22
carles.hernan...@isglobal.org<mailto:carles.hernan...@isglobal.org>
www.isglobal.org<http://www.isglobal.org> | 
www.carleshf.com<http://www.carleshf.com>

We are pleased to tell you that after three years of a strategic alliance 
between ISGlobal and CREAL, both institutions have merged. The resulting 
institution, which retains the ISGlobal name, will build upon the existing 
areas of excellence to become a world-class player in research, education and 
innovation in Global Health. More info at http://ow.ly/krQd301Nj3w

On 21 October 2017 at 19:23, Herv� Pag�s 
mailto:hpa...@fredhutch.org>> wrote:
Thanks Carles for the update.

Please do "Reply All" on further communications. Thanks!

Regards,
H.


On 10/21/2017 12:50 AM, Carles Hern�ndez wrote:
Dear Herv�,


Yesterday I connacted Nitesh because it seems that I have some permision
problems with my user. We keep in mind that we msut solve this as fast
as possible.


Kidnr egards,

Carles Hernandez-Ferrer
Bioinformatic Analyst / PhD Student
*ISGlobal*
Barcelona Institute for Global Health - Campus Mar
Barcelona Biomedical Research Park (PRBB) (office 183.01 A)
Doctor Aiguader, 88
08003 Barcelona, Spain
Tel. +34 93 214 73 22
carles.hernan...@isglobal.org<mailto:carles.hernan...@isglobal.org> 
<mailto:carles.hernan...@isglobal.org<mailto:carles.hernan...@isglobal.org>>
www.isglobal.org<http://www.isglobal.org>
<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.isglobal.org&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=UE8YU4mmMrQG59VPEhHJQf3-VLQMLyzKZv9ZsmH74IA&s=KqEXQCfBzLuIGKqv-nudfrAMBK9vvNp9cwbDMpKrBOw&e=>
| www.carleshf.com<http://www.carleshf.com>
<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.carleshf.com&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=UE8YU4mmMrQG59VPEhHJQf3-VLQMLyzKZv9ZsmH74IA&s=OfujD4doFtTBBAvjVFo0Ig9y4wpvkm1Gmbm2kzt4fZk&e=>
/
//We are pleased to tell you that after three years of a strategic
alliance between ISGlobal and CREAL, both institutions have merged. The
resulting institution, which retains the ISGlobal name, will build upon
the existing areas of excellence to become a world-class player in
research, education and innovation in Global Health. More info at
http://ow.ly/krQd301Nj3w
<https://urldefense.proofpoint.com/v2/url?u=http-3A__ow.ly_krQd301Nj3w&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=UE8YU4mmMrQG59VPEhHJQf3-VLQMLyzKZv9ZsmH74IA&s=VyLQQzXOB1B-TsSyjAg7nJREJIPNSHILQW4-0-QIjWQ&e=>/

On 21 October 2017 at 09:02, Herv� Pag�s 
mailto:hpa...@fredhutch.org>
<mailto:hpa...@fredhutch.org<mailto:hpa...@fredhutch.org>>> wrote:

Hi omicRexposome/BRGEdata developers,

When the BRGEdata package was accepted, we added the brgedata git
repo to the Bioconductor git server:

https://git.bioconductor.org/packages/brgedata

<https://urldefense.proofpoint.com/v2/url?u=https-3A__git.bioconductor.org_packages_brgedata&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=UE8YU4mmMrQG59VPEhHJQf3-VLQMLyzKZv9ZsmH74IA&s=HfuDh_Ddt-7u86QmKJK_vCohdqotR7-D8ei1GSOjKK0&e=>

Unfortunately at the time we did this, the name of the git repo didn't
match the name of the package (brgedata vs BRGEdata). This is causing
problems in our build system and is preventing the package from showing
up on the daily build report for data-experiment packages:

https://bioconductor.org/checkResults/3.6/data-experiment-LATEST/

<https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_3.6_data-2Dexperiment-2DLATEST_&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAv

Re: [Bioc-devel] EXTERNAL: Permission denied (publickey) while pushing changes to Github

[Turaga, Nitesh]

Hi 

Your key should have access now. Please try again. 

Best,

Nitesh 

> On Oct 24, 2017, at 7:01 AM, Sokratis Kariotis  
> wrote:
> 
> Hey all, I am trying to push som changes to my newly accepted packages
> (pcxn,pcxnData) and get this:
> 
> ''Permission denied (publickey).
> fatal: Could not read from remote repository.
> 
> Please make sure you have the correct access rights
> and the repository exists.''
> 
> If it helps my 'git remote -v' results are the following:
> 
> origin  https://github.com/hidelab/pcxnData.git (fetch)
> origin  https://github.com/hidelab/pcxnData.git (push)
> upstreamg...@git.bioconductor.org:packages/pcxnData.git (fetch)
> upstreamg...@git.bioconductor.org:packages/pcxnData.git (push)
> 
> Thanks in advance!
> -- 
> Sokratis Kariotis
> Scientific Programmer
> Hidelab
> Sheffield Institute for Translational Neuroscience
> 385a Glossop Rd, Sheffield, S10 2HQ
> 
>   [[alternative HTML version deleted]]
> 
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[Bioc-devel] Reset packages with duplicate commits

[Turaga, Nitesh]

Hi Maintainers,

You are being notified because we have identified duplicate commits in your 
packages. Only the last “merge” commit is the one causing the issues in both 
these packages. The two packages are listed below.

- affyPLM
- Rdisop

If you are receiving this message, then you must follow the procedure we list 
in 


http://bioconductor.org/developers/how-to/git/sync-existing-repositories/. 

Specifically point #8,


http://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-.

This allows you to maintain your repository in GitHub, and sync with the 
existing Bioconductor repository, WITHOUT duplicate commits after the merge 
process. It’s important to do this to maintain a clean git repository. Feel 
free to ask any questions you have about this process on the bioc-devel mailing 
list, or in reply to this thread. 

Best regards,

Nitesh 

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Re: [Bioc-devel] push access to bioconductor repository-reg.

[Turaga, Nitesh]

Hi Shweta,

I’m cc-ing bioc-devel on this as well. There are other members of the team in 
the future who could possibly help you with your questions. 

You seem to have three public keys on our

find . -name "shwetagopaul92.pub" -exec cat {} \;  

ssh-rsa 
B3NzaC1yc2EDAQABAAABAQDRU2oyo0iT2qVP3d8ciLYMbpPjkoVyS06AdJDvEcV7MUqHaTTRtz6TEIoVchQPskYn7D3c+UDxYty8pOXQ5M7gETRhbeewuEabSHV77jmzdgXj3AizE77bffAz3KA98Ibz1up+z065/qHMR8hZUpm3hw1kAVMyeiOvk2bRrowcJoewP7KtArgMTNBaecFLcV2xmOncHGBlC2FM7svwwRxa0zfhiMtV0RRlb9totAl+A/WrdVoHkHpPl96Jm9yvHN4FoZyD0acaXpQiKVEamhyANegZ/J+2pNan9JkMiqTF8Rdh/e6LHLBwxd3mpnMkJOOIYwexixWHUZtuAeNot53P

ssh-rsa 
B3NzaC1yc2EDAQABAAABAQCfQ+7dozCd9jrQ+nPnzfAAa9Nf4KjfDP1oXSFc8hHE+0UZZHxqSdubzZvrfJaNUT95Z2Uey17GRy4OYtd4ven2qTY3wWNI4Vgpjs/olqNqHQLyIF/uIe2LsiLwUzFh/rQQiOfHJkLvOcOU1CqiuAfqqHLPK4lP1X8vrnnMhA7oEAaJGBbIOEDlcCyJfFc8IY05UJsoxut61APZ4SowiVyhWfLYoQKh8R5OeQOj0h0ARTbkQvHIWE20ZUY0XPpz5Bm9kmjtavwhkTcrapKFJ527PTiPYjgWQwqVvkBus9JJv+zodkdumMNdDEuji498pDWsCNy7TH5BG10pr18AJel5

ssh-rsa 
B3NzaC1yc2EDAQABAAABAQDCSq5kTCW4ObxX83RAwgi7eQRpWxMsOQxRdVooWRa+5NygGLA7OkLBkqgF8b5zdfQ+vSBGHgSDRFnINqAd313wQ/V9f2VoCNXxo/FGhkpc6nrdtVUTCHL2rtihY/KZNS1V6/16b6GWmsUE2yux8PRxYtbnK5TMNFAGkt4s2eBJYH8FEGVLYk0De4K+mQDDlXvKPDgGvoUYHVlCKXijvvLN4RnUw4FtGles8fa8XBEtZz574kYqUWo5RhwNgCiRVysKhpp/FUs3RqYRZCwDhnLOdvbQYCBAz7efcMAjuXheVwXAYWdh8wpZcGyftimvZy380UgWnoZuER1Hl9rWUDip


Again, it’s all about using the correct private key. Look into 
http://bioconductor.org/developers/how-to/git/faq/ , specifically #15 to set up 
your config file to access the correct private key.

Best,

Nitesh 


> On Oct 26, 2017, at 11:04 AM, Shweta Gopaulakrishnan 
>  wrote:
> 
> Hi Nitesh, 
> 
> I updated my public key on github yesterday. I have also submitted the google 
> form with the new public key to bioconductor. I am still not having the 
> permission to fetch contents from the Bioconductor repository. 
> Please could you let me know the public key you have on your database now?
> 
> Thank you! 
> 
> On Wed, Oct 25, 2017 at 12:15 PM, Shweta Gopaulakrishnan 
>  wrote:
> Hi Nitesh,
> 
> Thank you for your response. 
> I did have a private key corresponding to a different public key. I have 
> updated github and Bioconductor with the new public key. 
> 
> Thank you! 
> 
> On Wed, Oct 25, 2017 at 9:49 AM, Turaga, Nitesh 
>  wrote:
> Hi Vincent,
> 
> 
> The RELEASE_3_6 branch does not exist yet, it is still called “master”. You 
> may push your changes there. You can see all the available branches by trying
> 
> `git branch -a`
> 
> We will notify bioc-devel once the new branch is created, towards end of the 
> month.
> 
> Shweta, has access to restfulSE and restfulSEData, with the public key
> 
> ssh-rsa 
> B3NzaC1yc2EDAQABAAABAQDRU2oyo0iT2qVP3d8ciLYMbpPjkoVyS06AdJDvEcV7MUqHaTTRtz6TEIoVchQPskYn7D3c+UDxYty8pOXQ5M7gETRhbeewuEabSHV77jmzdgXj3AizE77bffAz3KA98Ibz1up+z065/qHMR8hZUpm3hw1kAVMyeiOvk2bRrowcJoewP7KtArgMTNBaecFLcV2xmOncHGBlC2FM7svwwRxa0zfhiMtV0RRlb9totAl+A/WrdVoHkHpPl96Jm9yvHN4FoZyD0acaXpQiKVEamhyANegZ/J+2pNan9JkMiqTF8Rdh/e6LHLBwxd3mpnMkJOOIYwexixWHUZtuAeNot53P
> 
> It is important that Shweta use the private key, which corresponds to that 
> public key. This often happens when people change computers, or 
> delete/overwrite the keys in their `~/.ssh` folder.
> 
> Best,
> 
> Nitesh
> 
> 
> > On Oct 25, 2017, at 5:56 AM, Vincent Carey  
> > wrote:
> >
> > Hi Nitesh -- could you have a look at this?  I think since the submission 
> > process was successful
> > Shweta's key must be known to the system.
> >
> > For my own parody package I wanted to try to push a change to current 3.6 
> > build system but found
> >
> >  * [new branch]  RELEASE_3_4  -> upstream/RELEASE_3_4
> >
> >  * [new branch]  RELEASE_3_5  -> upstream/RELEASE_3_5
> >
> >  * [new branch]  master   -> upstream/master
> >
> > %vjcair> git checkout -b RELEASE_3_5 upstream/RELEASE_3_5
> >
> > Branch RELEASE_3_5 set up to track remote branch RELEASE_3_5 from upstream.
> >
> > Switched to a new branch 'RELEASE_3_5'
> >
> > %vjcair> git checkout -b RELEASE_3_6 upstream/RELEASE_3_6
> >
> > fatal: 'upstream/RELEASE_3_6' is not a commit and a branch 'RELEASE_3_6' 
> > cannot be created from it
> >
> > %vjcair> git branch
> >
> > * RELEASE_3_5
> >
> >   master
> >
> >
> >
> >
> > -- Forwarded message --
> > From: Shweta Gopaulakrishnan 
> > Date: Tue, Oct 24, 2017 at 5:17 PM
> > Subject: push access to bioconductor repository-reg.
> > To: Vincent Carey 
> >

Re: [Bioc-devel] issues with access to my Bioconductor repository IntramiRExploreR

[Turaga, Nitesh]

We have the following public key in our system

ssh-rsa 
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

This is the one you submitted to the google form, and this is the one that was 
added.

If you want to link your GitHub ID you have to resubmit to the google form.

Best,

Nitesh 


> On Oct 27, 2017, at 3:36 PM, Surajit Bhattacharya 
>  wrote:
> 
> Thanks Lori. The problem still persists.
> 
> $ git remote add upstream 
> g...@git.bioconductor.org:packages/IntramiRExploreR.git
> $ git fetch upstream
> Permission denied (publickey).
> fatal: Could not read from remote repository.
> 
> Please make sure you have the correct access rights
> and the repository exists.
> 
> 
> I have the ssh keys updated in my github account, still the problem persists. 
> Can you guide me regarding the same.
> 
> 
> Thanks,
> 
> Surajit
> 
> 
> From: Shepherd, Lori 
> Sent: Friday, October 27, 2017 7:40:08 AM
> To: Surajit Bhattacharya; bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] issues with access to my Bioconductor repository 
> IntramiRExploreR
> 
> 
> Hello,
> 
> 
> It looks like when you submitted your package we were still in svn and had 
> provided a svn id that was associated with your package. This was the id that 
> we would have originally requested in the form for rsa keys.
> 
> 
> We have changed the id on our system to match your github id and you should 
> have access now.
> 
> 
> Lori Shepherd
> 
> Bioconductor Core Team
> 
> Roswell Park Cancer Institute
> 
> Department of Biostatistics & Bioinformatics
> 
> Elm & Carlton Streets
> 
> Buffalo, New York 14263
> 
> 
> From: Bioc-devel  on behalf of Surajit 
> Bhattacharya 
> Sent: Thursday, October 26, 2017 6:11:18 PM
> To: bioc-devel@r-project.org
> Subject: [Bioc-devel] issues with access to my Bioconductor repository 
> IntramiRExploreR
> 
> Hello,
> 
> 
> I was trying to make some final changes to my package yesterday (changing the 
> README file with the link to the bioconductor page, instead of my github 
> repository), but am getting errors in accessing the bioconductor repository.
> 
> I followed the flow given in the webpage:
> 
> 
> ##Added the bioconductor git
> 
> $ git remote add upstream 
> g...@git.bioconductor.org:packages/IntramiRExploreR.git
> 
> ##Fetching from upstream
> 
> $ git fetch upstream
> 
> Permission denied (publickey).
> 
> fatal: Could not read from remote repository.
> 
> 
> 
> Please make sure you have the correct access rights
> 
> and the repository exists.
> 
> ##Remote -v
> 
> $ git remote -v
> 
> origin  
> https://github.com/sbhattacharya3/IntramiRExploreR.git
>  (fetch)
> 
> origin  
> https://github.com/sbhattacharya3/IntramiRExploreR.git
>  (push)
> 
> upstreamg...@git.bioconductor.org:packages/IntramiRExploreR.git 
> (fetch)
> 
> upstreamg...@git.bioconductor.org:packages/IntramiRExploreR.git (push)
> 
> 
> I have added my public key to the bioconductor list earlier as told then. Can 
> you please guidre me regarding the same.
> 
> 
> Thanks,
> 
> Surajit
> 
> 
> 
>[[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> This email message may contain legally privileged 

Re: [Bioc-devel] Package un-deprecation

[Turaga, Nitesh]

Hi, 

You have to wait till tomorrow to see if you package builds successfully. 

Hopefully your package builds, and there is a landing page.

