date:20210727

Re: [Bioc-devel] pre-receive hook declined

2021-07-27 Thread Clay Wright

Well at least it’s an embarrassingly easy fix!

Thanks all for the responses.


On Tue, Jul 27, 2021 at 8:06 PM Vincent Carey 
wrote:

> hi you can't update 3.12  3.x is frozen when 3.(x+1) becomes release
> perhaps the error message can be clarified
>
> On Tue, Jul 27, 2021 at 3:44 PM Clay Wright  wrote:
>
>> Hi,
>>
>> I am now encountering the following similar error trying to push a bugfix
>> to my package. Does my account also need a similar update to Victor and
>> Mike? Or is this something on my end? I just finally updated my github
>> personal access tokens, maybe that's the issue? I haven't tried a fresh
>> clone of the repository yet.
>>
>>
>> git push origin RELEASE_3_12
>>
>> Enumerating objects: 17, done.
>> Counting objects: 100% (17/17), done.
>> Delta compression using up to 4 threads
>> Compressing objects: 100% (12/12), done.
>> Writing objects: 100% (12/12), 1.48 KiB | 151.00 KiB/s, done.
>> Total 12 (delta 9), reused 0 (delta 0), pack-reused 0
>> remote: FATAL: W refs/heads/RELEASE_3_12 packages/flowTime r.wright DENIED
>> by fallthru
>> remote: error: hook declined to update refs/heads/RELEASE_3_12
>> To git.bioconductor.org:packages/flowTime.git
>>  ! [remote rejected] RELEASE_3_12 -> RELEASE_3_12 (hook declined)
>> error: failed to push some refs to 'git.bioconductor.org:
>> packages/flowTime.git'
>>
>>
>> Thanks!
>> Clay
>>
>>
>> On Fri, Jul 2, 2021 at 1:30 PM Victor Yuan  wrote:
>>
>> > It works for me as well now. Thanks!
>> >
>> > On Thu, Jul 1, 2021 at 8:21 AM Michael Love <
>> michaelisaiahl...@gmail.com>
>> > wrote:
>> >
>> > > That works for me. Thanks.
>> > >
>> > > Mike
>> > >
>> > > On Thu, Jul 1, 2021 at 2:07 PM Nitesh Turaga 
>> > > wrote:
>> > > >
>> > > > Hi
>> > > >
>> > > > Please try again. You should not see this error anymore.
>> > > >
>> > > > This was a mistake on our end.
>> > > >
>> > > > Best,
>> > > >
>> > > > Nitesh
>> > > >
>> > > >
>> > > >
>> > > > Nitesh Turaga
>> > > > Scientist II, Department of Data Science,
>> > > > Bioconductor Core Team Member
>> > > > Dana Farber Cancer Institute
>> > > >
>> > > > > On Jul 1, 2021, at 1:49 AM, Michael Love <
>> > michaelisaiahl...@gmail.com>
>> > > wrote:
>> > > > >
>> > > > > I'm getting a similar error, trying to push commits for a new
>> package
>> > > > > submission. So this is my first attempt to push to Bioc git
>> servers
>> > > > > for this package.
>> > > > >
>> > > > > After following instructions from
>> > > > >
>> https://bioconductor.org/developers/how-to/git/new-package-workflow/
>> > > > > ...
>> > > > >
>> > > > > spatialDmelxsim git:(main) > git push upstream main:master
>> > > > > Enumerating objects: 20, done.
>> > > > > Counting objects: 100% (20/20), done.
>> > > > > Delta compression using up to 8 threads
>> > > > > Compressing objects: 100% (10/10), done.
>> > > > > Writing objects: 100% (12/12), 1.60 KiB | 1.60 MiB/s, done.
>> > > > > Total 12 (delta 5), reused 0 (delta 0), pack-reused 0
>> > > > > remote: Traceback (most recent call last):
>> > > > > remote:   File
>> > > "hooks/pre-receive.h00-pre-receive-hook-dataexp-workflow",
>> > > > > line 90, in 
>> > > > > remote: apply_hooks(hooks_dict)
>> > > > > remote:   File
>> > > "hooks/pre-receive.h00-pre-receive-hook-dataexp-workflow",
>> > > > > line 72, in apply_hooks
>> > > > > remote: if hooks_dict["pre-receive-hook-merge-markers"]:  #
>> > enable
>> > > hook
>> > > > > remote: KeyError: 'pre-receive-hook-merge-markers'
>> > > > > To git.bioconductor.org:packages/spatialDmelxsim
>> > > > > ! [remote rejected] main -> master (pre-receive hook declined)
>> > > > > error: failed to push some refs to
>> > > > > 'git.bioconductor.org:packages/spatialDmelxsim'
>> > > >
>> > >
>> >
>> > [[alternative HTML version deleted]]
>> >
>> > ___
>> > Bioc-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
> The information in this e-mail is intended only for th...{{dropped:16}}

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Re: [Bioc-devel] pre-receive hook declined

2021-07-27 Thread Vincent Carey

hi you can't update 3.12  3.x is frozen when 3.(x+1) becomes release
perhaps the error message can be clarified

On Tue, Jul 27, 2021 at 3:44 PM Clay Wright  wrote:

> Hi,
>
> I am now encountering the following similar error trying to push a bugfix
> to my package. Does my account also need a similar update to Victor and
> Mike? Or is this something on my end? I just finally updated my github
> personal access tokens, maybe that's the issue? I haven't tried a fresh
> clone of the repository yet.
>
>
> git push origin RELEASE_3_12
>
> Enumerating objects: 17, done.
> Counting objects: 100% (17/17), done.
> Delta compression using up to 4 threads
> Compressing objects: 100% (12/12), done.
> Writing objects: 100% (12/12), 1.48 KiB | 151.00 KiB/s, done.
> Total 12 (delta 9), reused 0 (delta 0), pack-reused 0
> remote: FATAL: W refs/heads/RELEASE_3_12 packages/flowTime r.wright DENIED
> by fallthru
> remote: error: hook declined to update refs/heads/RELEASE_3_12
> To git.bioconductor.org:packages/flowTime.git
>  ! [remote rejected] RELEASE_3_12 -> RELEASE_3_12 (hook declined)
> error: failed to push some refs to 'git.bioconductor.org:
> packages/flowTime.git'
>
>
> Thanks!
> Clay
>
>
> On Fri, Jul 2, 2021 at 1:30 PM Victor Yuan  wrote:
>
> > It works for me as well now. Thanks!
> >
> > On Thu, Jul 1, 2021 at 8:21 AM Michael Love  >
> > wrote:
> >
> > > That works for me. Thanks.
> > >
> > > Mike
> > >
> > > On Thu, Jul 1, 2021 at 2:07 PM Nitesh Turaga 
> > > wrote:
> > > >
> > > > Hi
> > > >
> > > > Please try again. You should not see this error anymore.
> > > >
> > > > This was a mistake on our end.
> > > >
> > > > Best,
> > > >
> > > > Nitesh
> > > >
> > > >
> > > >
> > > > Nitesh Turaga
> > > > Scientist II, Department of Data Science,
> > > > Bioconductor Core Team Member
> > > > Dana Farber Cancer Institute
> > > >
> > > > > On Jul 1, 2021, at 1:49 AM, Michael Love <
> > michaelisaiahl...@gmail.com>
> > > wrote:
> > > > >
> > > > > I'm getting a similar error, trying to push commits for a new
> package
> > > > > submission. So this is my first attempt to push to Bioc git servers
> > > > > for this package.
> > > > >
> > > > > After following instructions from
> > > > >
> https://bioconductor.org/developers/how-to/git/new-package-workflow/
> > > > > ...
> > > > >
> > > > > spatialDmelxsim git:(main) > git push upstream main:master
> > > > > Enumerating objects: 20, done.
> > > > > Counting objects: 100% (20/20), done.
> > > > > Delta compression using up to 8 threads
> > > > > Compressing objects: 100% (10/10), done.
> > > > > Writing objects: 100% (12/12), 1.60 KiB | 1.60 MiB/s, done.
> > > > > Total 12 (delta 5), reused 0 (delta 0), pack-reused 0
> > > > > remote: Traceback (most recent call last):
> > > > > remote:   File
> > > "hooks/pre-receive.h00-pre-receive-hook-dataexp-workflow",
> > > > > line 90, in 
> > > > > remote: apply_hooks(hooks_dict)
> > > > > remote:   File
> > > "hooks/pre-receive.h00-pre-receive-hook-dataexp-workflow",
> > > > > line 72, in apply_hooks
> > > > > remote: if hooks_dict["pre-receive-hook-merge-markers"]:  #
> > enable
> > > hook
> > > > > remote: KeyError: 'pre-receive-hook-merge-markers'
> > > > > To git.bioconductor.org:packages/spatialDmelxsim
> > > > > ! [remote rejected] main -> master (pre-receive hook declined)
> > > > > error: failed to push some refs to
> > > > > 'git.bioconductor.org:packages/spatialDmelxsim'
> > > >
> > >
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> [[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] pre-receive hook declined

2021-07-27 Thread Kern, Lori

The current Bioconductor release is RELEASE_3_13 not RELEASE_3_12.  Past 
release branches are frozen and will not accept commits.  You should only be 
updating RELEASE_3_13 and master branches for this release cycle.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Clay Wright 

Sent: Tuesday, July 27, 2021 3:44 PM
To: bioc-devel 
Subject: Re: [Bioc-devel] pre-receive hook declined

Hi,

I am now encountering the following similar error trying to push a bugfix
to my package. Does my account also need a similar update to Victor and
Mike? Or is this something on my end? I just finally updated my github
personal access tokens, maybe that's the issue? I haven't tried a fresh
clone of the repository yet.


git push origin RELEASE_3_12

Enumerating objects: 17, done.
Counting objects: 100% (17/17), done.
Delta compression using up to 4 threads
Compressing objects: 100% (12/12), done.
Writing objects: 100% (12/12), 1.48 KiB | 151.00 KiB/s, done.
Total 12 (delta 9), reused 0 (delta 0), pack-reused 0
remote: FATAL: W refs/heads/RELEASE_3_12 packages/flowTime r.wright DENIED
by fallthru
remote: error: hook declined to update refs/heads/RELEASE_3_12
To git.bioconductor.org:packages/flowTime.git
 ! [remote rejected] RELEASE_3_12 -> RELEASE_3_12 (hook declined)
error: failed to push some refs to 'git.bioconductor.org:
packages/flowTime.git'


Thanks!
Clay


On Fri, Jul 2, 2021 at 1:30 PM Victor Yuan  wrote:

> It works for me as well now. Thanks!
>
> On Thu, Jul 1, 2021 at 8:21 AM Michael Love 
> wrote:
>
> > That works for me. Thanks.
> >
> > Mike
> >
> > On Thu, Jul 1, 2021 at 2:07 PM Nitesh Turaga 
> > wrote:
> > >
> > > Hi
> > >
> > > Please try again. You should not see this error anymore.
> > >
> > > This was a mistake on our end.
> > >
> > > Best,
> > >
> > > Nitesh
> > >
> > >
> > >
> > > Nitesh Turaga
> > > Scientist II, Department of Data Science,
> > > Bioconductor Core Team Member
> > > Dana Farber Cancer Institute
> > >
> > > > On Jul 1, 2021, at 1:49 AM, Michael Love <
> michaelisaiahl...@gmail.com>
> > wrote:
> > > >
> > > > I'm getting a similar error, trying to push commits for a new package
> > > > submission. So this is my first attempt to push to Bioc git servers
> > > > for this package.
> > > >
> > > > After following instructions from
> > > > https://secure-web.cisco.com/1zG69ZBuzV7x_en4chlgvb19YLMqAEk7U6ai5rDu9xpBwEhrMQex-fuviwZN6iTPYZAIuOYCT0y6swy9R-VpAohluoUDSNinbE8mr04UYClOnZRG_-58QOWQNJRHe1BwNZmeuwGL-ZcbYY4sgiXNhG-V1YcEvftuYFXf4emiBzFXb61tjbZlguHr39q93KL6enc_y5jtLkynm1DW_tXA9qeB_CZu2TqpngRUGfAqpO6iNeSM0rpLMIxlhTC-ZXp-MEoIdT5o9qhWz29dCeo04_fa2veI2o0uKB3JcbsfhepF3VBeKF3G7tWlSEuME4Lv5/https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fnew-package-workflow%2F
> > > > ...
> > > >
> > > > spatialDmelxsim git:(main) > git push upstream main:master
> > > > Enumerating objects: 20, done.
> > > > Counting objects: 100% (20/20), done.
> > > > Delta compression using up to 8 threads
> > > > Compressing objects: 100% (10/10), done.
> > > > Writing objects: 100% (12/12), 1.60 KiB | 1.60 MiB/s, done.
> > > > Total 12 (delta 5), reused 0 (delta 0), pack-reused 0
> > > > remote: Traceback (most recent call last):
> > > > remote:   File
> > "hooks/pre-receive.h00-pre-receive-hook-dataexp-workflow",
> > > > line 90, in 
> > > > remote: apply_hooks(hooks_dict)
> > > > remote:   File
> > "hooks/pre-receive.h00-pre-receive-hook-dataexp-workflow",
> > > > line 72, in apply_hooks
> > > > remote: if hooks_dict["pre-receive-hook-merge-markers"]:  #
> enable
> > hook
> > > > remote: KeyError: 'pre-receive-hook-merge-markers'
> > > > To git.bioconductor.org:packages/spatialDmelxsim
> > > > ! [remote rejected] main -> master (pre-receive hook declined)
> > > > error: failed to push some refs to
> > > > 'git.bioconductor.org:packages/spatialDmelxsim'
> > >
> >
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://secure-web.cisco.com/1pgqiCMe5IoIMpivDRv93WyaWnkPF_i8E2tWaoA374pIpXIPd7TPONLnD6TzKpuv5Yg3ruIxtF6pHIrp4F_Y_qS1BR-UpEDwq1S1z3s5XjHR3upqp3b_7--EM_Ae4V7iEqFujioz16Chp5jaJsTHGYj0GoRjkE2owlb4OnGqFubSHwIrXYrigAVweUpU46uOJjUz3N3ScU2BWTCfXGDdGYXzMC0l6TF__FFRc0sV8hpmFr0Tk8aOvECW9WvZtgpbk8c9Fv0L0gYoRt0hkutHzqm3dfWox6YpM8A5p7QIERxij-wUDelbblMtY1hdgOliR/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
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Re: [Bioc-devel] pre-receive hook declined