 Nitesh 


> On Oct 30, 2017, at 6:57 AM, sergi.pic...@upc.edu wrote:
> 
> Dear Nitesh, 
> 
> We were able to fix the error on MAIT under the bioc-devel official docker. 
> We pushed upstream two days ago to meet the deadline, but the system has not 
> seen the changes and no build has been issued since then. 
> What should we do?
> 
> Thank you for your help, 
> 
> Quoting sergi.pic...@upc.edu:
> 
>> Dear Nitesh,
>> 
>> The build has not been triggered yet, is everything correct?
>> 
>> Thank you,
>> 
>> Quoting "Turaga, Nitesh" :
>> 
>>> The builds are “nightly builds” i.e they trigger in the evening time EST. 
>>> Please wait till tomorrow to see your build report.
>>>  
>>> 
>>>> On Oct 26, 2017, at 11:16 AM, sergi.pic...@upc.edu wrote:
>>>> 
>>>> We have bumped the version and removed the ^M characters.
>>>> 
>>>> This did not trigger the build by the time I am writing now, though.
>>>> 
>>>> 
>>>> Thank you,
>>>> 
>>>> Quoting "Turaga, Nitesh" :
>>>> 
>>>>> Please issue another version bump.
>>>>> 
>>>>> It might also help if you removed the ^M characters after the version 
>>>>> bump.
>>>>> 
>>>>>> On Oct 26, 2017, at 10:37 AM, sergi.pic...@upc.edu wrote:
>>>>>> 
>>>>>> Yes, as far as I know.
>>>>>> 
>>>>>> Running:
>>>>>> 
>>>>>> git clone g...@git.bioconductor.org:packages/MAIT
>>>>>> 
>>>>>> and showing the DESCRIPTION file yields to
>>>>>> 
>>>>>> Version: 1.11.3
>>>>>> 
>>>>>> Is this right? Thank you,
>>>>>> 
>>>>>> Quoting "Turaga, Nitesh" :
>>>>>> 
>>>>>>> Did you push to upstream i.e g...@git.bioconductor.org?
>>>>>>> 
>>>>>>> And did you bump the version?
>>>>>>> 
>>>>>>>> On Oct 26, 2017, at 9:06 AM, sergi.pic...@upc.edu wrote:
>>>>>>>> 
>>>>>>>> Dear Nitesh,
>>>>>>>> 
>>>>>>>> We have pushed one changeset to 
>>>>>>>> g...@git.bioconductor.org:packages/MAIT, but I cannot see an updated 
>>>>>>>> build report on 
>>>>>>>> http://bioconductor.org/checkResults/devel/bioc-LATEST/MAIT/
>>>>>>>> 
>>>>>>>> Are we doing something wrong or is it a matter of time that it builds 
>>>>>>>> automatically?
>>>>>>>> 
>>>>>>>> Thank you,
>>>>>>>> 
>>>>>>>> Quoting "Turaga, Nitesh" :
>>>>>>>> 
>>>>>>>>> Hi,
>>>>>>>>> 
>>>>>>>>> Your package MAIT still fails the builds for the devel branch.
>>>>>>>>> 
>>>>>>>>> Please check it as soon as possible.
>>>>>>>>> 
>>>>>>>>> http://bioconductor.org/checkResults/devel/bioc-LATEST/MAIT/
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> This needs to be resolved before 29th October.
>>>>>>>>> 
>>>>>>>>> Best,
>>>>>>>>> 
>>>>>>>>> Nitesh
>>>>>>>>> 
>>>>>>>>>> On Sep 29, 2017, at 10:39 AM, sergi.pic...@upc.edu wrote:
>>>>>>>>>> 
>>>>>>>>>> Dear Bioconductor team,
>>>>>>>>>> 
>>>>>>>>>> Our lab is in charge of maintaining the MAIT package.
>>>>>>>>>> MAIT is about to get deprecated due to an error in its vignette.
>>>>>>>>>> We have a fix for it, and would also add a new author/maintainer to 
>>>>>>>>>> patch it.
>>>>>>>>>> Which steps do we need to follow?
>>>>>>>>>> 
>>>>>>>>>> Thank you for your help,
>>>>

Re: [Bioc-devel] EXTERNAL: Re: name of git repo for brgedata/BRGEdata package

[Turaga, Nitesh]

It seems you have submitted a bad id and key to the form.  

1. For GitHub ID, it needs to submit  as `carleshf`, not `github.com/carleshf`. 

2. the SSH key needs the `ssh-rsa` header in front of the key. It was submitted 
without it. 

Please resubmit. 

Your entries need to be,

Email : carles.hernan...@isglobal.org
SNV account: carleshf
Github: carleshf



> On Oct 24, 2017, at 9:11 AM, Carles Hernández  
> wrote:
> 
> Dear Nitesh,
> 
> 
> I checked again if I can fetch the repo in order to push the properly changes 
> to "brgedata" (and to "omicRexposome"). As you can see:
> 
> chernandez@workstation01 MINGW64 ~/Projects/BRGEdata (master)
> $ git fetch --all
> Fetching origin
> Fetching upstream
> Permission denied (publickey).
> fatal: Could not read from remote repository.
> 
> Please make sure you have the correct access rights
> and the repository exists.
> error: Could not fetch upstream
> 
> 
> Kind regards,
> 
> Carles Hernandez-Ferrer
> Bioinformatic Analyst / PhD Student
> ISGlobal
> Barcelona Institute for Global Health - Campus Mar
> Barcelona Biomedical Research Park (PRBB) (office 183.01 A)
> Doctor Aiguader, 88
> 08003 Barcelona, Spain
> Tel. +34 93 214 73 22
> carles.hernan...@isglobal.org
> www.isglobal.org | www.carleshf.com
> 
> We are pleased to tell you that after three years of a strategic alliance 
> between ISGlobal and CREAL, both institutions have merged. The resulting 
> institution, which retains the ISGlobal name, will build upon the existing 
> areas of excellence to become a world-class player in research, education and 
> innovation in Global Health. More info at http://ow.ly/krQd301Nj3w
> 
> On 21 October 2017 at 19:23, Hervé Pagès  wrote:
> Thanks Carles for the update.
> 
> Please do "Reply All" on further communications. Thanks!
> 
> Regards,
> H.
> 
> 
> On 10/21/2017 12:50 AM, Carles Hernández wrote:
> Dear Hervé,
> 
> 
> Yesterday I connacted Nitesh because it seems that I have some permision
> problems with my user. We keep in mind that we msut solve this as fast
> as possible.
> 
> 
> Kidnr egards,
> 
> Carles Hernandez-Ferrer
> Bioinformatic Analyst / PhD Student
> *ISGlobal*
> Barcelona Institute for Global Health - Campus Mar
> Barcelona Biomedical Research Park (PRBB) (office 183.01 A)
> Doctor Aiguader, 88
> 08003 Barcelona, Spain
> Tel. +34 93 214 73 22
> carles.hernan...@isglobal.org 
> www.isglobal.org
> 
> | www.carleshf.com
> 
> /
> //We are pleased to tell you that after three years of a strategic
> alliance between ISGlobal and CREAL, both institutions have merged. The
> resulting institution, which retains the ISGlobal name, will build upon
> the existing areas of excellence to become a world-class player in
> research, education and innovation in Global Health. More info at
> http://ow.ly/krQd301Nj3w
> /
> 
> On 21 October 2017 at 09:02, Hervé Pagès  > wrote:
> 
> Hi omicRexposome/BRGEdata developers,
> 
> When the BRGEdata package was accepted, we added the brgedata git
> repo to the Bioconductor git server:
> 
> https://git.bioconductor.org/packages/brgedata
> 
> 
> 
> Unfortunately at the time we did this, the name of the git repo didn't
> match the name of the package (brgedata vs BRGEdata). This is causing
> problems in our build system and is preventing the package from showing
> up on the daily build report for data-experiment packages:
> 
> https://bioconductor.org/checkResults/3.6/data-experiment-LATEST/
> 
> 
> 
> This in turn is causing the omicRexposome package to fail on the daily
> builds:
> 
> https://bioconductor.org/checkResults/3.6/bioc-LAT

Re: [Bioc-devel] I can't merge the changes by bioc team with my accepted package

[Turaga, Nitesh]

You submitted your key very recently. We process the keys every 24 hours, at 
12pm EST.

Please be patient.

Nitesh 

> On Oct 31, 2017, at 5:54 PM, Arman Shahrisa  
> wrote:
> 
> Hi,
> 
> I�m the maintainer of the package �cbaf�. It�s a new package for bioc v 3.6.
> 
> I�m trying to pull changes that are created during package publication.
> 
> I�m doing according to
> 
> https://bioconductor.org/developers/how-to/git/new-package-workflow/
> 
> and
> 
> https://bioconductor.org/developers/how-to/git/pull-upstream-changes/
> 
> When I run the following command
> 
>> git merge upstream/master
> 
> This message appears:
> 
>> merge: upstream/master � not something we can merge
> 
> Why?
> 
> Best regards,
> Arman
> 
>   [[alternative HTML version deleted]]
> 
> ___
> 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 
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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Re: [Bioc-devel] package access GitHub

[Turaga, Nitesh]

There are no updates given from that google form.

Did you try to access your package? 

> On Nov 1, 2017, at 1:45 PM, Valeriia Sherina  wrote:
> 
> Dear Bioconductor,
> 
> I am a maintainer of the package "nondetecs" on Bioconductor. I know that
> Bioconcuctor transitioned to GitHub submittions. I filled up a form "git /
> svn transition: ssh keys"  to get access to my package, but since last
> Wednesday have not gotten any updates on that.
> 
> I am hoping you might be able to help me.
> Thank you for your time.
> 
> With best regards,
> Valeriia Sherina
> 
>   [[alternative HTML version deleted]]
> 
> ___
> 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 
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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Re: [Bioc-devel] Package update not showing on Bioc 3.6 webpage

[Turaga, Nitesh]

Hi Kushal,

Can you please try,

ssh -T g...@git.bioconductor.org -v


Are you using the correct private key to your corresponding public key on our 
machine?

If not, please check the FAQ section 
bioconductor.org/developers/how-to/git/faq/ point#15. You can set up a config 
file to use the correct private key.

A snippet of your public key on our machine is,

ssh-rsa 
B3NzaC1yc2EDAQABAAACAQC8EgObkc/OI4nc8NE0sL4COb6uNaBIURhJoSyisz8i8/KWum0xFhav7ouDpMoZz0lgnlRaIYIRquJx0R44ojDcsN45TBR8Rna4PNBscVJEsbonD0k3wi2OBySgwxTzL5aZl99HzuAzthAPzFuskZDHahws9sPUtWMxioI6D5ZktVOb/QJbDJdFHFPXcd8l90wRJN0eGJXX9excJBDU57ufEgDBx9vGv85GTwJjP4UQYLyjDIap2CbrdC+7nJ95fa7YcNUj2znVFcrNnkW9

Best,

Nitesh 


> On Nov 1, 2017, at 2:23 PM, kushal kumar dey  wrote:
> 
> Hi Herve,
> 
> Thanks for clarifying on the matter. I followed your instructions and did *git
> cherry-pick* to make the following changes
> 
> - fix a bug in one of the functions
> - add a citation
> - fix the readme
> 
> I bumped the version number from 1.4.0 to 1.4.1 and tried to push to the
> release branch, but I when I run the command,
> 
> git push upstream RELEASE_3_6
> 
> I meet with the following error
> 
> *fatal: remote error: FATAL: W any packages/CountClust nobody DENIED by
> fallthru*
> 
> *(or you mis-spelled the reponame)*
> 
> 
> You can check the branch I want to push on my Github
> 
> 
> 
> *https://github.com/kkdey/CountClust/tree/RELEASE_3_6
> *
> 
> 
> This is my output from *git remote -v *
> 
> *origin https://github.com/kkdey/CountClust.git
>  (fetch)*
> 
> *origin https://github.com/kkdey/CountClust.git
>  (push)*
> 
> *upstream https://git.bioconductor.org/packages/CountClust
>  (fetch)*
> 
> *upstream https://git.bioconductor.org/packages/CountClust
>  (push)*
> 
> 
> Can you please let me know what I am doing wrong here and how I can update
> the release version?
> 
> 
> Thank you so much!
> 
> 
> Kushal
> 
> 
> 
> 
> 
> On 30 October 2017 at 17:50, Hervé Pagès  wrote:
> 
>> Hi Kushal,
>> 
>> If you push changes without bumping the version of your package,
>> the update won't propagate.
>> 
>> You only bumped the version to 1.5.1 today so you need to wait
>> about 24 hours before seeing this reflected on the landing page
>> for CountClust.
>> 
>> Also please note that you did the version bump plus a few other
>> commits (6 commits in total) in master today **after** we created
>> the RELEASE_3_6 branch so these changes will only propagate to
>> BioC 3.7 (the new devel version of BioC, starting tomorrow).
>> If you want these changes to also propagate to the BioC 3.6 release
>> you'll need to push them to the RELEASE_3_6 branch. This is
>> typically done with 'git cherry-pick' as documented here:
>> 
>> 
>> https://bioconductor.org/developers/how-to/git/bug-fix-in-
>> release-and-devel/
>> 
>> Cheers,
>> H.
>> 
>> 
>> On 10/30/2017 02:41 PM, kushal kumar dey wrote:
>> 
>>> Hi all,
>>> 
>>> I am the author and maintainer of the CountClust package. I recently
>>> submitted an update (version 1.5.1) to the package through
>>> Bioconductor Git  and I can access this updated version when I clone the
>>> source repository
>>> 
>>> git clone https://urldefense.proofpoint.com/v2/url?u=https-3A__git.bio
>>> conductor.org_packages_CountClust&d=DwICAg&c=eRAMFD45gAfqt84
>>> VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=-x3S
>>> 8Sl0fsASITg_-ULMYIykoPk6Y0PqK2NoRjC43iA&s=YBM0DldFbCkrEBnHaB
>>> n5X8-jb1yhm_GmSUWL6SIGLmo&e=
>>> 
>>> However, the updated version is not available in the official Bioconductor
>>> 3.6 page, which still shows the version 1.3.0.
>>> 
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bio
>>> conductor.org_packages_3.6_bioc_html_CountClust.html&d=DwICA
>>> g&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvS
>>> XAJJKaaPhzWA&m=-x3S8Sl0fsASITg_-ULMYIykoPk6Y0PqK2NoRjC43iA&
>>> s=UfPX4T5l4JBfXBumCcQ-5YOm59i_xfX2OEILrQ3I2u0&e=
>>> 
>>> Can you please let me know if the page has not been updated for the
>>> packages yet or if I would need to do something at my end to update the
>>> version reported on the page?
>>> 
>>> Thanks so much
>>> 
>>> 
>> --
>> Hervé Pagès
>> 
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Ce
>> nter
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>> 
>> E-mail: hpa...@fredhutch.org
>> Phone:  (206) 667-5791
>> Fax:(206) 667-1319
>> 
> 
> 
> 
> -- 
> Kushal K. Dey
> Graduate Student
> 5 th Year, Department of Statistics
> University of Chicago
> Contact: +1 312-709-0680 | kk...@uchicago.edu
> 
>   [[alternative HTML version deleted]]
> 
> __

Re: [Bioc-devel] Package update not showing on Bioc 3.6 webpage

[Turaga, Nitesh]

Hi Kushal,

You also need to use the “SSH” protocol, and not the “HTTPS” protocol.

Your upstream should be g...@git.bioconductor.org:packages/CountClust

Best,

Nitesh 

> On Nov 1, 2017, at 5:06 PM, Turaga, Nitesh  
> wrote:
> 
> Hi Kushal,
> 
> Can you please try,
> 
>   ssh -T g...@git.bioconductor.org -v
> 
> 
> Are you using the correct private key to your corresponding public key on our 
> machine?
> 
> If not, please check the FAQ section 
> bioconductor.org/developers/how-to/git/faq/ point#15. You can set up a config 
> file to use the correct private key.
> 
> A snippet of your public key on our machine is,
> 
> ssh-rsa 
> B3NzaC1yc2EDAQABAAACAQC8EgObkc/OI4nc8NE0sL4COb6uNaBIURhJoSyisz8i8/KWum0xFhav7ouDpMoZz0lgnlRaIYIRquJx0R44ojDcsN45TBR8Rna4PNBscVJEsbonD0k3wi2OBySgwxTzL5aZl99HzuAzthAPzFuskZDHahws9sPUtWMxioI6D5ZktVOb/QJbDJdFHFPXcd8l90wRJN0eGJXX9excJBDU57ufEgDBx9vGv85GTwJjP4UQYLyjDIap2CbrdC+7nJ95fa7YcNUj2znVFcrNnkW9
> 
> Best,
> 
> Nitesh 
> 
> 
>> On Nov 1, 2017, at 2:23 PM, kushal kumar dey  wrote:
>> 
>> Hi Herve,
>> 
>> Thanks for clarifying on the matter. I followed your instructions and did 
>> *git
>> cherry-pick* to make the following changes
>> 
>> - fix a bug in one of the functions
>> - add a citation
>> - fix the readme
>> 
>> I bumped the version number from 1.4.0 to 1.4.1 and tried to push to the
>> release branch, but I when I run the command,
>> 
>> git push upstream RELEASE_3_6
>> 
>> I meet with the following error
>> 
>> *fatal: remote error: FATAL: W any packages/CountClust nobody DENIED by
>> fallthru*
>> 
>> *(or you mis-spelled the reponame)*
>> 
>> 
>> You can check the branch I want to push on my Github
>> 
>> 
>> 
>> *https://github.com/kkdey/CountClust/tree/RELEASE_3_6
>> <https://github.com/kkdey/CountClust/tree/RELEASE_3_6>*
>> 
>> 
>> This is my output from *git remote -v *
>> 
>> *origin https://github.com/kkdey/CountClust.git
>> <https://github.com/kkdey/CountClust.git> (fetch)*
>> 
>> *origin https://github.com/kkdey/CountClust.git
>> <https://github.com/kkdey/CountClust.git> (push)*
>> 
>> *upstream https://git.bioconductor.org/packages/CountClust
>> <https://git.bioconductor.org/packages/CountClust> (fetch)*
>> 
>> *upstream https://git.bioconductor.org/packages/CountClust
>> <https://git.bioconductor.org/packages/CountClust> (push)*
>> 
>> 
>> Can you please let me know what I am doing wrong here and how I can update
>> the release version?
>> 
>> 
>> Thank you so much!
>> 
>> 
>> Kushal
>> 
>> 
>> 
>> 
>> 
>> On 30 October 2017 at 17:50, Hervé Pagès  wrote:
>> 
>>> Hi Kushal,
>>> 
>>> If you push changes without bumping the version of your package,
>>> the update won't propagate.
>>> 
>>> You only bumped the version to 1.5.1 today so you need to wait
>>> about 24 hours before seeing this reflected on the landing page
>>> for CountClust.
>>> 
>>> Also please note that you did the version bump plus a few other
>>> commits (6 commits in total) in master today **after** we created
>>> the RELEASE_3_6 branch so these changes will only propagate to
>>> BioC 3.7 (the new devel version of BioC, starting tomorrow).
>>> If you want these changes to also propagate to the BioC 3.6 release
>>> you'll need to push them to the RELEASE_3_6 branch. This is
>>> typically done with 'git cherry-pick' as documented here:
>>> 
>>> 
>>> https://bioconductor.org/developers/how-to/git/bug-fix-in-
>>> release-and-devel/
>>> 
>>> Cheers,
>>> H.
>>> 
>>> 
>>> On 10/30/2017 02:41 PM, kushal kumar dey wrote:
>>> 
>>>> Hi all,
>>>> 
>>>> I am the author and maintainer of the CountClust package. I recently
>>>> submitted an update (version 1.5.1) to the package through
>>>> Bioconductor Git  and I can access this updated version when I clone the
>>>> source repository
>>>> 
>>>> git clone https://urldefense.proofpoint.com/v2/url?u=https-3A__git.bio
>>>> conductor.org_packages_CountClust&d=DwICAg&c=eRAMFD45gAfqt84
>>>> VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=-x3S
>>>> 8Sl0fsASITg_-ULMYIykoPk6Y0PqK2NoRjC43iA&s=YBM0DldFbCkrEBnHaB
>>>> n5X8-jb1yhm_GmSUWL6SIGLmo&e=

Re: [Bioc-devel] switching to git

[Turaga, Nitesh]

Hi,

You do not receive an email after submitting your key. 

We have added the latest set of keys, 

Please try again.

Nitesh 

> On Nov 7, 2017, at 8:06 PM, Peter Haverty  wrote:
> 
> I'm working on using the new git setup. I've provided my GitHub user name
> to BioC's form, so that my public key can be used with BioC's git. I
> believe I was supposed to receive an email after that was set up, but I
> have not. Is there something else I need to do?
> 
> Regards,
> Pete
> 
> 
> Peter M. Haverty, Ph.D.
> Genentech, Inc.
> phave...@gene.com
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] EXTERNAL: Re: Rnits Bioconductor package

[Turaga, Nitesh]

I’ve added your correct submission.

Please try again

> On Nov 8, 2017, at 1:41 PM, Ramos Perez, Marcel 
>  wrote:
> 
> Hi Dipen, 
> Please make sure that your GitHub and Subversion usernames were entered 
> correctly in the form.
> 
> I have copied Nitesh, as he can verify that they are valid and assist you 
> further.
> 
> 
> Regards,
> 
> Marcel 
> 
> 
> On 11/08/2017 01:33 PM, Dipen Sangurdekar wrote:
>> Hi Marcel,
>> 
>> I have been trying to push my local git repos to git.bioconductor.org. I 
>> have added my public ssh key to bioconductor google form twice already, but 
>> I still get the following error
>> 
>> $ git remote -v
>> 
>> upstream g...@git.bioconductor.org:packages/Rnits (fetch)
>> 
>> upstream g...@git.bioconductor.org:packages/Rnits (push)
>> 
>> 
>> 
>> $ git push upstream master
>> 
>> FATAL: W any packages/Rnits dipenps DENIED by fallthru
>> 
>> (or you mis-spelled the reponame)
>> 
>> fatal: Could not read from remote repository.
>> 
>> 
>> 
>> Please make sure you have the correct access rights
>> 
>> and the repository exists.
>> 
>> 
>> 
>> Is there any avenue I can pursue to follow up on this issue? I couldn't find 
>> any help by looking on the bioconductor site.
>> 
>> 
>> 
>> Thanks,
>> 
>> Dipen
>> 
>> 
>> 
>> 
>> On Sun, Oct 1, 2017 at 9:14 PM, Marcel Ramos 
>>  wrote:
>> Hi Dipen, 
>> The most recent build does not reflect your changes. 
>> http://bioconductor.org/checkResults/devel/bioc-LATEST/Rnits/
>> Please commit your changes to Bioconductor's git repository. 
>> For instructions, please see: https://bioconductor.org/developers/how-to/git/
>> 
>> Best regards,
>> 
>> Marcel 
>> 
>> On 09/27/2017 04:02 PM, Dipen Sangurdekar wrote:
>>> Thanks - I have pushed changes to version 1.11 (second link) on github. Is 
>>> the build on dev version done nightly?
>>> I need to find where I uploaded the code for version 1.10.0 (first link). 
>>> The bug is because the link to the GEO file the code uses in the vignette 
>>> doesn't exist on NCBI's site anymore. 
>>> 
>>> Dipen
>>> 
>>> 
>>> 
>>> On Wed, Sep 27, 2017 at 3:28 PM, Marcel Ramos 
>>>  wrote:
>>> Hi Dipen P. Sangurdekar, 
>>> I am contacting you concerning the `Rnits` package, on the release and/or 
>>> development 
>>> branch of Bioconductor, for which you are listed as the maintainer. 
>>> The latest build/check report shows that your package is failing on one or 
>>> more platforms. 
>>> Please resolve the issues for your package's continued inclusion in 
>>> Bioconductor. 
>>> http://bioconductor.org/checkResults/release/bioc-LATEST/Rnits/
>>> http://bioconductor.org/checkResults/devel/bioc-LATEST/Rnits/
>>> 
>>> Please let me know if you have any questions. 
>>> Regards,
>>> 
>>> Marcel
>>> 
>>> 
>>> -- 
>>> Marcel Ramos
>>> Bioconductor Core Team
>>> Roswell Park Cancer Institute
>>> Department of Biostatistics & Bioinformatics
>>> 
>>> 
>>> 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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Re: [Bioc-devel] Issues with access to Bioconductor repository: multiClust

[Turaga, Nitesh]

Hi,

My record shows that you’ve submitted your key at (Tuesday) 14/11/2017 
15:35:17.  We process the keys around noon every day (EST). You should have 
received a notification on the google form after submission that it takes 1 
business day.

I’ll make an exception and reprocess this now. You should have access. 

Best

Nitesh 

> On Nov 14, 2017, at 5:20 PM, Nathan Lawlor  wrote:
> 
> Hello,
> 
> I originally submitted the package "multiClust" to Bioconductor through svn
> (my user SVN id was: "n.lawlor").
> 
> On Monday (11/14/2017) I completed the git/svn transition form: (
> https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform)
> providing my github user id: "nlawlor" and an ssh key which I added to my
> github account.
> 
> I am able to access the bioconductor git repository for multiClust however
> I am unable to push any changes to that repository.
> 
> Here are what my existing remotes look like:
> 
> git remote -v
> 
> origin g...@github.com:nlawlor/multiClust.git (fetch)
> 
> origin g...@github.com:nlawlor/multiClust.git (push)
> 
> upstream g...@git.bioconductor.org:packages/multiClust.git (fetch)
> 
> upstream g...@git.bioconductor.org:packages/multiClust.git (push)
> 
> 
> I'm able to push any changes to my origin remote, but when I do: "git push
> upstream master"
> 
> 
> I receive the following error:
> 
> 
> FATAL: W any packages/multiClust nlawlor DENIED by fallthru
> 
> (or you mis-spelled the reponame)
> 
> fatal: Could not read from remote repository.
> 
> 
> Please make sure you have the correct access rights
> 
> and the repository exists.
> 
> 
> Is it possible that my id in the bioconductor system is still using the svn
> user (n.lawlor) and has not been updated to the github id (nlawlor)?
> 
> 
> Thank you,
> 
> Nathan
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] Query bioconductor.org for what the current release version is?

[Turaga, Nitesh]

Hi Henrik,

Try https://www.bioconductor.org/config.yaml

You should have the essential information in there—

 release_version: "3.6"

Hope this is what you are looking for.

Nitesh 

> On Nov 16, 2017, at 8:09 PM, Henrik Bengtsson  
> wrote:
> 
> Hi.  Is there a way, without using R, to query bioconductor.org (or
> any other reliable/maintained resources) for what the current release
> version of Bioconductor is?  Something like:
> 
> $ curl https://bioconductor.org/api/version
> 3.6
> 
> or possibly something fancy like:
> 
> $ curl https://bioconductor.org/api/version.json
> {"version":["3.6"],"date":["2017-10-31"],"depends":["R (>= 3.4.2)"]}
> 
> Thanks.
> 
> Henrik
> 
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Re: [Bioc-devel] Git access

[Turaga, Nitesh]

We changed this policy as of yesterday to reduce confusion for people who are 
submitting keys.

Have you tried to access your package (ROTS) ? We have a key on file for you. 

If you have submitted your key a while ago, then my suggestion would be try to 
first access your package.


Best,

Nitesh  

> On Nov 17, 2017, at 8:52 AM, Fatemehsadat Seyednasrollah  
> wrote:
> 
> Sorry forgot to mention the google form was sent 29th of Oct.
> 
> BR,
> Fatemeh
> 
> From: Bioc-devel  on behalf of Fatemehsadat 
> Seyednasrollah 
> Sent: Friday, November 17, 2017 3:44 PM
> To: bioc-devel@r-project.org
> Subject: [Bioc-devel] Git access
> 
> Hi,
> 
> Based on the question #17 from the below link:
> https://bioconductor.org/developers/how-to/git/faq/
> 
> I need to receive an email from maintai...@bioconductor.org, regarding 
> confirmation of addition or invalid entry after submitting the SSH key to the 
> google form. But I havent. What should I do?
> 
> 
> Best regards,
> Fatemeh
> 
> 
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Re: [Bioc-devel] Git access

[Turaga, Nitesh]

Hi Fatemah,

You can try the new key to see if that is the one assigned. Have you tried it? 

If not, then you’d probably have to resubmit a new key. 

Best,

Nitesh 

> On Nov 17, 2017, at 9:26 AM, Fatemehsadat Seyednasrollah  
> wrote:
> 
> Thanks! though I have sent the key around three weeks ago.
> Actually, I have sent two keys. The latest one is the one which was sent on 
> 29th Oct. How can I be sure if the latest key is assigned? I dont have access 
> to the first key anymore.
> And yes I am trying to get access to ROTS git.
> 
> Best,
> Fatemeh
> ________
> From: Turaga, Nitesh 
> Sent: Friday, November 17, 2017 4:20 PM
> To: Fatemehsadat Seyednasrollah
> Cc: bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] Git access
> 
> We changed this policy as of yesterday to reduce confusion for people who are 
> submitting keys.
> 
> Have you tried to access your package (ROTS) ? We have a key on file for you.
> 
> If you have submitted your key a while ago, then my suggestion would be try 
> to first access your package.
> 
> 
> Best,
> 
> Nitesh
> 
>> On Nov 17, 2017, at 8:52 AM, Fatemehsadat Seyednasrollah  
>> wrote:
>> 
>> Sorry forgot to mention the google form was sent 29th of Oct.
>> 
>> BR,
>> Fatemeh
>> 
>> From: Bioc-devel  on behalf of 
>> Fatemehsadat Seyednasrollah 
>> Sent: Friday, November 17, 2017 3:44 PM
>> To: bioc-devel@r-project.org
>> Subject: [Bioc-devel] Git access
>> 
>> Hi,
>> 
>> Based on the question #17 from the below link:
>> https://bioconductor.org/developers/how-to/git/faq/
>> 
>> I need to receive an email from maintai...@bioconductor.org, regarding 
>> confirmation of addition or invalid entry after submitting the SSH key to 
>> the google form. But I havent. What should I do?
>> 
>> 
>> Best regards,
>> Fatemeh
>> 
>> 
>> ___
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>> 
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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 
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> distribution, or use of this email message is prohibited.  If you have 
> received this message in error, please notify the sender immediately by 
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Re: [Bioc-devel] cherry picking fixes to release

[Turaga, Nitesh]

Hi Michael, 

Thanks for catching this. It is updated now.

Best



> On Dec 3, 2017, at 1:18 PM, Michael Lawrence  
> wrote:
> 
> Was the website ever updated for this? I don't see the 
> 
> git checkout -b  upstream/
> 
> which has to be done the first time patching a release.
> 
> On Tue, Oct 3, 2017 at 11:19 AM, Turaga, Nitesh 
>  wrote:
> Thanks for the heads up. I will fix the documentation on the website.
> 
> Best,
> 
> Nitesh
> 
> > On Oct 3, 2017, at 2:17 PM, Michael Lawrence  
> > wrote:
> >
> > Yes, that seems to have fixed it. Thanks for your help.
> >
> > I guess the guide on the Bioc website needs to be tweaked.
> >
> > Michael
> >
> > On Tue, Oct 3, 2017 at 11:15 AM, Turaga, Nitesh
> >  wrote:
> >> I’m just guessing, but I think “git” is trying to work on the upstream 
> >> RELEASE_3_5 directly.
> >>
> >> Maybe try,
> >>
> >>git fetch —all
> >>git checkout -b RELASE_3_5 upstream/RELEASE_3_5   ## This will 
> >> create a local branch RELEASE_3_5 which follows your upstream/RELEASE_3_5
> >>
> >> This should not have that detached head state.
> >>
> >> Nitesh
> >>
> >>
> >>
> >>> On Oct 3, 2017, at 2:11 PM, Turaga, Nitesh 
> >>>  wrote:
> >>>
> >>> Hi Micheal,
> >>>
> >>> This is very interesting, I’m never run across it.
> >>>
> >>> Can you tell me what package you are working on, and I’ll try your 
> >>> commands as a user. (I won’t push anything, just want to reproduce the 
> >>> error)
> >>>
> >>> Best,
> >>>
> >>> Nitesh
> >>>> On Oct 3, 2017, at 1:51 PM, Michael Lawrence  
> >>>> wrote:
> >>>>
> >>>> Hi Nitesh,
> >>>>
> >>>> I tried following your guide to fixing bugs in devel and release, but
> >>>> I hit a hurdle.
> >>>>
> >>>> I did a git fetch --all. Then a git branch RELEASE_3_5.
> >>>>
> >>>> But I end up in a weird detached head state.
> >>>>
> >>>> bash-3.2$ git branch
> >>>> * (HEAD detached from origin/RELEASE_3_5)
> >>>> master
> >>>>
> >>>> Do you have any ideas?
> >>>>
> >>>> Thanks,
> >>>> Michael
> >>>
> >>
> >>
> >>
> >> 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, 
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> 



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Re: [Bioc-devel] pushing from github to bioconductor, skipping local machine

[Turaga, Nitesh]

Hi Tyler,

AFAIK, this is not possible. You need a local repository with valid credentials 
on that local machine to be able to push to the bioconductor server. 