2021-07-27 Thread Nitesh Turaga

Hi,

This is because all commits to RELEASE_3_12 have been blocked during the 
release of Bioconductor 3.13.

You can now only commit/push to RELEASE_3_13 and devel.

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Jul 27, 2021, at 3:44 PM, Clay Wright  wrote:
> 
> Hi,
> 
> I am now encountering the following similar error trying to push a bugfix
> to my package. Does my account also need a similar update to Victor and
> Mike? Or is this something on my end? I just finally updated my github
> personal access tokens, maybe that's the issue? I haven't tried a fresh
> clone of the repository yet.
> 
> 
> git push origin RELEASE_3_12
> 
> Enumerating objects: 17, done.
> Counting objects: 100% (17/17), done.
> Delta compression using up to 4 threads
> Compressing objects: 100% (12/12), done.
> Writing objects: 100% (12/12), 1.48 KiB | 151.00 KiB/s, done.
> Total 12 (delta 9), reused 0 (delta 0), pack-reused 0
> remote: FATAL: W refs/heads/RELEASE_3_12 packages/flowTime r.wright DENIED
> by fallthru
> remote: error: hook declined to update refs/heads/RELEASE_3_12
> To git.bioconductor.org:packages/flowTime.git
> ! [remote rejected] RELEASE_3_12 -> RELEASE_3_12 (hook declined)
> error: failed to push some refs to 'git.bioconductor.org:
> packages/flowTime.git'
> 
> 
> Thanks!
> Clay
> 
> 
> On Fri, Jul 2, 2021 at 1:30 PM Victor Yuan  wrote:
> 
>> It works for me as well now. Thanks!
>> 
>> On Thu, Jul 1, 2021 at 8:21 AM Michael Love 
>> wrote:
>> 
>>> That works for me. Thanks.
>>> 
>>> Mike
>>> 
>>> On Thu, Jul 1, 2021 at 2:07 PM Nitesh Turaga 
>>> wrote:
 
 Hi
 
 Please try again. You should not see this error anymore.
 
 This was a mistake on our end.
 
 Best,
 
 Nitesh
 
 
 
 Nitesh Turaga
 Scientist II, Department of Data Science,
 Bioconductor Core Team Member
 Dana Farber Cancer Institute
 
> On Jul 1, 2021, at 1:49 AM, Michael Love <
>> michaelisaiahl...@gmail.com>
>>> wrote:
> 
> I'm getting a similar error, trying to push commits for a new package
> submission. So this is my first attempt to push to Bioc git servers
> for this package.
> 
> After following instructions from
> https://bioconductor.org/developers/how-to/git/new-package-workflow/
> ...
> 
> spatialDmelxsim git:(main) > git push upstream main:master
> Enumerating objects: 20, done.
> Counting objects: 100% (20/20), done.
> Delta compression using up to 8 threads
> Compressing objects: 100% (10/10), done.
> Writing objects: 100% (12/12), 1.60 KiB | 1.60 MiB/s, done.
> Total 12 (delta 5), reused 0 (delta 0), pack-reused 0
> remote: Traceback (most recent call last):
> remote:   File
>>> "hooks/pre-receive.h00-pre-receive-hook-dataexp-workflow",
> line 90, in 
> remote: apply_hooks(hooks_dict)
> remote:   File
>>> "hooks/pre-receive.h00-pre-receive-hook-dataexp-workflow",
> line 72, in apply_hooks
> remote: if hooks_dict["pre-receive-hook-merge-markers"]:  #
>> enable
>>> hook
> remote: KeyError: 'pre-receive-hook-merge-markers'
> To git.bioconductor.org:packages/spatialDmelxsim
> ! [remote rejected] main -> master (pre-receive hook declined)
> error: failed to push some refs to
> 'git.bioconductor.org:packages/spatialDmelxsim'
 
>>> 
>> 
>>[[alternative HTML version deleted]]
>> 
>> ___
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>> 
> 
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> 
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Re: [Bioc-devel] pre-receive hook declined

2021-07-27 Thread Clay Wright

Hi,

I am now encountering the following similar error trying to push a bugfix
to my package. Does my account also need a similar update to Victor and
Mike? Or is this something on my end? I just finally updated my github
personal access tokens, maybe that's the issue? I haven't tried a fresh
clone of the repository yet.


git push origin RELEASE_3_12

Enumerating objects: 17, done.
Counting objects: 100% (17/17), done.
Delta compression using up to 4 threads
Compressing objects: 100% (12/12), done.
Writing objects: 100% (12/12), 1.48 KiB | 151.00 KiB/s, done.
Total 12 (delta 9), reused 0 (delta 0), pack-reused 0
remote: FATAL: W refs/heads/RELEASE_3_12 packages/flowTime r.wright DENIED
by fallthru
remote: error: hook declined to update refs/heads/RELEASE_3_12
To git.bioconductor.org:packages/flowTime.git
 ! [remote rejected] RELEASE_3_12 -> RELEASE_3_12 (hook declined)
error: failed to push some refs to 'git.bioconductor.org:
packages/flowTime.git'