You would have to find a way to set up a machine from which you can push to our 
server.

Best,

Nitesh 

> On Dec 4, 2017, at 12:50 PM, Tyler Smith  wrote:
> 
> Hi,
> 
> I think I have set up proper access to the Bioconductor git repos, and
> cloned the repos into a separate github repository. Bioconductor has my
> ssh key, and I've also added this key to GitHub.
> 
> The only hitch in my development workflow is that my work network blocks
> the SSH/git port, so I can't use the git protocol to access the
> bioconductor repository. I can send my changes over https to github. Is
> it possible to send changes from GitHub to Bioconductor directly? That
> is, to instruct git to transfer from GitHub to Bioconductor without me
> needing to send anything from my local machine direct to Bioconductor. 
> 
> All the help I turn up with Google shows how to send local -> github or
> local -> upstream, I need github -> upstream.
> 
> Thanks,
> 
> Tyler
> 
> -- 
> plantarum.ca
> 
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Re: [Bioc-devel] DaMiRseq: error while pushing

[Turaga, Nitesh]

Hi Mattia,

If you read the “error” and “hint” messages carefully, it says do a 

> hint: (e.g., 'git pull ...') before pushing again.

Did you try that?

Best,

Nitesh 

> On Dec 12, 2017, at 10:21 AM, Mattia Chiesa  wrote:
> 
> Dear All,
> I am the mantainer of the DaMiRseq package.
> I performed some relevant modificantions in the package (i.e. added 
> functions, added the CITATION file, updated vignette and NEWS file) and now 
> I'm ready to push (from a local folder to github and Bioconductor).
> So, as usually, I typed:
> git add .
> git commit -m "message"
> git push origin master
> git push upstream master
> (and typed the password)
> 
> Everything was ok for github (origin) but for Bioconductor an error occured:
> 
> Enter passphrase for key '/c/Users/mchiesa/.ssh/id_rsa':
> To git.bioconductor.org:packages/DaMiRseq.git
> ! [rejected]master -> master (fetch first)
> error: failed to push some refs to 
> 'g...@git.bioconductor.org:packages/DaMiRseq.git'
> hint: Updates were rejected because the remote contains work that you do
> hint: not have locally. This is usually caused by another repository pushing
> hint: to the same ref. You may want to first integrate the remote changes
> hint: (e.g., 'git pull ...') before pushing again.
> hint: See the 'Note about fast-forwards' in 'git push --help' for details.
> 
> What should I do?
> Thanks in advance,
> Mattia
> 
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] Question about Access to Bioconductor through Git

[Turaga, Nitesh]

Hi George,

If you’ve had an SVN id before, then you would have to submit that. I’ve 
checked your submission and you have to submit just your SVN ID, not the 
password. Please try and check for this.

Otherwise, there is no way for us to associate your package with your Github 
ID. 

Best,

Nitesh 



> On Dec 12, 2017, at 8:25 PM, George Wu  wrote:
> 
> Hi Bioc-Devel List,
> 
> I am having trouble pushing to the git bioconductor repository, most likely
> due to not requesting for access correctly.
> 
> I was able to follow the instructions to open a github account and link the
> github repository to the one on my local machine, and then sync both with
> the g...@git.bioconductor.org for my package. I also submitted the
> information and had my key added to have access to push.
> 
> When I tried to push my changes I got the following messages:
> 
> *"*
> *FATAL: W any packages/... DENIED by fallthru*
> *(or you mis-spelled the reponame)*
> *fatal: Could not read from remote repository.*
> 
> *Please make sure you have the correct access rights*
> *and the repository exists.*
> *"*
> 
> 
> My guess is that I submitted my key incorrectly? I used to have a SVN
> account a long time ago, but do not remember the details, so I put my
> GitHub id. And then I copy-pasted directly using '*clip < ~/.ssh/id_rsa.pub*'
> to add my key. The key should work because I used the process to link to my
> github account from my local machine. Did I make a mistake somewhere?
> 
> Thanks for your help in advance,
> George
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] git push to Bioconductor failing

[Turaga, Nitesh]

Hi Gabriel,

You seem to have not submitted your SVN ID. Please submit your key along with 
that information.

Best

Nitesh 

> On Dec 15, 2017, at 12:50 PM, Hoffman, Gabriel  
> wrote:
> 
> Hi,
> 
> I am having an issue pushing changes from my git repo to Bioconductor.  I can 
> push changes to Github just fine.
> 
> 
> Here my push command fails.
> 
> 
>> git push upstream
> 
> FATAL: W any packages/variancePartition gabrielhoffman DENIED by fallthru
> 
> (or you mis-spelled the reponame)
> 
> fatal: Could not read from remote repository.
> 
> 
> Please make sure you have the correct access rights
> 
> and the repository exists.
> 
> I have the proper upstream location set
> 
> 
>> git remote -v
> 
> origin https://github.com/GabrielHoffman/variancePartition.git (fetch)
> 
> origin https://github.com/GabrielHoffman/variancePartition.git (push)
> 
> upstream g...@git.bioconductor.org:packages/variancePartition (fetch)
> 
> upstream g...@git.bioconductor.org:packages/variancePartition (push)
> 
> 
> But it seems like I don't have write access to this repo.
> 
> 
>> ssh -T g...@git.bioconductor.org | grep variancePartition
> 
> R  packages/variancePartition
> 
> 
> 
> I have registered my SSH RSA key with Bioconductor, and I have received the 
> emails saying it was approved.  But I still do not have write access.
> 
> 
> Do you have any suggestions to debug this?
> 
> 
> Thanks,
> 
> - Gabriel
> 
> 
> 
> 
> --
> 
> Gabriel Hoffman, Ph.D.
> 
> 
> 
> Assistant Professor
> 
> Icahn Institute for Genomics and Multiscale Biology
> 
> Department of Genetics and Genomic Sciences
> 
> Icahn School of Medicine at Mount Sinai
> 
> 
> 
> gabriel.hoff...@mssm.edu
> 
> 
> 
> 1425 Madison Avenue
> 
> New York, NY 10029
> 
> Icahn Building L3-70B
> 
> 212-659-1635
> 
> 
> http://gabrielhoffman.github.io
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] Updating bioconductor after computer transfer - problem

[Turaga, Nitesh]

Hi Chris,

We have a key already for you. It is possible you are using the wrong key to 
access git.bioconductor.org. 

ssh-rsa 
B3NzaC1yc2EDAQABAAABAQCv4h33vFVuXjQqddBgjU2398YglnXpOPL1xgU1t63JQ+bJWOQx2wl

That is the prefix of the key we have on file for you. One way is to submit a 
new key, if you don’t have access to the private key corresponding to your 
public key. You should have access once that new key is in our system. 

Best

Nitesh

> On Dec 15, 2017, at 2:06 AM, Christopher John  
> wrote:
> 
> Hi
> 
> I have recently copy and pasted my github directory from my old PC to a new
> PC. I can update the github still fine, but bioconductor I get an error:
> 
> christopher@RA-MAP:~/M3C$ git remote -v
> originhttps://github.com/crj32/M3C (fetch)
> originhttps://github.com/crj32/M3C (push)
> upstreamg...@git.bioconductor.org:packages/M3C.git (fetch)
> upstreamg...@git.bioconductor.org:packages/M3C.git (push)
> 
> .. the usual commands
> 
> christopher@RA-MAP:~/M3C$ git push origin master
> Username for 'https://github.com': crj32
> Password for 'https://cr...@github.com':
> Everything up-to-date
> 
> christopher@RA-MAP:~/M3C$ git push upstream master
> Permission denied (publickey).
> fatal: Could not read from remote repository.
> Please make sure you have the correct access rights
> and the repository exists.
> 
> I guessed this was to do with the ssh key not being update to date with the
> one from the new PC. So I followed the directions on this site and got my
> local ssh key, added it to the github, then sent the ssh key off to the
> bioconductor through the google forms page. Still no luck, same error. Was
> this the correct thing to do?
> 
> https://bioconductor.org/developers/how-to/git/maintain-github-bioc/
> 
> Thanks,
> 
> Chris
> 
>   [[alternative HTML version deleted]]
> 
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[Bioc-devel] RSS feed on bioconductor.org/developers/gitlog

[Turaga, Nitesh]

Hello Maintainers,

Happy new year! 

The GIT logs are available as RSS feeds, or as markdown on the website at 

http://bioconductor.org/developers/gitlog/ 

This is across all the packages on the bioconductor git server. It allows 
developers to keep track of their package development, and for the community to 
keep track of their favorite packages. The website shows only the most recent 
200 commits.

Please note that the website rebuilds every 20 mins, so it will take 20 mins 
for your commit to show up on the website.


Best,


Nitesh Turaga
Bioconductor Core Team

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Re: [Bioc-devel] RSS feed on bioconductor.org/developers/gitlog

[Turaga, Nitesh]

Hi,

The links on each feed point back to the bioconductor home page. There is no 
log file for each package separately. This was a design choice.

Best,

Nitesh 

> On Jan 3, 2018, at 9:39 AM, Lluís Revilla  wrote:
> 
> Great work and happy new year!!
> 
> I checked both RSS feeds and the random links I tried all point to the home 
> page of Bioconductor. 
> I am unsure if the links in the feed should point to a section on the gitlog 
> page or to any other page (or is an issue on my end). 
> 
> Thanks,
> 
> Lluís
> 
> 
> On 2 January 2018 at 21:38, Turaga, Nitesh  
> wrote:
> Hello Maintainers,
> 
> Happy new year!
> 
> The GIT logs are available as RSS feeds, or as markdown on the website at
> 
> http://bioconductor.org/developers/gitlog/
> 
> This is across all the packages on the bioconductor git server. It allows 
> developers to keep track of their package development, and for the community 
> to keep track of their favorite packages. The website shows only the most 
> recent 200 commits.
> 
> Please note that the website rebuilds every 20 mins, so it will take 20 mins 
> for your commit to show up on the website.
> 
> 
> Best,
> 
> 
> Nitesh Turaga
> Bioconductor Core Team
> 
> 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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> 



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Re: [Bioc-devel] git help

[Turaga, Nitesh]

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 
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  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  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.
> 



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Re: [Bioc-devel] git help

[Turaga, Nitesh]

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  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 
>> 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  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  
>>>>> 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

Re: [Bioc-devel] RSS feed on bioconductor.org/developers/gitlog

[Turaga, Nitesh]

Hi,

The order of the commits, is when the maintainer “pushes” to our git server. 

Most recent commit is at the top. 

We increased the limit to 500.

Best,

Nitesh 

> On Jan 5, 2018, at 9:16 AM, Felix Ernst  wrote:
> 
> Hi Nitesh,
>  
> Happy new year as well.
>  
> I was wondering, what the sorting order is. I can’t seem to figure it out. 
>  
> Is it supposed to be ordered? Date and name of package? The first break on 
> the page is near rhdf5 and semisup.
>  
> Cheers,
> Felix
>  
>  
>  
> Von: Turaga, Nitesh
> Gesendet: Dienstag, 2. Januar 2018 21:56
> An: bioc-devel
> Betreff: [Bioc-devel] RSS feed on bioconductor.org/developers/gitlog
>  
> Hello Maintainers,
>  
> Happy new year!
>  
> The GIT logs are available as RSS feeds, or as markdown on the website at
> 
> http://bioconductor.org/developers/gitlog/ 
>  
> This is across all the packages on the bioconductor git server. It allows 
> developers to keep track of their package development, and for the community 
> to keep track of their favorite packages. The website shows only the most 
> recent 200 commits.
>  
> Please note that the website rebuilds every 20 mins, so it will take 20 mins 
> for your commit to show up on the website.
>  
>  
> Best,
>  
>  
> Nitesh Turaga
> Bioconductor Core Team
>  
> 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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Re: [Bioc-devel] git help

[Turaga, Nitesh]

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  
> 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  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 
>>> 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  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  
>>>>>> 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

Re: [Bioc-devel] Can I push a new branch to Bioconductor git?

[Turaga, Nitesh]

Hi Stian,

You cannot push to any branch other than “master” and RELEASE_3_6. Bioconductor 
regulates the branches that are available on our GIT server. 

You cannot push an additional branch, we recommend you do that on your GitHub, 
and merge with master when you are ready, and then push to Bioconductor.

You also seem to have duplicate commits on your repository. You should probably 
take a look at why that is happening.

Best,

Nitesh 

> On Jan 7, 2018, at 5:43 AM, Stian Lågstad  wrote:
> 
> I'm trying to push a new branch with some changes to origin, but I'm
> getting this error:
> 
> ```
> ➜  chimeraviz-bioconductor git:(starfusionffpm) git push --set-upstream
> origin starfusionffpm
> Counting objects: 7, done.
> Delta compression using up to 8 threads.
> Compressing objects: 100% (7/7), done.
> Writing objects: 100% (7/7), 998 bytes | 0 bytes/s, done.
> 
> Total 7 (delta 5), 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: . Provide the error, the package name and
> remote: any other details we might need.
> remote:
> remote: Use
> remote:
> remote: git show 248742bd41a1b1d862d29e612baa067c50c55e5b
> remote: git show 81ee14920be186caf4f2949e7dacfad68db64ed2
> remote:
> remote: to see body of commits.
> remote:
> To g...@git.bioconductor.org:packages/chimeraviz
> 
> ! [remote rejected] starfusionffpm -> starfusionffpm (pre-receive hook
> declined)
> error: failed to push some refs to 'g...@git.bioconductor.org:
> packages/chimeraviz'
> ```
> 
> I'm not syncing anything with an existing Github repository. I just wanted
> to store a couple of changes that I might merge into master later.
> 
> I haven't done anything locally since my last successful push to master, so
> I should be in sync:
> ```
> ➜  chimeraviz-bioconductor git:(starfusionffpm) git checkout master
> Switched to branch 'master'
> Your branch is up-to-date with 'origin/master'.
> ➜  chimeraviz-bioconductor git:(master) git pull
> Already up-to-date.
> ➜  chimeraviz-bioconductor git:(master) git branch -a
>  RELEASE_3_6
> * master
>  starfusionffpm
>  remotes/origin/HEAD -> origin/master
>  remotes/origin/RELEASE_3_5
>  remotes/origin/RELEASE_3_6
>  remotes/origin/master
> ➜  chimeraviz-bioconductor git:(master) git checkout RELEASE_3_6
> Switched to branch 'RELEASE_3_6'
> Your branch is up-to-date with 'origin/RELEASE_3_6'.
> ➜  chimeraviz-bioconductor git:(RELEASE_3_6) git pull
> Already up-to-date.
> ```
> 
> Are we allowed to push new branches to Bioconductor, or should we avoid
> doing that?
> 
> -- 
> Stian Lågstad
> +47 41 80 80 25
> 
>   [[alternative HTML version deleted]]
> 
> ___
> 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 
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Re: [Bioc-devel] git help

[Turaga, Nitesh]

Hi Kevin,

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


commit fb5868c2fdfa607b52e467881212b3619a8b0ae9 (HEAD -> master)
Author: Hervé Pagès 
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: Hervé Pagès 
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  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  
>>> 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  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 
>>>>> 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  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 

Re: [Bioc-devel] git help

[Turaga, Nitesh]

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 
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: Hervé Pagès 
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: Hervé Pagès 
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 
Date:   Fri Jun 30 20:12:52 2017 +

Merge branch 'master' into devel

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

##
Same for the RELEASE branch. 
##

commit 7111f07cc9c32977f1eca63a0f2a25cb1092f7be (HEAD -> RELEASE_3_6)
Author: khoran 
Date:   Sun Jan 7 10:14:49 2018 -0800

set version for release branch

commit a2615e98aff83130f6129abc02132a65d99689b9
Author: Hervé Pagès 
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 
Date:   Fri Jun 30 20:12:52 2017 +

Merge branch 'master' into devel

git-svn-id: 
file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChemmineR@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  
> 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: Hervé Pagès 
> 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: Hervé Pagès 
> 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  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 
>>>>  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  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

Re: [Bioc-devel] git help

[Turaga, Nitesh]

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  
> 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 
> 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: Hervé Pagès 
> 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: Hervé Pagès 
> 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 
> Date:   Fri Jun 30 20:12:52 2017 +
> 
>Merge branch 'master' into devel
> 
>git-svn-id: 
> file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChemmineR@130816
>  bc3139a8-67e5-0310-9ffc-ced21a209358
> 
> ##
> Same for the RELEASE branch. 
> ##
> 
> commit 7111f07cc9c32977f1eca63a0f2a25cb1092f7be (HEAD -> RELEASE_3_6)
> Author: khoran 
> Date:   Sun Jan 7 10:14:49 2018 -0800
> 
>set version for release branch
> 
> commit a2615e98aff83130f6129abc02132a65d99689b9
> Author: Hervé Pagès 
> 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 
> Date:   Fri Jun 30 20:12:52 2017 +
> 
>Merge branch 'master' into devel
> 
>git-svn-id: 
> file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChemmineR@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  
>> 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: Hervé Pagès 
>> 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: Hervé Pagès 
>> 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  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 
>>>>>  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 

Re: [Bioc-devel] git help

[Turaga, Nitesh]

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  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  
>>> 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 
>>> 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: Hervé Pagès 
>>> 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: Hervé Pagès 
>>> 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 
>>> Date:   Fri Jun 30 20:12:52 2017 +
>>> 
>>>Merge branch 'master' into devel
>>> 
>>>git-svn-id: 
>>> file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChemmineR@130816
>>>  bc3139a8-67e5-0310-9ffc-ced21a209358
>>> 
>>> ##
>>> Same for the RELEASE branch.
>>> ##
>>> 
>>> commit 7111f07cc9c32977f1eca63a0f2a25cb1092f7be (HEAD -> RELEASE_3_6)
>>> Author: khoran 
>>> Date:   Sun Jan 7 10:14:49 2018 -0800
>>> 
>>>set version for release branch
>>> 
>>> commit a2615e98aff83130f6129abc02132a65d99689b9
>>> Author: Hervé Pagès 
>>> 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 
>>> Date:   Fri Jun 30 20:12:52 2017 +
>>> 
>>>Merge branch 'master' into devel
>>> 
>>>git-svn-id: 
>>> file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChemmineR@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  
>>>> 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: Hervé Pagès 
>>>> 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: Hervé Pagès 
>>>> 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,
>>

Re: [Bioc-devel] Duplicate commit error when pushing to annotatr upstream/master

[Turaga, Nitesh]

Hi Raymond,

I’m trying to figure out why your problem was caused. The duplicates are coming 
from this commit (ea6c6421b074dbc9411bd6d00547b90bb6168d31), which is a merge. 
But I’m what I’m trying to figure out is how you’ve been able to push with 
duplicate commits after that merge.

Please give me sometime.

I will get back to you.

Best,

Nitesh 

> On Jan 8, 2018, at 2:19 PM, Raymond Cavalcante  wrote:
> 
> Hello,
> 
> I’m running into the following error when trying to push some changes to 
> annotatr upstream/master:
> 
>> rcavalca$ git push upstream master
>> Counting objects: 6, done.
>> Delta compression using up to 8 threads.
>> Compressing objects: 100% (6/6), done.
>> Writing objects: 100% (6/6), 854 bytes | 854.00 KiB/s, done.
>> Total 6 (delta 5), 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: . Provide the error, the package name and
>> remote: any other details we might need.
>> remote: 
>> remote: Use
>> remote: 
>> remote: git show ffdb09d480c01535466e89b99e22535672e362a7
>> remote: git show 333da75f93af1ca7f5cb9a8443a1d5c963f21280
>> remote: 
>> remote: to see body of commits.
>> remote: 
>> To git.bioconductor.org:packages/annotatr.git
>> ! [remote rejected] master -> master (pre-receive hook declined)
>> error: failed to push some refs to 
>> 'g...@git.bioconductor.org:packages/annotatr.git'
> 
> 
> The two commits that are highlighted in the error message are "bump x.y.z 
> versions to odd y after creation of 3_5 branch" commits. I was always 
> confused about the git-svn bridge, but these twin commits are an artifact of 
> that system, I think. The commit that I was trying to push to upstream/master 
> is unrelated to those two commits, and I have committed other items in the 
> new git way prior to the 3.6 release with no issue.
> 
> I tried the suggested solution 
> (https://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-
>  
> ),
>  but there is a note "This works only if you haven’t pushed the change 
> causing the issue to the Bioconductor repository." I fall into this case.
> 
> If anyone has any suggestions for how to deal with this, I would appreciate 
> the help. If more information is required, please say so.
> 
> Thanks,
> Raymond Cavalcante
>   [[alternative HTML version deleted]]
> 
> ___
> 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 
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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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Re: [Bioc-devel] No write permissions to push changes to my devel package

[Turaga, Nitesh]

Hi,

You have submitted a wrong entry to the google form. 

Your package was issued an SVN ID, without submitting that we have no way of 
knowing that your submission is linked to the package BPRMeth. Please resubmit 
with the correct information as requested by the google form. 

Best,

Nitesh 


> On Jan 11, 2018, at 5:29 PM, Andreas Kapouranis 
>  wrote:
> 
> Hi,
> 
> I have developed a package BPRMeth in Bioconductor and now I want to make
> changes however it seems that I *do not have write permissions* to my own
> package in g...@git.bioconductor.org
> 
> I submitted my github ID (which contains my public SSH keys) to the google
> form (however I still have not received an email back).
> 
> When running:
> 
>> ssh -T g...@git.bioconductor.org
> 
> hello andreaskapou, this is ...
> 
> ...
> 
> R   packages/BPRMeth
> 
> ...
> 
> It shows I have only read permission and *not write permission* to my
> package BPRMeth.
> 
> For completeness here is the output of
> *git clone -v*
> 
> origin g...@github.com:andreaskapou/BPRMeth.git (fetch)
> 
> origin g...@github.com:andreaskapou/BPRMeth.git (push)
> 
> upstream g...@git.bioconductor.org:packages/BPRMeth.git (fetch)
> 
> upstream g...@git.bioconductor.org:packages/BPRMeth.git (push)
> 
> Thanks,
> CAK
> 
> --
> Chantriolnt - Andreas Kapourani
> PhD Candidate in Data Science,
> School of Informatics,
> University of Edinburgh
> http://homepages.inf.ed.ac.uk/s1263191/
> e-mail  : C.A.Kapourani.ed.ac.uk
>: kapouranis.andr...@gmail.com
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] Changing package maintainer: git credentials

[Turaga, Nitesh]

Hi Liz,

Please submit your GitHub Id twice in the google form. 

Once for the Github ID field, and another time for the SVN ID field. 

Is, n.harmston no longer a maintainer for that package? In which case I can 
update the entry and switch you to become the maintainer. Please cc him in the 
reply to this email. 

Best,

Nitesh 

> On Jan 13, 2018, at 2:48 PM, Liz Ing-Simmons  wrote:
> 
> Hi there,
> 
> I am a maintainer for the GenomicInteractions package, and I'd like to set
> up git access so that I can update the package. However I never had my own
> svn credentials, so I'm not sure what to put into the Google form. I
> couldn't figure out who to contact about this so I thought I'd ask here.
> 
> If it's helpful, the svn username for the previous maintainer is
> n.harmston, my github username is liz-is, and Github knows my ssh key.
> 
> Thanks,
> 
> Liz
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] "Duplicate commits" after when pushing change right after doing a clean `git clone g...@git.bioconductor.org:packages/chimeraviz`

[Turaga, Nitesh]

Hi Stian,

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

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

Best,

Nitesh 


> On Jan 13, 2018, at 12:35 PM, Stian Lågstad  wrote:
> 
> Hi,
> 
> Could someone help me get past the duplicate commits error? I'm not sure
> what to do.
> 
> These are the steps I've taken:
> 
> 1. Clone the repository. `git clone g...@git.bioconductor.org:packa
> ges/chimeraviz`
> 2. Make a small change in master + attempt to push it, and got this:
> ```
> ➜  chimeraviz-bioconductor git:(master) git push
> 
> Counting objects: 4, done.
> Delta compression using up to 8 threads.
> Compressing objects: 100% (4/4), done.
> Writing objects: 100% (4/4), 422 bytes | 0 bytes/s, done.
> 
> Total 4 (delta 3), reused 0 (delta 0)
> remote: Error: duplicate commits.
> remote:
> remote: There are duplicate commits in your commit history, These cannot be
> remote: pushed to the Bioconductor git server. Please make sure that this is
> remote: resolved.
> remote:
> remote: Take a look at the documentation to fix this,
> remote: https://bioconductor.org/developers/how-to/git/sync-
> existing-repositories/,
> remote: particularly, point #8 (force Bioconductor master to Github master).
> remote:
> remote: For more information, or help resolving this issue, contact
> remote: . Provide the error, the package name and
> remote: any other details we might need.
> remote:
> remote: Use
> remote:
> remote: git show 248742bd41a1b1d862d29e612baa067c50c55e5b
> remote: git show 81ee14920be186caf4f2949e7dacfad68db64ed2
> remote:
> remote: to see body of commits.
> remote:
> To g...@git.bioconductor.org:packages/chimeraviz
> 
> ! [remote rejected] master -> master (pre-receive hook declined)
> ```
> 
> I do see what looks like duplicate commits in the git log. For
> example ba964db26ac49e86a5374e0dc3040769ae799113
> and 8a49e3cdd1ce5257879d752aeead83813c6a4044, which are both from Sat Apr 8
> 17:45:42 2017. But I've been successful in making changes after april last
> year.
> 
> -- 
> Stian Lågstad
> +47 41 80 80 25
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] Problems creating a new GitHub repository for an existing Bioconductor package

[Turaga, Nitesh]

Hi,

Please keep following the instructions. You are on the right track. 

The keys have been processed and you should be able to add your upstream now.

Best,

Nitesh 

> On Jan 16, 2018, at 4:48 AM, Pau Bellot Pujalte  wrote:
> 
> Dear Bioconductor devel team,
> 
> I'm Pau bellot, author and maintainer of netbenchmark package
> . I
> have received some bug reports about my package and in the process of
> fixing them I have discovered that I did not migrate from SVN to GIT. I'm
> following the steps in
> https://bioconductor.org/developers/how-to/git/maintain-github-bioc/ but I
> don't succeed:
> 
>> git remote add upstream g...@git.bioconductor.org:packages/netbenchmark.git
>>> git fetch upstream
>> Permission denied (publickey).
>> fatal: Could not read from remote repository.
>> Please make sure you have the correct access rights and the repository
>> exists.
> 
> 
> Could you please help me to migrate to git?
> Thanks,
> Pau
> 
> Pd:  I have filled out the Google form for maintainers
> .
> Pd2: I have created a public repository in my git:
> https://github.com/paubellot/netbenchmark
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] Duplicate commits in Bioconductor commit history

[Turaga, Nitesh]

Hi Laurent,

After checking your package, it’s very hard to get rid of the duplicate commits 
at this stage of development. I don’t think it should effect the build process 
of your package. 

The only thing it might effect is, when you look back at a later time to 
specific commit which is duplicated there might be confusion for developers. 
Just as a helpful tip, duplicate commits happen when you “merge” different 
sources. So, be careful while merging in the future from a remote.

I’ve enabled you to push to your repository, so this does not hold up your 
development. 

Best,

Nitesh 

> On Jan 16, 2018, at 10:15 AM, Laurent Gatto  wrote:
> 
> 
> Dear all,
> 
> There are duplicated commit in the Bioconductor commit history of the
> qcmetrics package, which stop me from pushing additional changes. Here
> is an illustration of the problem:
> 
> $ git clone g...@git.bioconductor.org:packages/qcmetrics.git
> Cloning into 'qcmetrics'...
> cd remote: Counting objects: 973, done.
> remote: Compressing objects: 100% (429/429), done.
> remote: Total 973 (delta 614), reused 800 (delta 510)
> Receiving objects: 100% (973/973), 4.73 MiB | 1.82 MiB/s, done.
> Resolving deltas: 100% (614/614), done.
> Checking connectivity... done.
> $ cd qcmetrics
> $ echo >> DESCRIPTION
> $ git commit -am "just a test" 
> [master 209d6e3] just a test
> 1 file changed, 1 insertion(+)
> $ git push
> Counting objects: 23, done.
> Delta compression using up to 4 threads.
> Compressing objects: 100% (3/3), done.
> Writing objects: 100% (3/3), 280 bytes | 0 bytes/s, done.
> Total 3 (delta 2), reused 0 (delta 0)
> remote: Error: duplicate commits.
> remote: 
> remote: There are duplicate commits in your commit history, These cannot be
> remote: pushed to the Bioconductor git server. Please make sure that this is
> remote: resolved.
> remote: 
> remote: Take a look at the documentation to fix this,
> remote: 
> https://bioconductor.org/developers/how-to/git/sync-existing-repositories/,
> remote: particularly, point #8 (force Bioconductor master to Github master).
> remote: 
> remote: For more information, or help resolving this issue, contact
> remote: . Provide the error, the package name and
> remote: any other details we might need.
> remote: 
> remote: Use
> remote: 
> remote: git show fe33ea0a9221f5dbeea0581d1d2381df965d10ce
> remote: git show 2b089e21267bccbe23416bf756bff01036623aec
> remote: 
> remote: to see body of commits.
> remote: 
> To g...@git.bioconductor.org:packages/qcmetrics.git
> ! [remote rejected] master -> master (pre-receive hook declined)
> error: failed to push some refs to 
> 'g...@git.bioconductor.org:packages/qcmetrics.git'
> 
> If I look at the documentation suggested above, I understand that this
> is relevant for duplicated commits in github and bioconductor
> histories.
> 
> Any idea how to address this within Bioconductor?
> 
> Thank you in advance.
> 
> Laurent
> 
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Re: [Bioc-devel] "Duplicate commits" after when pushing change right after doing a clean `git clone g...@git.bioconductor.org:packages/chimeraviz`

[Turaga, Nitesh]

Hi Stian,

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

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

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

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

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

Best,

Nitesh 


> On Jan 13, 2018, at 8:36 PM, Turaga, Nitesh  
> wrote:
> 
> Hi Stian,
> 
> I’m looking into it. Your commit history seems to have a discontinuous 
> history of duplicates + non-duplicates caused by merge from different 
> sources. I’m yet to figure out how to solve this situation.
> 
> I will get back to you within a couple of days. 
> 
> Best,
> 
> Nitesh 
> 
> 
>> On Jan 13, 2018, at 12:35 PM, Stian Lågstad  wrote:
>> 
>> Hi,
>> 
>> Could someone help me get past the duplicate commits error? I'm not sure
>> what to do.
>> 
>> These are the steps I've taken:
>> 
>> 1. Clone the repository. `git clone g...@git.bioconductor.org:packa
>> ges/chimeraviz`
>> 2. Make a small change in master + attempt to push it, and got this:
>> ```
>> ➜  chimeraviz-bioconductor git:(master) git push
>> 
>> Counting objects: 4, done.
>> Delta compression using up to 8 threads.
>> Compressing objects: 100% (4/4), done.
>> Writing objects: 100% (4/4), 422 bytes | 0 bytes/s, done.
>> 
>> Total 4 (delta 3), reused 0 (delta 0)
>> remote: Error: duplicate commits.
>> remote:
>> remote: There are duplicate commits in your commit history, These cannot be
>> remote: pushed to the Bioconductor git server. Please make sure that this is
>> remote: resolved.
>> remote:
>> remote: Take a look at the documentation to fix this,
>> remote: https://bioconductor.org/developers/how-to/git/sync-
>> existing-repositories/,
>> remote: particularly, point #8 (force Bioconductor master to Github master).
>> remote:
>> remote: For more information, or help resolving this issue, contact
>> remote: . Provide the error, the package name and
>> remote: any other details we might need.
>> remote:
>> remote: Use
>> remote:
>> remote: git show 248742bd41a1b1d862d29e612baa067c50c55e5b
>> remote: git show 81ee14920be186caf4f2949e7dacfad68db64ed2
>> remote:
>> remote: to see body of commits.
>> remote:
>> To g...@git.bioconductor.org:packages/chimeraviz
>> 
>> ! [remote rejected] master -> master (pre-receive hook declined)
>> ```
>> 
>> I do see what looks like duplicate commits in the git log. For
>> example ba964db26ac49e86a5374e0dc3040769ae799113
>> and 8a49e3cdd1ce5257879d752aeead83813c6a4044, which are both from Sat Apr 8
>> 17:45:42 2017. But I've been successful in making changes after april last
>> year.
>> 
>> -- 
>> Stian Lågstad
>> +47 41 80 80 25
>> 
>>  [[alternative HTML version deleted]]
>> 
>> ___
>> 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 
> 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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Re: [Bioc-devel] Duplicate commit error when pushing to annotatr upstream/master

[Turaga, Nitesh]

Hi Raymond,

I have fixed your repository on Bioconductor, and you are able to push changes 
again. 