Thanks!
Clay


On Fri, Jul 2, 2021 at 1:30 PM Victor Yuan  wrote:

> It works for me as well now. Thanks!
>
> On Thu, Jul 1, 2021 at 8:21 AM Michael Love 
> wrote:
>
> > That works for me. Thanks.
> >
> > Mike
> >
> > On Thu, Jul 1, 2021 at 2:07 PM Nitesh Turaga 
> > wrote:
> > >
> > > Hi
> > >
> > > Please try again. You should not see this error anymore.
> > >
> > > This was a mistake on our end.
> > >
> > > Best,
> > >
> > > Nitesh
> > >
> > >
> > >
> > > Nitesh Turaga
> > > Scientist II, Department of Data Science,
> > > Bioconductor Core Team Member
> > > Dana Farber Cancer Institute
> > >
> > > > On Jul 1, 2021, at 1:49 AM, Michael Love <
> michaelisaiahl...@gmail.com>
> > wrote:
> > > >
> > > > I'm getting a similar error, trying to push commits for a new package
> > > > submission. So this is my first attempt to push to Bioc git servers
> > > > for this package.
> > > >
> > > > After following instructions from
> > > > https://bioconductor.org/developers/how-to/git/new-package-workflow/
> > > > ...
> > > >
> > > > spatialDmelxsim git:(main) > git push upstream main:master
> > > > Enumerating objects: 20, done.
> > > > Counting objects: 100% (20/20), done.
> > > > Delta compression using up to 8 threads
> > > > Compressing objects: 100% (10/10), done.
> > > > Writing objects: 100% (12/12), 1.60 KiB | 1.60 MiB/s, done.
> > > > Total 12 (delta 5), reused 0 (delta 0), pack-reused 0
> > > > remote: Traceback (most recent call last):
> > > > remote:   File
> > "hooks/pre-receive.h00-pre-receive-hook-dataexp-workflow",
> > > > line 90, in 
> > > > remote: apply_hooks(hooks_dict)
> > > > remote:   File
> > "hooks/pre-receive.h00-pre-receive-hook-dataexp-workflow",
> > > > line 72, in apply_hooks
> > > > remote: if hooks_dict["pre-receive-hook-merge-markers"]:  #
> enable
> > hook
> > > > remote: KeyError: 'pre-receive-hook-merge-markers'
> > > > To git.bioconductor.org:packages/spatialDmelxsim
> > > > ! [remote rejected] main -> master (pre-receive hook declined)
> > > > error: failed to push some refs to
> > > > 'git.bioconductor.org:packages/spatialDmelxsim'
> > >
> >
>
> [[alternative HTML version deleted]]
>
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Re: [Bioc-devel] EXTERNAL: R: Bioconductor package DaMiRseq

2021-07-27 Thread Marcel Ramos

Hi Mattia,

Make sure you are pushing to git.bioconductor.org in addition to GitHub. 
I still see

Maintainer: Mattia Chiesa 

in the git.bioconductor.org repo:

https://code.bioconductor.org/browse/DaMiRseq/blob/master/DESCRIPTION

Best,

Marcel

On 7/27/21 11:00 AM, Mattia Chiesa wrote:
> Sorry Nitesh but maybe I missed something.
> I activated Bioc Credential; I checked the ssh keys in .ssh/id_rsa.pub 
> (before generating a newest one) and it was the same in my BiocCredential 
> profile. I changed the mantainer's mail in DESCRIPTION directly by Github.  
> But nothing changes: I've got again the error.
>
> 
> Da: Nitesh Turaga 
> Inviato: martedì 27 luglio 2021 16:10
> A: Mattia Chiesa 
> Cc: bioc-devel 
> Oggetto: Re: [Bioc-devel] Bioconductor package DaMiRseq
>
> Please add your SSH keys and you’ll gain access to your package.
>
> Once you get access, change the maintainer email address in the DESCRIPTION 
> file of the package.
>
> Best,
>
>
> Nitesh Turaga
> Scientist II, Department of Data Science,
> Bioconductor Core Team Member
> Dana Farber Cancer Institute
>
>> On Jul 27, 2021, at 10:09 AM, Mattia Chiesa  wrote:
>>
>> Yes I'm still using my istitutional mail. I've just activated the Bioc 
>> Credintials.
>> Da: Nitesh Turaga 
>> Inviato: martedì 27 luglio 2021 16:01
>> A: Mattia Chiesa 
>> Oggetto: Re: [Bioc-devel] Bioconductor package DaMiRseq
>>
>> Hi
>>
>> I guess the question is are you still using the email I referred to in the 
>> previous email? Do you still have access to it?
>>
>> If so, you can activate your BiocCredentials account with that.
>>
>> Nitesh Turaga
>> Scientist II, Department of Data Science,
>> Bioconductor Core Team Member
>> Dana Farber Cancer Institute
>>
>>> On Jul 27, 2021, at 9:47 AM, Mattia Chiesa  wrote:
>>>
>>> Sorry, but I really do not remember. Probably Yes! when we moved from SVN 
>>> to GIT, I used my istitutional mail. However, I have never had problems in 
>>> the past updating my packages by GitBash.
>>> How can I fix it now?
>>> Thanks Nitesh
>>> Mattia
>>>
>>>
>>>
>>> Da: Nitesh Turaga 
>>> Inviato: martedì 27 luglio 2021 15:38
>>> A: Mattia Chiesa 
>>> Cc: bioc-devel@r-project.org 
>>> Oggetto: Re: [Bioc-devel] Bioconductor package DaMiRseq
>>>
>>> Hi
>>>
>>> Are you using mattia.chi...@cardiologicomonzino.it to activate your 
>>> BiocCredentials account?
>>>
>>> It seems this email is not the same as the one on the maintainer on the 
>>> DESCRIPTION file of the package.
>>>
>>> Best,
>>>
>>> Nitesh
>>>
>>> Nitesh Turaga
>>> Scientist II, Department of Data Science,
>>> Bioconductor Core Team Member
>>> Dana Farber Cancer Institute
>>>
 On Jul 27, 2021, at 9:25 AM, Mattia Chiesa  
 wrote:

 Dear all,
 I need to update my package 
 (DaMiRseq)
  in order to fix a bug that makes the package fail in devel and release.
 I tried, as usual, to pull the latest version of package with:
 git pull upstream master
 but a connection error occurs:
 ssh_exchange_identification: read: Connection reset by peer
 fatal: Could not read from remote repository.
 Please make sure you have the correct access rights
 and the repository exists.

 I asked to Lori who kindly invites me to write you. What should I do?
 In addition, I cannot activate the Bioconductor Git Credentials,  even 
 though I mantain the package since 2017.