Duplicate commits are caused because of “merge” commits from remotes. Please 
make sure that before you push from hence forth, or merge, that the duplicate 
commit issue doesn’t reoccur.


Best,

Nitesh 

> On Jan 9, 2018, at 1:30 PM, Turaga, Nitesh  
> wrote:
> 
> Hi Raymond,
> 
> I’m trying to figure out why your problem was caused. The duplicates are 
> coming from this commit (ea6c6421b074dbc9411bd6d00547b90bb6168d31), which is 
> a merge. But I’m what I’m trying to figure out is how you’ve been able to 
> push with duplicate commits after that merge.
> 
> Please give me sometime.
> 
> I will get back to you.
> 
> Best,
> 
> Nitesh 
> 
>> On Jan 8, 2018, at 2:19 PM, Raymond Cavalcante  wrote:
>> 
>> Hello,
>> 
>> I’m running into the following error when trying to push some changes to 
>> annotatr upstream/master:
>> 
>>> rcavalca$ git push upstream master
>>> Counting objects: 6, done.
>>> Delta compression using up to 8 threads.
>>> Compressing objects: 100% (6/6), done.
>>> Writing objects: 100% (6/6), 854 bytes | 854.00 KiB/s, done.
>>> Total 6 (delta 5), 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: . Provide the error, the package name and
>>> remote: any other details we might need.
>>> remote: 
>>> remote: Use
>>> remote: 
>>> remote: git show ffdb09d480c01535466e89b99e22535672e362a7
>>> remote: git show 333da75f93af1ca7f5cb9a8443a1d5c963f21280
>>> remote: 
>>> remote: to see body of commits.
>>> remote: 
>>> To git.bioconductor.org:packages/annotatr.git
>>> ! [remote rejected] master -> master (pre-receive hook declined)
>>> error: failed to push some refs to 
>>> 'g...@git.bioconductor.org:packages/annotatr.git'
>> 
>> 
>> The two commits that are highlighted in the error message are "bump x.y.z 
>> versions to odd y after creation of 3_5 branch" commits. I was always 
>> confused about the git-svn bridge, but these twin commits are an artifact of 
>> that system, I think. The commit that I was trying to push to 
>> upstream/master is unrelated to those two commits, and I have committed 
>> other items in the new git way prior to the 3.6 release with no issue.
>> 
>> I tried the suggested solution 
>> (https://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-
>>  
>> <https://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github->),
>>  but there is a note "This works only if you haven’t pushed the change 
>> causing the issue to the Bioconductor repository." I fall into this case.
>> 
>> If anyone has any suggestions for how to deal with this, I would appreciate 
>> the help. If more information is required, please say so.
>> 
>> Thanks,
>> Raymond Cavalcante
>>  [[alternative HTML version deleted]]
>> 
>> ___
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>> 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 
> 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 
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Re: [Bioc-devel] "Duplicate commits" after when pushing change right after doing a clean `git clone g...@git.bioconductor.org:packages/chimeraviz`

[Turaga, Nitesh]

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

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

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

Your’s is a very unique case.

Best,

Nitesh 

> On Jan 17, 2018, at 1:22 PM, Stian Lågstad  wrote:
> 
> I usually create a seperate branch for work, which I merge into master when 
> I'm happy with the result. Will that be a problem? Should I rebase instead to 
> avoid it?
> 
> Thank you.
> 
> On Wed, Jan 17, 2018 at 6:48 PM, Turaga, Nitesh 
>  wrote:
> Hi Stian,
> 
> I’ve enabled you to push to your repository on Bioconductor.
> 
> Your duplicate commit history weaves in and out because of merges along the 
> way from your GitHub repository. At this point, there is very little I can do 
> to help unless I spend a lot of time on your package, manually fixing the 
> history.
> 
> The duplicate commits should not effect your package development, and you 
> should continue with it. It does not effect the build process as well.
> 
> If you feel like this is something you can fix from your end, by using “git 
> reset” and “git cherry-pick” you should feel free to fix. Let me know when 
> you are successful, and I can help you push the updated repo.
> 
> For the future, duplicate commits are caused by “merge” commands. You might 
> want to search for those if you want to know which commits are causing these 
> duplicates.
> 
> Best,
> 
> Nitesh
> 
> 
> > On Jan 13, 2018, at 8:36 PM, Turaga, Nitesh  
> > wrote:
> >
> > Hi Stian,
> >
> > I’m looking into it. Your commit history seems to have a discontinuous 
> > history of duplicates + non-duplicates caused by merge from different 
> > sources. I’m yet to figure out how to solve this situation.
> >
> > I will get back to you within a couple of days.
> >
> > Best,
> >
> > Nitesh
> >
> >
> >> On Jan 13, 2018, at 12:35 PM, Stian Lågstad  wrote:
> >>
> >> Hi,
> >>
> >> Could someone help me get past the duplicate commits error? I'm not sure
> >> what to do.
> >>
> >> These are the steps I've taken:
> >>
> >> 1. Clone the repository. `git clone g...@git.bioconductor.org:packa
> >> ges/chimeraviz`
> >> 2. Make a small change in master + attempt to push it, and got this:
> >> ```
> >> ➜  chimeraviz-bioconductor git:(master) git push
> >>
> >> Counting objects: 4, done.
> >> Delta compression using up to 8 threads.
> >> Compressing objects: 100% (4/4), done.
> >> Writing objects: 100% (4/4), 422 bytes | 0 bytes/s, done.
> >>
> >> Total 4 (delta 3), reused 0 (delta 0)
> >> remote: Error: duplicate commits.
> >> remote:
> >> remote: There are duplicate commits in your commit history, These cannot be
> >> remote: pushed to the Bioconductor git server. Please make sure that this 
> >> is
> >> remote: resolved.
> >> remote:
> >> remote: Take a look at the documentation to fix this,
> >> remote: https://bioconductor.org/developers/how-to/git/sync-
> >> existing-repositories/,
> >> remote: particularly, point #8 (force Bioconductor master to Github 
> >> master).
> >> remote:
> >> remote: For more information, or help resolving this issue, contact
> >> remote: . Provide the error, the package name and
> >> remote: any other details we might need.
> >> remote:
> >> remote: Use
> >> remote:
> >> remote: git show 248742bd41a1b1d862d29e612baa067c50c55e5b
> >> remote: git show 81ee14920be186caf4f2949e7dacfad68db64ed2
> >> remote:
> >> remote: to see body of commits.
> >> remote:
> >> To g...@git.bioconductor.org:packages/chimeraviz
> >>
> >> ! [remote rejected] master -> master (pre-receive hook declined)
> >> ```
> >>
> >> I do see what looks like duplicate commits in the git log. For
> >> example ba964db26ac49e86a5374e0dc3040769ae799113
> >> and 8a49e3cdd1ce5257879d752aeead83813c6a4044, which are both from Sat Apr 8
> >> 17:45:42 2017. But I've been successful in making changes after april last
> >> year.
> >>
> >> --
> >> Stian Lågstad
> >> +47 41 80 80 25
> >>
> >>  [[alternative HTML version deleted]]
> >>
>

Re: [Bioc-devel] git permission denied to synapter repository

[Turaga, Nitesh]

Hi Sebastian,

You did not do anything wrong. Laurent is the only one listed on the package so 
far. I will add you to it.

Laurent, just a heads up, I’m adding Sebastian to the “synapter" package. 

Best,

Nitesh 

> On Jan 17, 2018, at 4:07 PM, Sebastian Gibb  wrote:
> 
> Dear Bioconductor admins,
> 
> I am the (co-)maintainer of the synapter package.
> 
> I tried to push some changes the first time after the conversion to git and 
> got
> the following error:
> 
> ```
>> git push upstream master
> FATAL: W any packages/synapter s.gibb DENIED by fallthru
> (or you mis-spelled the reponame)
> fatal: Could not read from remote repository.
> 
> Please make sure you have the correct access rights
> and the repository exists.
> ```
> 
> s.gibb was my svn username on bioc. AFAIK the access to my other repositories
> (cleaver, topdownr) works as expected.
> 
> Did I something wrong?
> 
> Best wishes,
> 
> Sebastian
> 
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Re: [Bioc-devel] unable to push to bioconductor git

[Turaga, Nitesh]

Hi Davy,

omicsPrint has only m.iterson registered on our git server. 

I guess you are pulling and cloning using the “HTTPS” protocol instead of the 
SSH. It should reject you if you ask to clone using “git clone 
g...@git.bioconductor.org:packages/omicsPrint”. Please use the correct 
protocol, and if you have any further questions check out the FAQ section. 
(bioconductor.org/developers/how-to/git/faq/)

I will add you to the package. You should have access now. 

Best,

Nitesh 

> On Jan 18, 2018, at 4:46 AM, Davy Cats  wrote:
> 
> Dear bioconductor admins,
> 
> I am the maintainer of the omicsPrint package. Up until now the original
> creator of the package has been pushing all changes to the bioconductor
> git. When I try to push changes to the bioconductor git, however, I get the
> following message:
> 
> FATAL: W any packages/omicsPrint DavyCats DENIED by fallthru
> (or you mis-spelled the reponame)
> fatal: Could not read from remote repository.
> 
> Please make sure you have the correct access rights
> and the repository exists.
> 
> I have filled in the google form and my public ssh key is available through
> github. I am capable of pulling/cloning from the bioconductor git, so I'm
> assuming I don't have write permissions for the repository?
> 
> Best regards,
> Davy Cats
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] need git push permission for mtbls2

[Turaga, Nitesh]

Hi Stephan,

The key seems to be correct. You should have read and write access to that 
package.

I missed the fact that it was an experiment data package and not a software 
package. 

Thanks,

Nitesh 

> On Jan 19, 2018, at 3:29 AM, Neumann, Steffen  wrote:
> 
> Hi BioC team,
> 
> I have R W for several packages I am involved in, 
> but not for mtbls2 that I maintain. Please add W 
> for "s.neumann" for mtbls2 as well, or is there 
> any mistake on my side ? 
> 
> Thanks in advance, 
> yours, 
> Steffen
> 
> 
> R W   packages/msdata
> R packages/mtbls2
> R W   packages/mzR
> 
> sneumann@msbi-corei:/.../mtbls2$ git remote -v
> origing...@github.com:sneumann/mtbls2.git (fetch)
> origing...@github.com:sneumann/mtbls2.git (push)
> upstream  g...@git.bioconductor.org:packages/mtbls2.git (fetch)
> upstream  g...@git.bioconductor.org:packages/mtbls2.git (push)
> 
> -- 
> 
> IPB HalleAG Massenspektrometrie & Bioinformatik
> Dr. Steffen Neumann  http://www.IPB-Halle.DE
> Weinberg 3   http://msbi.bic-gh.de
> 06120 Halle  Tel. +49 (0) 345 5582 - 1470
>  +49 (0) 345 5582 - 0
> sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
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Re: [Bioc-devel] Duplicate commits for hpar was [Re: Duplicate commits in Bioconductor commit history]

[Turaga, Nitesh]

Hi Laurent,

If you check the package “hpar” with a fresh clone from git@git.bioconductor, 
you’ll see that it doesn’t have any duplicate commits now. 

I think only your local repository has duplicate commits. You’d have to fix 
this issue on your side. 

Best regards,

Nitesh 

> On Jan 19, 2018, at 11:37 AM, Laurent Gatto  wrote:
> 
> 
> Dear Nitesh,
> 
> I have the exact same issue with hpar:
> 
> Counting objects: 454, done.
> Delta compression using up to 4 threads.
> Compressing objects: 100% (167/167), done.
> Writing objects: 100% (359/359), 1.87 MiB | 0 bytes/s, done.
> Total 359 (delta 225), reused 314 (delta 186)
> remote: Resolving deltas: 100% (225/225), completed with 26 local objects.
> 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: . Provide the error, the package name and
> remote: any other details we might need.
> remote: 
> remote: Use
> remote: 
> remote: git show c7e7f60cf62745d1ef56c6e4afa2e125583bafb2
> remote: git show dfb82cec06e8b56d4b01ab0c313c658240ad1bae
> remote: 
> remote: to see body of commits.
> remote: 
> To g...@git.bioconductor.org:packages/hpar.git
> ! [remote rejected] master -> master (pre-receive hook declined)
> error: failed to push some refs to 
> 'g...@git.bioconductor.org:packages/hpar.git'
> 
> 
> I believe this is due to the old git-svn bridge, that resulted in the
> duplicated commits - via the git-svn bridge and then me merging into
> master on github.
> 
> Could you sort this out on your end so that I can fix my package,
> please.
> 
> Thank you very much in advance.
> 
> Best wishes,
> 
> Laurent
> 
> On 17 January 2018 17:40, Turaga, Nitesh wrote:
> 
>> Hi Laurent,
>> 
>> After checking your package, it’s very hard to get rid of the duplicate 
>> commits at this stage of development. I don’t think it should effect the 
>> build process of your package. 
>> 
>> The only thing it might effect is, when you look back at a later time to 
>> specific commit which is duplicated there might be confusion for developers. 
>> Just as a helpful tip, duplicate commits happen when you “merge” different 
>> sources. So, be careful while merging in the future from a remote.
>> 
>> I’ve enabled you to push to your repository, so this does not hold up your 
>> development. 
>> 
>> Best,
>> 
>> Nitesh 
>> 
>>> On Jan 16, 2018, at 10:15 AM, Laurent Gatto  wrote:
>>> 
>>> 
>>> Dear all,
>>> 
>>> There are duplicated commit in the Bioconductor commit history of the
>>> qcmetrics package, which stop me from pushing additional changes. Here
>>> is an illustration of the problem:
>>> 
>>> $ git clone g...@git.bioconductor.org:packages/qcmetrics.git
>>> Cloning into 'qcmetrics'...
>>> cd remote: Counting objects: 973, done.
>>> remote: Compressing objects: 100% (429/429), done.
>>> remote: Total 973 (delta 614), reused 800 (delta 510)
>>> Receiving objects: 100% (973/973), 4.73 MiB | 1.82 MiB/s, done.
>>> Resolving deltas: 100% (614/614), done.
>>> Checking connectivity... done.
>>> $ cd qcmetrics
>>> $ echo >> DESCRIPTION
>>> $ git commit -am "just a test" 
>>> [master 209d6e3] just a test
>>> 1 file changed, 1 insertion(+)
>>> $ git push
>>> Counting objects: 23, done.
>>> Delta compression using up to 4 threads.
>>> Compressing objects: 100% (3/3), done.
>>> Writing objects: 100% (3/3), 280 bytes | 0 bytes/s, done.
>>> Total 3 (delta 2), reused 0 (delta 0)
>>> remote: Error: duplicate commits.
>>> remote: 
>>> remote: There are duplicate commits in your commit history, These cannot be
>>> remote: pushed to the Bioconductor git server. Please make sure that this is
>>> remote: resolved.
>>> remote: 
>>> remote: Take a look at the documentation to fix this,
>>> remote: 
>>> https://bioconductor.org/developers/how-to/git/sync-existing-repositories/,
>>> remote: particularly, point #8 (force Biocon

Re: [Bioc-devel] Duplicate commits for hpar was [Re: Duplicate commits in Bioconductor commit history]

[Turaga, Nitesh]

The pre-receive hook is catching the duplicate commits on your local repository 
and preventing the push from contaminating the bioconductor version of the 
repository.

If you need help fixing your local repository, feel free to ask questions. Try 
to follow the link in error message and see if you can work through that.

Best regards,

Nitesh 



> On Jan 19, 2018, at 12:43 PM, ni41435_ca  
> wrote:
> 
> Hi Laurent,
> 
> If you check the package “hpar” with a fresh clone from git@git.bioconductor, 
> you’ll see that it doesn’t have any duplicate commits now. 
> 
> I think only your local repository has duplicate commits. You’d have to fix 
> this issue on your side. 
> 
> Best regards,
> 
> Nitesh 
> 
>> On Jan 19, 2018, at 11:37 AM, Laurent Gatto  wrote:
>> 
>> 
>> Dear Nitesh,
>> 
>> I have the exact same issue with hpar:
>> 
>> Counting objects: 454, done.
>> Delta compression using up to 4 threads.
>> Compressing objects: 100% (167/167), done.
>> Writing objects: 100% (359/359), 1.87 MiB | 0 bytes/s, done.
>> Total 359 (delta 225), reused 314 (delta 186)
>> remote: Resolving deltas: 100% (225/225), completed with 26 local objects.
>> 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: . Provide the error, the package name and
>> remote: any other details we might need.
>> remote: 
>> remote: Use
>> remote: 
>> remote: git show c7e7f60cf62745d1ef56c6e4afa2e125583bafb2
>> remote: git show dfb82cec06e8b56d4b01ab0c313c658240ad1bae
>> remote: 
>> remote: to see body of commits.
>> remote: 
>> To g...@git.bioconductor.org:packages/hpar.git
>> ! [remote rejected] master -> master (pre-receive hook declined)
>> error: failed to push some refs to 
>> 'g...@git.bioconductor.org:packages/hpar.git'
>> 
>> 
>> I believe this is due to the old git-svn bridge, that resulted in the
>> duplicated commits - via the git-svn bridge and then me merging into
>> master on github.
>> 
>> Could you sort this out on your end so that I can fix my package,
>> please.
>> 
>> Thank you very much in advance.
>> 
>> Best wishes,
>> 
>> Laurent
>> 
>> On 17 January 2018 17:40, Turaga, Nitesh wrote:
>> 
>>> Hi Laurent,
>>> 
>>> After checking your package, it’s very hard to get rid of the duplicate 
>>> commits at this stage of development. I don’t think it should effect the 
>>> build process of your package. 
>>> 
>>> The only thing it might effect is, when you look back at a later time to 
>>> specific commit which is duplicated there might be confusion for 
>>> developers. Just as a helpful tip, duplicate commits happen when you 
>>> “merge” different sources. So, be careful while merging in the future from 
>>> a remote.
>>> 
>>> I’ve enabled you to push to your repository, so this does not hold up your 
>>> development. 
>>> 
>>> Best,
>>> 
>>> Nitesh 
>>> 
>>>> On Jan 16, 2018, at 10:15 AM, Laurent Gatto  wrote:
>>>> 
>>>> 
>>>> Dear all,
>>>> 
>>>> There are duplicated commit in the Bioconductor commit history of the
>>>> qcmetrics package, which stop me from pushing additional changes. Here
>>>> is an illustration of the problem:
>>>> 
>>>> $ git clone g...@git.bioconductor.org:packages/qcmetrics.git
>>>> Cloning into 'qcmetrics'...
>>>> cd remote: Counting objects: 973, done.
>>>> remote: Compressing objects: 100% (429/429), done.
>>>> remote: Total 973 (delta 614), reused 800 (delta 510)
>>>> Receiving objects: 100% (973/973), 4.73 MiB | 1.82 MiB/s, done.
>>>> Resolving deltas: 100% (614/614), done.
>>>> Checking connectivity... done.
>>>> $ cd qcmetrics
>>>> $ echo >> DESCRIPTION
>>>> $ git commit -am "just a test" 
>>>> [master 209d6e3] just a test
>>&g

Re: [Bioc-devel] Duplicate commits for hpar was [Re: Duplicate commits in Bioconductor commit history]

[Turaga, Nitesh]

You want to follow 

http://bioconductor.org/developers/how-to/git/sync-existing-repositories/

And look at #8 in that page,

http://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-

You should follow this and try once more.

Nitesh 

> On Jan 19, 2018, at 12:54 PM, Laurent Gatto  wrote:
> 
> 
> On 19 January 2018 17:47, Turaga, Nitesh wrote:
> 
>> The pre-receive hook is catching the duplicate commits on your local
>> repository and preventing the push from contaminating the bioconductor
>> version of the repository.
>> 
>> If you need help fixing your local repository, feel free to ask
>> questions. Try to follow the link in error message and see if you can
>> work through that.
> 
> A fresh clone from github, new and fetched remotes from bioc gives me
> 
> $ git push
> To g...@git.bioconductor.org:packages/hpar.git
> ! [rejected]master -> master (non-fast-forward)
> error: failed to push some refs to 
> 'g...@git.bioconductor.org:packages/hpar.git'
> hint: Updates were rejected because a pushed branch tip is behind its remote
> hint: counterpart. Check out this branch and integrate the remote changes
> hint: (e.g. 'git pull ...') before pushing again.
> hint: See the 'Note about fast-forwards' in 'git push --help' for details.
> 
> But it works when I clone from bioc directly.
> 
> I'll look into this another day, as I have to go now.
> 
> Thank you for your help.
> 
> Best wishes,
> 
> Laurent
> 
>> Best regards,
>> 
>> Nitesh 
>> 
>> 
>> 
>>> On Jan 19, 2018, at 12:43 PM, ni41435_ca  
>>> wrote:
>>> 
>>> Hi Laurent,
>>> 
>>> If you check the package “hpar” with a fresh clone from 
>>> git@git.bioconductor, you’ll see that it doesn’t have any duplicate commits 
>>> now. 
>>> 
>>> I think only your local repository has duplicate commits. You’d have to fix 
>>> this issue on your side. 
>>> 
>>> Best regards,
>>> 
>>> Nitesh 
>>> 
>>>> On Jan 19, 2018, at 11:37 AM, Laurent Gatto  wrote:
>>>> 
>>>> 
>>>> Dear Nitesh,
>>>> 
>>>> I have the exact same issue with hpar:
>>>> 
>>>> Counting objects: 454, done.
>>>> Delta compression using up to 4 threads.
>>>> Compressing objects: 100% (167/167), done.
>>>> Writing objects: 100% (359/359), 1.87 MiB | 0 bytes/s, done.
>>>> Total 359 (delta 225), reused 314 (delta 186)
>>>> remote: Resolving deltas: 100% (225/225), completed with 26 local objects.
>>>> 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: . Provide the error, the package name and
>>>> remote: any other details we might need.
>>>> remote: 
>>>> remote: Use
>>>> remote: 
>>>> remote: git show c7e7f60cf62745d1ef56c6e4afa2e125583bafb2
>>>> remote: git show dfb82cec06e8b56d4b01ab0c313c658240ad1bae
>>>> remote: 
>>>> remote: to see body of commits.
>>>> remote: 
>>>> To g...@git.bioconductor.org:packages/hpar.git
>>>> ! [remote rejected] master -> master (pre-receive hook declined)
>>>> error: failed to push some refs to 
>>>> 'g...@git.bioconductor.org:packages/hpar.git'
>>>> 
>>>> 
>>>> I believe this is due to the old git-svn bridge, that resulted in the
>>>> duplicated commits - via the git-svn bridge and then me merging into
>>>> master on github.
>>>> 
>>>> Could you sort this out on your end so that I can fix my package,
>>>> please.
>>>> 
>>>> Thank you very much in advance.
>>>> 
>>>> Best wishes,
>>>> 
>>>> Laurent
>>>> 
>>>> On 17 January 2018 17:40, Turaga, Nites

Re: [Bioc-devel] Push to git not updating correctly

[Turaga, Nitesh]

Hi,

I have checked your package and have not seen a commit after 

commit 84c72291990fadd47b657b410e37b52d6b68f008
Author: Clare Pacini 
Date:   Tue Oct 31 15:52:53 2017 +

Update egs


Please make sure you are pushing not just to your GitHub, but also to the 
bioconductor git repo. 

Best,

Nitesh 


> On Jan 19, 2018, at 10:24 AM, Clare Pacini  wrote:
> 
> Hi all,
> 
> I have pushed changes to the DrugVsDisease repository and have been able to 
> verify these changes are present in the git repository (after adding it to my 
> GitHub account and checking for the changes). However, it seems that an old 
> version is still be checked in the daily reports - and are reporting TIMEOUT 
> issues.
> 
> Any ideas as to what I am missing here?
> 
> Thanks
> 
> Clare
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Re: [Bioc-devel] Permission denied when fetching from BioC GitHub repository

[Turaga, Nitesh]

Hi 

Only packages maintained by Bioconductor are at that location 
gitHub.com/Bioconductor.  Your package is not maintained by the core-team in 
Bioconductor, so, it does not belong in that location.

We follow the same process as all the maintainers, we have a Github repo to 
take advantage of the social coding practices, and the canonical Bioconductor 
git server which acts as the central server for bioconductor packages.

I hope this answers your question.

Best,

Nitesh 

> On Jan 24, 2018, at 11:24 AM, Federico C  wrote:
> 
> Hi Valerie,
> 
> the ssh key has now been setup and it works. I had some issues with merging 
> but at the end I decided to force BioC master to GitHub master (following 
> https://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-
>  
> ).
>  Afterwards, I pushed the bug fix to both origin and upstream remotes (master 
> branch). Indeed:
> 
> | => git status
> On branch master
> Your branch is up-to-date with 'upstream/master'.
> 
> nothing to commit, working tree clean
> 
> However, shouldn’t wavClusteR be listed at https://github.com/Bioconductor 
>  at this point?
> 
> Thanks a lot for your help.
> Best wishes,
> 
> Federico
> 
> 
> 
> 
> 
>> On 23 Jan 2018, at 20:50, Federico C  wrote:
>> 
>> Hi Valerie,
>> 
>> done. Thanks a lot,
>> 
>> Federico
>> 
>>> On 23 Jan 2018, at 20:18, Obenchain, Valerie 
>>> >> > wrote:
>>> 
>>> Hi Federico,
>>> 
>>> We don't have an ssh key on file for you. Please add one by following 
>>> instructions at the link below and use the ID of 'f.comoglio':
>>> 
>>> https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform
>>>  
>>> 
>>> 
>>> You will get an email in the next 24 hours if the submission was successful.
>>> 
>>> Valerie
>>> 
>>> On 01/23/2018 09:47 AM, Federico C wrote:
 Dear all,
 
 I’m trying to push a bug fix for wavClusteR to the BioC GitHub repository. 
 I currently pushed the latest package version to the devel and master 
 branch of my GitHub repository 
 (https://github.com/FedericoComoglio/wavClusteR 
  
  
 ).
 
 To sync these changes with the bioC GitHub repository, I have followed the 
 documentation at https://bioconductor.org/developers/how-to/git/ 
  
  
  . However, even though I 
 added an upstream remote to my repository and added a public key as 
 described, when I fetch updates from all (see 
 https://bioconductor.org/developers/how-to/git/sync-existing-repositories/ 
 
  
 
  
 )
  I get
 
 | => git fetch --all
 Fetching origin
 Fetching upstream
 g...@git.bioconductor.org  
  : 
 Permission denied (publickey).
 fatal: Could not read from remote repository.
 
 Please make sure you have the correct access rights
 and the repository exists.
 error: Could not fetch upstream
 
 Could you please help me with this issue?
 
 Thanks a lot for your time and patience.
 
 Best wishes,
 Federico
[[alternative HTML version deleted]]
 
 ___
 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 
>>> 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.
>> 
> 
> 
>   [[alternative HTML version deleted]]
> 
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Thi

Re: [Bioc-devel] Duplicate Commits in ASSIGN Package

[Turaga, Nitesh]

Hi David,

I can take a look at your package later today on your Github and update the 
version on Bioconductor if everything looks good. 

The reason you are not able to push is because we prevent “force” pushes on the 
bioconductor git server from maintainers.

Give me sometime and I’ll get back to you.

Best,

Nitesh 


> On Jan 24, 2018, at 12:48 PM, Jenkins, David  wrote:
> 
> Hi All,
> 
> I’m the maintainer of the ASSIGN package. It’s currently failing the devel 
> build and when I tried to push a fix for that I noticed that we have a lot of 
> duplicate commits in the history from a while back, I think from the git-svn 
> bridge.
> 
> I rebased and removed all of the duplicate commits and the deduped version is 
> on our github:
> 
> https://github.com/compbiomed/ASSIGN
> 
> Can you help me replace the duplicated version with the new version?
> 
> Thanks,
> 
> David
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] updating Bioconductor package that is already on Github

[Turaga, Nitesh]

Hi

You are using the wrong key.

The key we have on file for you is

ssh-rsa 
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


You should use a private key corresponding to that public key.

Best,

Nitesh 

> On Jan 26, 2018, at 12:05 PM, Simina Boca  wrote:
> 
> Dear all,
> Thank you to Sean, Lori, and Nitesh for helping me out with a package update 
> last year. I'm now trying to update another package, MultiMed. I have it set 
> up on Github https://github.com/SiminaB/MultiMed - you can see that the 
> contributors are Marc, Herve, and Dan Tenenbaum.
> However, I get the same error as I got before when doing "git push upstream 
> master":
> Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to 
> the list of known hosts.
> Enter passphrase for key '/c/Users/sboca/.ssh/id_rsa':
> FATAL: W any packages/swfdr SiminaB DENIED by fallthru
> (or you mis-spelled the reponame)
> fatal: Could not read from remote repository.
> 
> Please make sure you have the correct access rights
> and the repository exists.
> 
> Do I need to submit anything else or should BioC already know that I'm the 
> same person who is managing these packages?
> 
> Thanks so much!
> 
> Cheers,
> Simina
> 
> 
> On Tue, Sep 12, 2017 at 10:17 AM, Turaga, Nitesh 
>  wrote:
> Hi Simina,
> 
> Please try again now.
> 
> The issue was you didn’t submit your SVN ID “s.boca”. This is needed for 
> people who have been maintainers before the Git transition, to associate your 
> key to the package.
> 
> For new packages this issue doesn’t apply, because we just collect their 
> Github IDs.
> 
> Hope this helps.
> 
> Best,
> 
> Nitesh
> 
> > On Sep 11, 2017, at 2:50 PM, Simina Boca  wrote:
> >
> > Thank you again Sean and Lori! I am now past that initial stage. I now have
> > to resolve merge conflicts, primarily in the DESCRIPTION file. When
> > following the instructions here http://bioconductor.org/
> > developers/how-to/git/resolve-conflicts/ however, I ended up getting the
> > error below:
> >
> > ~\Documents\GitHub\swfdr [master ≡ +0 ~0 -1 !]> git push upstream master
> > Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to
> > the list of known hosts.
> > Enter passphrase for key '/c/Users/sboca/.ssh/id_rsa':
> > FATAL: W any packages/swfdr SiminaB DENIED by fallthru
> > (or you mis-spelled the reponame)
> > fatal: Could not read from remote repository.
> >
> > Please make sure you have the correct access rights
> > and the repository exists.
> >
> > Thank you so much!
> >
> > Best,
> > Simina
> >
> >
> > On Wed, Sep 6, 2017 at 10:56 AM, Simina Boca  wrote:
> >
> >> Thank you so much Sean and Lori! For some reason I thought the ssh key
> >> part was only relevant if the package was submitted via svn, which is why i
> >> had overlooked those instructions initially.
> >>
> >> Cheers,
> >> Simina
> >>
> >> On Wed, Sep 6, 2017 at 7:01 AM, Shepherd, Lori <
> >> lori.sheph...@roswellpark.org> wrote:
> >>
> >>> Have you submitted your ssh key
> >>>
> >>>
> >>> https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480v
> >>> o4tNufs0ziNyNmexegNZgNieIovbAA/viewform
> >>>
> >>> <https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform>
> >>> git / svn transition: ssh keys
> >>> <https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform>
> >>> docs.google.com
> >>> Use this form to link your existing svn credentials with access
> >>> permissions to the new Bioconductor git repository. To do this, we need an
> >>> ssh public key. You might have added these to github, see
> >>> https://github.com/your-github-id.keys. Alternatively, y

Re: [Bioc-devel] updating Bioconductor package that is already on Github

[Turaga, Nitesh]

Hi Simina,

I’m assuming your keys are stored in the folder “.ssh”. If that is the case, 
try,

 ssh-keygen -y -e -f 

That command will print out a public key. If that public key is the same as the 
one I’ve sent you, they you can use that. (Remember that public keys, don’t 
have “.pub” ending. If your public key is called “id_rsa.pub” then your private 
key is most likely, “id_rsa”). 