 Thanks in advance,
 Mattia

 Da: Kern, Lori 
 Inviato: marted� 27 luglio 2021 14:29
 A: Mattia Chiesa 
 Oggetto: Re: Bioconductor package DaMiRseq

 Regardless of whether it stems from a dependency package or not,  your 
 package is still failing in release and devel which is problematic.  If 
 the change is intentional from a dependent package, you would still have 
 to modify your code.  If you find it is from a dependent package and 
 consider it a bug,  I encourage you to reach out to their maintainer 
 directly as well.

 Please ask further git access issues on bioc-devel@r-project.org mailing 
 list as there are dedicated members of the team to assist with access. To 
 start,  make sure you have a valid ssh key on the computer you are using, 
 and that the key is uploaded to the git credentials app.  If you have not 
 activated the git credentials app, be sure to activate your account first. 
  Links to the app and other useful git workflow can be found here:
 http://bioconductor.org/developers/how-to/git/new-package-workflow/

 Cheers,

 Lori Shepherd

 Bioconductor Core Team

 Roswell Park Comprehensive Cancer Center

 Department of Biostatistics & Bioinformatics

 Elm & Carlton Streets

 Buffalo, New York 14263

[Bioc-devel] R: Bioconductor package DaMiRseq

2021-07-27 Thread Mattia Chiesa

Sorry Nitesh but maybe I missed something.
I activated Bioc Credential; I checked the ssh keys in .ssh/id_rsa.pub (before 
generating a newest one) and it was the same in my BiocCredential profile. I 
changed the mantainer's mail in DESCRIPTION directly by Github.  But nothing 
changes: I've got again the error.


Da: Nitesh Turaga 
Inviato: martedì 27 luglio 2021 16:10
A: Mattia Chiesa 
Cc: bioc-devel 
Oggetto: Re: [Bioc-devel] Bioconductor package DaMiRseq

Please add your SSH keys and you’ll gain access to your package.

Once you get access, change the maintainer email address in the DESCRIPTION 
file of the package.

Best,


Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Jul 27, 2021, at 10:09 AM, Mattia Chiesa  wrote:
>
> Yes I'm still using my istitutional mail. I've just activated the Bioc 
> Credintials.
> Da: Nitesh Turaga 
> Inviato: martedì 27 luglio 2021 16:01
> A: Mattia Chiesa 
> Oggetto: Re: [Bioc-devel] Bioconductor package DaMiRseq
>
> Hi
>
> I guess the question is are you still using the email I referred to in the 
> previous email? Do you still have access to it?
>
> If so, you can activate your BiocCredentials account with that.
>
> Nitesh Turaga
> Scientist II, Department of Data Science,
> Bioconductor Core Team Member
> Dana Farber Cancer Institute
>
> > On Jul 27, 2021, at 9:47 AM, Mattia Chiesa  wrote:
> >
> > Sorry, but I really do not remember. Probably Yes! when we moved from SVN 
> > to GIT, I used my istitutional mail. However, I have never had problems in 
> > the past updating my packages by GitBash.
> > How can I fix it now?
> > Thanks Nitesh
> > Mattia
> >
> >
> >
> > Da: Nitesh Turaga 
> > Inviato: martedì 27 luglio 2021 15:38
> > A: Mattia Chiesa 
> > Cc: bioc-devel@r-project.org 
> > Oggetto: Re: [Bioc-devel] Bioconductor package DaMiRseq
> >
> > Hi
> >
> > Are you using mattia.chi...@cardiologicomonzino.it to activate your 
> > BiocCredentials account?
> >
> > It seems this email is not the same as the one on the maintainer on the 
> > DESCRIPTION file of the package.
> >
> > Best,
> >
> > Nitesh
> >
> > Nitesh Turaga
> > Scientist II, Department of Data Science,
> > Bioconductor Core Team Member
> > Dana Farber Cancer Institute
> >
> > > On Jul 27, 2021, at 9:25 AM, Mattia Chiesa  
> > > wrote:
> > >
> > > Dear all,
> > > I need to update my package 
> > > (DaMiRseq)
> > >  in order to fix a bug that makes the package fail in devel and release.
> > > I tried, as usual, to pull the latest version of package with:
> > > git pull upstream master
> > > but a connection error occurs:
> > > ssh_exchange_identification: read: Connection reset by peer
> > > fatal: Could not read from remote repository.
> > > Please make sure you have the correct access rights
> > > and the repository exists.
> > >
> > > I asked to Lori who kindly invites me to write you. What should I do?
> > > In addition, I cannot activate the Bioconductor Git Credentials,  even 
> > > though I mantain the package since 2017.
> > >
> > > Thanks in advance,
> > > Mattia
> > >
> > >
> > > 
> > > Da: Kern, Lori 
> > > Inviato: marted� 27 luglio 2021 14:29
> > > A: Mattia Chiesa 
> > > Oggetto: Re: Bioconductor package DaMiRseq
> > >
> > > Regardless of whether it stems from a dependency package or not,  your 
> > > package is still failing in release and devel which is problematic.  If 
> > > the change is intentional from a dependent package, you would still have 
> > > to modify your code.  If you find it is from a dependent package and 
> > > consider it a bug,  I encourage you to reach out to their maintainer 
> > > directly as well.
> > >
> > > Please ask further git access issues on bioc-devel@r-project.org mailing 
> > > list as there are dedicated members of the team to assist with access. To 
> > > start,  make sure you have a valid ssh key on the computer you are using, 
> > > and that the key is uploaded to the git credentials app.  If you have not 
> > > activated the git credentials app, be sure to activate your account 
> > > first.  Links to the app and other useful git workflow can be found here:
> > > http://bioconductor.org/developers/how-to/git/new-package-workflow/
> > >
> > > Cheers,
> > >
> > >
> > >
> > >
> > >
> > > Lori Shepherd
> > >
> > > Bioconductor Core Team
> > >
> > > Roswell Park Comprehensive Cancer Center
> > >
> > > Department of Biostatistics & Bioinformatics
> > >
> > > Elm & Carlton Streets
> > >
> > > Buffalo, New York 14263
> > >
> > > 
> > > From: Mattia Chiesa 
> > > Sent: Tuesday, July 27, 2021 5:06 AM
> > > To: Kern, Lori 
> > > Subject: R: Bioconductor package DaMiRseq
> > >
> > > Dear Lori,
> > > Since I haven't modified DaMiRseq for several months, I think the the 
> > > problem could be related to some Damirseq

Re: [Bioc-devel] Bioconductor package DaMiRseq

2021-07-27 Thread Nitesh Turaga

Please add your SSH keys and you’ll gain access to your package.