If you have to configure your git login, please follow the link below to make 
sure that the same key is used

http://bioconductor.org/developers/how-to/git/faq/

Best,

Nitesh 


> On Jan 26, 2018, at 12:36 PM, Simina Boca  wrote:
> 
> Thank you Nitesh! Where should I use the private key? I only see the public 
> key mentioned here: 
> http://bioconductor.org/developers/how-to/git/maintain-github-bioc/ Sorry if 
> I'm missing something very obvious!
> 
> Best,
> Simina
> 
> On Fri, Jan 26, 2018 at 12:23 PM, Turaga, Nitesh 
>  wrote:
> Hi
> 
> You are using the wrong key.
> 
> The key we have on file for you is
> 
> ssh-rsa 
> 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
> 
> 
> You should use a private key corresponding to that public key.
> 
> Best,
> 
> Nitesh
> 
> > On Jan 26, 2018, at 12:05 PM, Simina Boca  wrote:
> >
> > Dear all,
> > Thank you to Sean, Lori, and Nitesh for helping me out with a package 
> > update last year. I'm now trying to update another package, MultiMed. I 
> > have it set up on Github https://github.com/SiminaB/MultiMed - you can see 
> > that the contributors are Marc, Herve, and Dan Tenenbaum.
> > However, I get the same error as I got before when doing "git push upstream 
> > master":
> > Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to 
> > the list of known hosts.
> > Enter passphrase for key '/c/Users/sboca/.ssh/id_rsa':
> > FATAL: W any packages/swfdr SiminaB DENIED by fallthru
> > (or you mis-spelled the reponame)
> > fatal: Could not read from remote repository.
> >
> > Please make sure you have the correct access rights
> > and the repository exists.
> >
> > Do I need to submit anything else or should BioC already know that I'm the 
> > same person who is managing these packages?
> >
> > Thanks so much!
> >
> > Cheers,
> > Simina
> >
> >
> > On Tue, Sep 12, 2017 at 10:17 AM, Turaga, Nitesh 
> >  wrote:
> > Hi Simina,
> >
> > Please try again now.
> >
> > The issue was you didn’t submit your SVN ID “s.boca”. This is needed for 
> > people who have been maintainers before the Git transition, to associate 
> > your key to the package.
> >
> > For new packages this issue doesn’t apply, because we just collect their 
> > Github IDs.
> >
> > Hope this helps.
> >
> > Best,
> >
> > Nitesh
> >
> > > On Sep 11, 2017, at 2:50 PM, Simina Boca  wrote:
> > >
> > > Thank you again Sean and Lori! I am now past that initial stage. I now 
> > > have
> > > to resolve merge conflicts, primarily in the DESCRIPTION file. When
> > > following the instructions here http://bioconductor.org/
> > > developers/how-to/git/resolve-conflicts/ however, I ended up getting the
> > > error below:
> > >
> > > ~\Documents\GitHub\swfdr [master ≡ +0 ~0 -1 !]> git push upstream master
> > > Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to
> > > the list of known hosts.
> > > Enter passphrase for key '/c/Users/sboca/.ssh/id_rsa':
> > > FATAL: W any packages/swfdr SiminaB DENIED by fallthru
> > > (or you mis-spelled the reponame)
> > > fatal: Could not read from remote repository.
> > >
> > > Please make sure you have the correct access rights
> > > and the repository exists.
> > >
> > > Thank you so much!
> > >
> > > Best,
> > > Simina
> > >
> > >

Re: [Bioc-devel] updating Bioconductor package that is already on Github

[Turaga, Nitesh]

Yes, that is the key we have. 

Please send me more information,( output of these commands)


git remote -v

ssh -T g...@git.bioconductor.org | grep swfdr

You might want to make sure you are using correct private key by setting up a 
config file in your SSH. (http://bioconductor.org/developers/how-to/git/faq/ 
section point 16)


Nitesh 

> On Jan 30, 2018, at 8:47 PM, Simina Boca  wrote:
> 
> Hi Nitesh,
> 
> I submitted this key as well a couple of days ago:
> ssh-rsa 
> 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
>  smb...@georgetown.edu
> Do you have this matched up with my account right now? I'm still getting the 
> error message when trying to push upstream.
> 
> Thanks so much for all your help!
> 
> Best,
> Simina
> 
> 
> On Sun, Jan 28, 2018 at 9:53 AM, Simina Boca  wrote:
> Thanks so much Nitesh! I had submitted my public key last time I did this (a 
> few months ago) so I thought I didn't have to do it again. However, for 
> whatever reason, the public key you sent is a bit different from mine (not 
> sure why, since I haven't generated any more since then). In any case, I just 
> used the google form to submit my public key.
> 
> Cheers,
> Simina
> 
> On Fri, Jan 26, 2018 at 12:44 PM, Turaga, Nitesh 
>  wrote:
> Hi Simina,
> 
> I’m assuming your keys are stored in the folder “.ssh”. If that is the case, 
> try,
> 
>  ssh-keygen -y -e -f 
> 
> That command will print out a public key. If that public key is the same as 
> the one I’ve sent you, they you can use that. (Remember that public keys, 
> don’t have “.pub” ending. If your public key is called “id_rsa.pub” then your 
> private key is most likely, “id_rsa”).
> 
> If you have to configure your git login, please follow the link below to make 
> sure that the same key is used
> 
> http://bioconductor.org/developers/how-to/git/faq/
> 
> Best,
> 
> Nitesh
> 
> 
> > On Jan 26, 2018, at 12:36 PM, Simina Boca  wrote:
> >
> > Thank you Nitesh! Where should I use the private key? I only see the public 
> > key mentioned here: 
> > http://bioconductor.org/developers/how-to/git/maintain-github-bioc/ Sorry 
> > if I'm missing something very obvious!
> >
> > Best,
> > Simina
> >
> > On Fri, Jan 26, 2018 at 12:23 PM, Turaga, Nitesh 
> >  wrote:
> > Hi
> >
> > You are using the wrong key.
> >
> > The key we have on file for you is
> >
> > ssh-rsa 
> > 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
> >
> >
> > You should use a private key corresponding to that public key.
> >
> > Best,
> >
> > Nitesh
> >
> > > On Jan 26, 2018, at 12:05 PM, Simina Boca  wrote:
> > >
> > > Dear all,
> > > Thank you to Sean, Lori, and Nitesh for helping me out with a package 
> > > update last year. I'm now trying to update another package, MultiMed. I 
> > > have it set up on Github https://github.com/SiminaB/MultiMed - you can 
> > > see that the contributors are Marc, Herve, and Dan Tenenbaum.
> > > However, I get the same error as I got before when doing "git push 
> > > upstream master":
> > > Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) 
> > > to the list of known hosts.
> > > Enter passphrase for key '/c/Users/sboca/.ssh/id_rsa&#

Re: [Bioc-devel] updating Bioconductor package that is already on Github

[Turaga, Nitesh]

Hi Simina,

You should have access now. The missing information in all the previous 
communications was the name of the package you were trying to access.

Nitesh
> On Jan 30, 2018, at 10:51 PM, Simina Boca  wrote:
> 
> Sure! This is for the MultiMed package, not swfdr, so I made that change 
> below:
> 
> ~\Documents\GitHub\MultiMed [master ≡]> git remote -v
> origin  https://github.com/SiminaB/MultiMed.git (fetch)
> origin  https://github.com/SiminaB/MultiMed.git (push)
> upstreamg...@git.bioconductor.org:packages/MultiMed.git (fetch)
> upstreamg...@git.bioconductor.org:packages/MultiMed.git (push)
> 
> ~\Documents\GitHub\MultiMed [master ≡]> ssh -T g...@git.bioconductor.org | 
> grep MultiMed
> Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to 
> the list of known hosts.
>  R  packages/MultiMed
> 
> The file containing my public key is named id_rsa.pub and the one containing 
> my private key is id_rsa, so I think that should be OK...
> 
> Best,
> Simina
> 
> 
> On Tue, Jan 30, 2018 at 9:36 PM, Turaga, Nitesh 
>  wrote:
> Yes, that is the key we have.
> 
> Please send me more information,( output of these commands)
> 
> 
> git remote -v
> 
> ssh -T g...@git.bioconductor.org | grep swfdr
> 
> You might want to make sure you are using correct private key by setting up a 
> config file in your SSH. (http://bioconductor.org/developers/how-to/git/faq/ 
> section point 16)
> 
> 
> Nitesh
> 
> > On Jan 30, 2018, at 8:47 PM, Simina Boca  wrote:
> >
> > Hi Nitesh,
> >
> > I submitted this key as well a couple of days ago:
> > ssh-rsa 
> > 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
> >  smb...@georgetown.edu
> > Do you have this matched up with my account right now? I'm still getting 
> > the error message when trying to push upstream.
> >
> > Thanks so much for all your help!
> >
> > Best,
> > Simina
> >
> >
> > On Sun, Jan 28, 2018 at 9:53 AM, Simina Boca  wrote:
> > Thanks so much Nitesh! I had submitted my public key last time I did this 
> > (a few months ago) so I thought I didn't have to do it again. However, for 
> > whatever reason, the public key you sent is a bit different from mine (not 
> > sure why, since I haven't generated any more since then). In any case, I 
> > just used the google form to submit my public key.
> >
> > Cheers,
> > Simina
> >
> > On Fri, Jan 26, 2018 at 12:44 PM, Turaga, Nitesh 
> >  wrote:
> > Hi Simina,
> >
> > I’m assuming your keys are stored in the folder “.ssh”. If that is the 
> > case, try,
> >
> >  ssh-keygen -y -e -f 
> >
> > That command will print out a public key. If that public key is the same as 
> > the one I’ve sent you, they you can use that. (Remember that public keys, 
> > don’t have “.pub” ending. If your public key is called “id_rsa.pub” then 
> > your private key is most likely, “id_rsa”).
> >
> > If you have to configure your git login, please follow the link below to 
> > make sure that the same key is used
> >
> > http://bioconductor.org/developers/how-to/git/faq/
> >
> > Best,
> >
> > Nitesh
> >
> >
> > > On Jan 26, 2018, at 12:36 PM, Simina Boca  wrote:
> > >
> > > Thank you Nitesh! Where should I use the private key? I only see the 
> > > public key mentioned here: 
> > > http://bioconductor.org/developers/how-to/git/maintain-github-bioc/ Sorry 
> > > if I'm missing something very obvious!
> > >
> > > Best,
> > > Simina
> > >
> > > On Fri, Jan 26, 2018 at 12:23 PM, Turaga, Nitesh 
> > >  wrote:
> > > Hi
> > >
> > > You are using the wrong key.
> > >
> > > The key we have on file for you is
> > >
> > > ssh-rsa 
> > > B3NzaC1yc2EDAQABAAACAQDk1ywCtjVfC0wewYRCvzEiAac3so7nnRISC6

Re: [Bioc-devel] Duplicate Commits in ASSIGN Package

[Turaga, Nitesh]

Hi David,

Your master branch is fine now. I have updated bioconductor to reflect your 
master branch. 

But you need to do the same thing to RELEASE_3_6 as well. There are duplicate 
commits on that branch.

Please let me know once you have fixed your RELEASE_3_6.

Best,

Nitesh 

> On Jan 31, 2018, at 11:50 AM, Jenkins, David  wrote:
> 
> Hi Nitesh,
> 
> Any updates on this? Thanks for your help.
> 
> David
> 
> On 1/24/18, 2:08 PM, "Turaga, Nitesh"  wrote:
> 
>Hi David,
> 
>I can take a look at your package later today on your Github and update 
> the version on Bioconductor if everything looks good. 
> 
>The reason you are not able to push is because we prevent “force” pushes 
> on the bioconductor git server from maintainers.
> 
>Give me sometime and I’ll get back to you.
> 
>Best,
> 
>Nitesh 
> 
> 
>> On Jan 24, 2018, at 12:48 PM, Jenkins, David  wrote:
>> 
>> Hi All,
>> 
>> I’m the maintainer of the ASSIGN package. It’s currently failing the devel 
>> build and when I tried to push a fix for that I noticed that we have a lot 
>> of duplicate commits in the history from a while back, I think from the 
>> git-svn bridge.
>> 
>> I rebased and removed all of the duplicate commits and the deduped version 
>> is on our github:
>> 
>> https://github.com/compbiomed/ASSIGN
>> 
>> Can you help me replace the duplicated version with the new version?
>> 
>> Thanks,
>> 
>> David
>> 
>>  [[alternative HTML version deleted]]
>> 
>> ___
>> 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 
> 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 
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> 



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Re: [Bioc-devel] Duplicate Commits in ASSIGN Package

[Turaga, Nitesh]

Should be all fixed now. 


Best,

Nitesh 
> On Jan 31, 2018, at 12:31 PM, Jenkins, David  wrote:
> 
> Sorry about that, the RELEASE_3_6 branch on our github should be fixed now:
> https://github.com/compbiomed/ASSIGN/commits/RELEASE_3_6
> 
> Thanks,
> 
> David
> 
> On 1/31/18, 12:00 PM, "Turaga, Nitesh"  wrote:
> 
>Hi David,
> 
>Your master branch is fine now. I have updated bioconductor to reflect 
> your master branch. 
> 
>But you need to do the same thing to RELEASE_3_6 as well. There are 
> duplicate commits on that branch.
> 
>Please let me know once you have fixed your RELEASE_3_6.
> 
>Best,
> 
>Nitesh 
> 
>> On Jan 31, 2018, at 11:50 AM, Jenkins, David  wrote:
>> 
>> Hi Nitesh,
>> 
>> Any updates on this? Thanks for your help.
>> 
>> David
>> 
>> On 1/24/18, 2:08 PM, "Turaga, Nitesh"  wrote:
>> 
>>   Hi David,
>> 
>>   I can take a look at your package later today on your Github and update 
>> the version on Bioconductor if everything looks good. 
>> 
>>   The reason you are not able to push is because we prevent “force” pushes 
>> on the bioconductor git server from maintainers.
>> 
>>   Give me sometime and I’ll get back to you.
>> 
>>   Best,
>> 
>>   Nitesh 
>> 
>> 
>>> On Jan 24, 2018, at 12:48 PM, Jenkins, David  wrote:
>>> 
>>> Hi All,
>>> 
>>> I’m the maintainer of the ASSIGN package. It’s currently failing the devel 
>>> build and when I tried to push a fix for that I noticed that we have a lot 
>>> of duplicate commits in the history from a while back, I think from the 
>>> git-svn bridge.
>>> 
>>> I rebased and removed all of the duplicate commits and the deduped version 
>>> is on our github:
>>> 
>>> https://github.com/compbiomed/ASSIGN
>>> 
>>> Can you help me replace the duplicated version with the new version?
>>> 
>>> Thanks,
>>> 
>>> David
>>> 
>>> [[alternative HTML version deleted]]
>>> 
>>> ___
>>> 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 
>> 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 
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recipient(s), you are hereby notified that any disclosure, copying, 
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this message in error, please notify the sender immediately by e-mail and 
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