Once you get access, change the maintainer email address in the DESCRIPTION 
file of the package. 

Best,


Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Jul 27, 2021, at 10:09 AM, Mattia Chiesa  wrote:
> 
> Yes I'm still using my istitutional mail. I've just activated the Bioc 
> Credintials.
> Da: Nitesh Turaga 
> Inviato: martedì 27 luglio 2021 16:01
> A: Mattia Chiesa 
> Oggetto: Re: [Bioc-devel] Bioconductor package DaMiRseq
>  
> Hi 
> 
> I guess the question is are you still using the email I referred to in the 
> previous email? Do you still have access to it?
> 
> If so, you can activate your BiocCredentials account with that. 
> 
> Nitesh Turaga
> Scientist II, Department of Data Science,
> Bioconductor Core Team Member
> Dana Farber Cancer Institute
> 
> > On Jul 27, 2021, at 9:47 AM, Mattia Chiesa  wrote:
> > 
> > Sorry, but I really do not remember. Probably Yes! when we moved from SVN 
> > to GIT, I used my istitutional mail. However, I have never had problems in 
> > the past updating my packages by GitBash.
> > How can I fix it now?
> > Thanks Nitesh
> > Mattia
> > 
> > 
> > 
> > Da: Nitesh Turaga 
> > Inviato: martedì 27 luglio 2021 15:38
> > A: Mattia Chiesa 
> > Cc: bioc-devel@r-project.org 
> > Oggetto: Re: [Bioc-devel] Bioconductor package DaMiRseq
> >  
> > Hi
> > 
> > Are you using mattia.chi...@cardiologicomonzino.it to activate your 
> > BiocCredentials account? 
> > 
> > It seems this email is not the same as the one on the maintainer on the 
> > DESCRIPTION file of the package. 
> > 
> > Best,
> > 
> > Nitesh 
> > 
> > Nitesh Turaga
> > Scientist II, Department of Data Science,
> > Bioconductor Core Team Member
> > Dana Farber Cancer Institute
> > 
> > > On Jul 27, 2021, at 9:25 AM, Mattia Chiesa  
> > > wrote:
> > > 
> > > Dear all,
> > > I need to update my package 
> > > (DaMiRseq)
> > >  in order to fix a bug that makes the package fail in devel and release.
> > > I tried, as usual, to pull the latest version of package with:
> > > git pull upstream master
> > > but a connection error occurs:
> > > ssh_exchange_identification: read: Connection reset by peer
> > > fatal: Could not read from remote repository.
> > > Please make sure you have the correct access rights
> > > and the repository exists.
> > > 
> > > I asked to Lori who kindly invites me to write you. What should I do?
> > > In addition, I cannot activate the Bioconductor Git Credentials,  even 
> > > though I mantain the package since 2017.
> > > 
> > > Thanks in advance,
> > > Mattia
> > > 
> > > 
> > > 
> > > Da: Kern, Lori 
> > > Inviato: marted� 27 luglio 2021 14:29
> > > A: Mattia Chiesa 
> > > Oggetto: Re: Bioconductor package DaMiRseq
> > > 
> > > Regardless of whether it stems from a dependency package or not,  your 
> > > package is still failing in release and devel which is problematic.  If 
> > > the change is intentional from a dependent package, you would still have 
> > > to modify your code.  If you find it is from a dependent package and 
> > > consider it a bug,  I encourage you to reach out to their maintainer 
> > > directly as well.
> > > 
> > > Please ask further git access issues on bioc-devel@r-project.org mailing 
> > > list as there are dedicated members of the team to assist with access. To 
> > > start,  make sure you have a valid ssh key on the computer you are using, 
> > > and that the key is uploaded to the git credentials app.  If you have not 
> > > activated the git credentials app, be sure to activate your account 
> > > first.  Links to the app and other useful git workflow can be found here:
> > > http://bioconductor.org/developers/how-to/git/new-package-workflow/
> > > 
> > > Cheers,
> > > 
> > > 
> > > 
> > > 
> > > 
> > > Lori Shepherd
> > > 
> > > Bioconductor Core Team
> > > 
> > > Roswell Park Comprehensive Cancer Center
> > > 
> > > Department of Biostatistics & Bioinformatics
> > > 
> > > Elm & Carlton Streets
> > > 
> > > Buffalo, New York 14263
> > > 
> > > 
> > > From: Mattia Chiesa 
> > > Sent: Tuesday, July 27, 2021 5:06 AM
> > > To: Kern, Lori 
> > > Subject: R: Bioconductor package DaMiRseq
> > > 
> > > Dear Lori,
> > > Since I haven't modified DaMiRseq for several months, I think the the 
> > > problem could be related to some Damirseq dependencies.
> > > Anyway, I tried to go deep into the problem, but when I type:
> > > git pull upstream master
> > > a connection error occurs:
> > > ssh_exchange_identification: read: Connection reset by peer
> > > fatal: Could not read from remote repository.
> > > Please make sure you have the correct access rights
> > > and the repository exists.
> > > 
> > > It's the first time I have experinced this problem. What should I do?
> > > Thanks In advance.

[Bioc-devel] R: Bioconductor package DaMiRseq

2021-07-27 Thread Mattia Chiesa

Sorry, but I really do not remember. Probably Yes! when we moved from SVN to 
GIT, I used my istitutional mail. However, I have never had problems in the 
past updating my packages by GitBash.
How can I fix it now?
Thanks Nitesh
Mattia




Da: Nitesh Turaga 
Inviato: martedì 27 luglio 2021 15:38
A: Mattia Chiesa 
Cc: bioc-devel@r-project.org 
Oggetto: Re: [Bioc-devel] Bioconductor package DaMiRseq

Hi

Are you using mattia.chi...@cardiologicomonzino.it to activate your 
BiocCredentials account?

It seems this email is not the same as the one on the maintainer on the 
DESCRIPTION file of the package.

Best,

Nitesh

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Jul 27, 2021, at 9:25 AM, Mattia Chiesa  wrote:
>
> Dear all,
> I need to update my package 
> (DaMiRseq)
>  in order to fix a bug that makes the package fail in devel and release.
> I tried, as usual, to pull the latest version of package with:
> git pull upstream master
> but a connection error occurs:
> ssh_exchange_identification: read: Connection reset by peer
> fatal: Could not read from remote repository.
> Please make sure you have the correct access rights
> and the repository exists.
>
> I asked to Lori who kindly invites me to write you. What should I do?
> In addition, I cannot activate the Bioconductor Git Credentials,  even though 
> I mantain the package since 2017.
>
> Thanks in advance,
> Mattia
>
>
> 
> Da: Kern, Lori 
> Inviato: marted� 27 luglio 2021 14:29
> A: Mattia Chiesa 
> Oggetto: Re: Bioconductor package DaMiRseq
>
> Regardless of whether it stems from a dependency package or not,  your 
> package is still failing in release and devel which is problematic.  If the 
> change is intentional from a dependent package, you would still have to 
> modify your code.  If you find it is from a dependent package and consider it 
> a bug,  I encourage you to reach out to their maintainer directly as well.
>
> Please ask further git access issues on bioc-devel@r-project.org mailing list 
> as there are dedicated members of the team to assist with access. To start,  
> make sure you have a valid ssh key on the computer you are using, and that 
> the key is uploaded to the git credentials app.  If you have not activated 
> the git credentials app, be sure to activate your account first.  Links to 
> the app and other useful git workflow can be found here:
> http://bioconductor.org/developers/how-to/git/new-package-workflow/
>
> Cheers,
>
>
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> 
> From: Mattia Chiesa 
> Sent: Tuesday, July 27, 2021 5:06 AM
> To: Kern, Lori 
> Subject: R: Bioconductor package DaMiRseq
>
> Dear Lori,
> Since I haven't modified DaMiRseq for several months, I think the the problem 
> could be related to some Damirseq dependencies.
> Anyway, I tried to go deep into the problem, but when I type:
> git pull upstream master
> a connection error occurs:
> ssh_exchange_identification: read: Connection reset by peer
> fatal: Could not read from remote repository.
> Please make sure you have the correct access rights
> and the repository exists.
>
> It's the first time I have experinced this problem. What should I do?
> Thanks In advance.
> Mattia
>
>
> 
> Da: Kern, Lori 
> Inviato: luned� 26 luglio 2021 16:55
> A: mattia.chi...@hotmail.it 
> Oggetto: Bioconductor package DaMiRseq
>
> We would like to bring to your attention that your package is failing to build
> or check on our release and devel build machines:
>
> Devel:
> http://bioconductor.org/checkResults/3.14/bioc-LATEST/DaMiRseq
>
> Release:
> http://bioconductor.org/checkResults/3.13/bioc-LATEST/DaMiRseq
>
> Would you mind taking a look at this? Don't hesitate to ask on the bioc-devel 
> mailing list if

Re: [Bioc-devel] Bioconductor package DaMiRseq

2021-07-27 Thread Nitesh Turaga

Hi

Are you using mattia.chi...@cardiologicomonzino.it to activate your 
BiocCredentials account? 

It seems this email is not the same as the one on the maintainer on the 
DESCRIPTION file of the package. 

Best,

Nitesh 

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Jul 27, 2021, at 9:25 AM, Mattia Chiesa  wrote:
> 
> Dear all,
> I need to update my package 
> (DaMiRseq)
>  in order to fix a bug that makes the package fail in devel and release.
> I tried, as usual, to pull the latest version of package with:
> git pull upstream master
> but a connection error occurs:
> ssh_exchange_identification: read: Connection reset by peer
> fatal: Could not read from remote repository.
> Please make sure you have the correct access rights
> and the repository exists.
> 
> I asked to Lori who kindly invites me to write you. What should I do?
> In addition, I cannot activate the Bioconductor Git Credentials,  even though 
> I mantain the package since 2017.
> 
> Thanks in advance,
> Mattia
> 
> 
> 
> Da: Kern, Lori 
> Inviato: marted� 27 luglio 2021 14:29
> A: Mattia Chiesa 
> Oggetto: Re: Bioconductor package DaMiRseq
> 
> Regardless of whether it stems from a dependency package or not,  your 
> package is still failing in release and devel which is problematic.  If the 
> change is intentional from a dependent package, you would still have to 
> modify your code.  If you find it is from a dependent package and consider it 
> a bug,  I encourage you to reach out to their maintainer directly as well.
> 
> Please ask further git access issues on bioc-devel@r-project.org mailing list 
> as there are dedicated members of the team to assist with access. To start,  
> make sure you have a valid ssh key on the computer you are using, and that 
> the key is uploaded to the git credentials app.  If you have not activated 
> the git credentials app, be sure to activate your account first.  Links to 
> the app and other useful git workflow can be found here:
> http://bioconductor.org/developers/how-to/git/new-package-workflow/
> 
> Cheers,
> 
> 
> 
> 
> 
> Lori Shepherd
> 
> Bioconductor Core Team
> 
> Roswell Park Comprehensive Cancer Center
> 
> Department of Biostatistics & Bioinformatics
> 
> Elm & Carlton Streets
> 
> Buffalo, New York 14263
> 
> 
> From: Mattia Chiesa 
> Sent: Tuesday, July 27, 2021 5:06 AM
> To: Kern, Lori 
> Subject: R: Bioconductor package DaMiRseq
> 
> Dear Lori,
> Since I haven't modified DaMiRseq for several months, I think the the problem 
> could be related to some Damirseq dependencies.
> Anyway, I tried to go deep into the problem, but when I type:
> git pull upstream master
> a connection error occurs:
> ssh_exchange_identification: read: Connection reset by peer
> fatal: Could not read from remote repository.
> Please make sure you have the correct access rights
> and the repository exists.
> 
> It's the first time I have experinced this problem. What should I do?
> Thanks In advance.
> Mattia
> 
> 
> 
> Da: Kern, Lori 
> Inviato: luned� 26 luglio 2021 16:55
> A: mattia.chi...@hotmail.it 
> Oggetto: Bioconductor package DaMiRseq
> 
> We would like to bring to your attention that your package is failing to build
> or check on our release and devel build machines:
> 
> Devel:
> http://bioconductor.org/checkResults/3.14/bioc-LATEST/DaMiRseq
> 
> Release:
> http://bioconductor.org/checkResults/3.13/bioc-LATEST/DaMiRseq
> 
> Would you mind taking a look at this? Don't hesitate to ask on the bioc-devel 
> mailing list if you have any question or need help.
> 
> This is very problematic.   If no action is taken over the next few weeks we 
> will begin the deprecation process for your package. We appreciate your 
> assistance on pushing changes to remedy these errors.
> 
> 
> 
> 
> Lori Shepherd
> 
> Bioconductor Core Team
> 
> Roswell Park Comprehensive Cancer Center
> 
> Department of Biostatistics & Bioinformatics
>

[Bioc-devel] R: Bioconductor package DaMiRseq

2021-07-27 Thread Mattia Chiesa

Dear all,
I need to update my package 
(DaMiRseq)
 in order to fix a bug that makes the package fail in devel and release.
I tried, as usual, to pull the latest version of package with:
 git pull upstream master
but a connection error occurs:
ssh_exchange_identification: read: Connection reset by peer
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exists.

I asked to Lori who kindly invites me to write you. What should I do?
In addition, I cannot activate the Bioconductor Git Credentials,  even though I 
mantain the package since 2017.

Thanks in advance,
Mattia



Da: Kern, Lori 
Inviato: marted� 27 luglio 2021 14:29
A: Mattia Chiesa 
Oggetto: Re: Bioconductor package DaMiRseq

Regardless of whether it stems from a dependency package or not,  your package 
is still failing in release and devel which is problematic.  If the change is 
intentional from a dependent package, you would still have to modify your code. 
 If you find it is from a dependent package and consider it a bug,  I encourage 
you to reach out to their maintainer directly as well.

Please ask further git access issues on bioc-devel@r-project.org mailing list 
as there are dedicated members of the team to assist with access. To start,  
make sure you have a valid ssh key on the computer you are using, and that the 
key is uploaded to the git credentials app.  If you have not activated the git 
credentials app, be sure to activate your account first.  Links to the app and 
other useful git workflow can be found here:
http://bioconductor.org/developers/how-to/git/new-package-workflow/

Cheers,





Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Mattia Chiesa 
Sent: Tuesday, July 27, 2021 5:06 AM
To: Kern, Lori 
Subject: R: Bioconductor package DaMiRseq

Dear Lori,
Since I haven't modified DaMiRseq for several months, I think the the problem 
could be related to some Damirseq dependencies.
Anyway, I tried to go deep into the problem, but when I type:
git pull upstream master
a connection error occurs:
ssh_exchange_identification: read: Connection reset by peer
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exists.

It's the first time I have experinced this problem. What should I do?
Thanks In advance.
Mattia



Da: Kern, Lori 
Inviato: luned� 26 luglio 2021 16:55
A: mattia.chi...@hotmail.it 
Oggetto: Bioconductor package DaMiRseq

We would like to bring to your attention that your package is failing to build
or check on our release and devel build machines:

Devel:
http://bioconductor.org/checkResults/3.14/bioc-LATEST/DaMiRseq

Release:
http://bioconductor.org/checkResults/3.13/bioc-LATEST/DaMiRseq

Would you mind taking a look at this? Don't hesitate to ask on the bioc-devel 
mailing list if you have any question or need help.

This is very problematic.   If no action is taken over the next few weeks we 
will begin the deprecation process for your package. We appreciate your 
assistance on pushing changes to remedy these errors.




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

This email message may contain legally privileged and/or confidential 
information. If you are not the intended recipient(s), or the employee or agent 
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Re: [Bioc-devel] BentoBox and BentoBoxData git.bioconductor repositories

2021-07-27 Thread Kramer, Nicole Emma

Hi Nitesh,

Thank you for all your help!

Best,
Nicole


--

Nicole Kramer

Ph.D. Student in Bioinformatics and Computational Biology

University of North Carolina at Chapel Hill

nekra...@live.unc.edu


From: Nitesh Turaga 
Sent: Monday, July 26, 2021 6:33 PM
To: Kramer, Nicole Emma 
Cc: bioc-devel 
Subject: Re: [Bioc-devel] BentoBox and BentoBoxData git.bioconductor 
repositories

Hello,

Please take a look at http://bioconductor.org/developers/how-to/git/faq/ #13 
onwards to see if any of those issues fix your problem.

There is nothing wrong on our end.

Best,

Nitesh

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Jul 26, 2021, at 6:28 PM, Kramer, Nicole Emma  
> wrote:
>
> I've also been having issues pushing to the BentoBoxData git.bioconductor.org 
> repo, but I do not have trouble with the BentoBox repo. Do I have the correct 
> permissions?
>
> Thank you,
> Nicole
>
> --
> Nicole Kramer
> Ph.D. Student in Bioinformatics and Computational Biology
> University of North Carolina at Chapel Hill
> nekra...@live.unc.edu
> From: Nitesh Turaga 
> Sent: Monday, July 26, 2021 4:48 PM
> To: Kramer, Nicole Emma 
> Cc: bioc-devel 
> Subject: Re: [Bioc-devel] BentoBox and BentoBoxData git.bioconductor 
> repositories
>
> Hi Nicole,
>
> Please sync your two repos now. You should be all set.
>
> Best,
>
> Nitesh Turaga
> Scientist II, Department of Data Science,
> Bioconductor Core Team Member
> Dana Farber Cancer Institute
>
> > On Jul 26, 2021, at 12:44 PM, Kramer, Nicole Emma  
> > wrote:
> >
> > Hi Nitesh,
> >
> > Thank you so much!
> >
> > Best,
> > Nicole
> >
> > --
> > Nicole Kramer
> > Ph.D. Student in Bioinformatics and Computational Biology
> > University of North Carolina at Chapel Hill
> > nekra...@live.unc.edu
> > From: Nitesh Turaga 
> > Sent: Monday, July 26, 2021 11:21 AM
> > To: Kramer, Nicole Emma 
> > Cc: bioc-devel@r-project.org 
> > Subject: Re: [Bioc-devel] BentoBox and BentoBoxData git.bioconductor 
> > repositories
> >
> > Hi Nicole,
> >
> > Thank you for cleaning the repos.
> >
> > I will do the force push for you, but you will have to re-sync the Github 
> > repo once it�s done.
> >
> > I�ll email you as soon as I�m done with the force push.
> >
> > Best,
> >
> > Nitesh
> >
> > Nitesh Turaga
> > Scientist II, Department of Data Science,
> > Bioconductor Core Team Member
> > Dana Farber Cancer Institute
> >
> > > On Jul 24, 2021, at 6:54 PM, Kramer, Nicole Emma  
> > > wrote:
> > >
> > > Hello,
> > >
> > > I am in the review process for the packages BentoBoxData and BentoBox and 
> > > I am attempting to make changes to these packages. However, they have 
> > > been cleaned for large data files and need to be reset at their 
> > > git.bioconductor.org locations. Would I be able to get these repos force 
> > > pushed?
> > >
> > > Thank you,
> > > Nicole Kramer
> > >
> > >
> > > --
> > >
> > > Nicole Kramer
> > >
> > > Ph.D. Student in Bioinformatics and Computational Biology
> > >
> > > University of North Carolina at Chapel Hill
> > >
> > > nekra...@live.unc.edu
> > >
> > >[[alternative HTML version deleted]]
> > >
> > > ___
> > > Bioc-devel@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel


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