Re: [Bioc-devel] DMCHMM package new dev release

2018-09-05 Thread Shepherd, Lori 
We now see the changes on the git.bioconductor.org server.  The changes should 
be reflected in tomorrows build report.


Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Farhad Shokoohi 
Sent: Wednesday, September 5, 2018 9:46:21 AM
To: Shepherd, Lori
Cc: Obenchain, Valerie; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] DMCHMM package new dev release

Hello,

I followed every command.
Everything is up to date.



MacBook-Pro:DMCHMM Farhad$ git remote add upstream 
g...@git.bioconductor.org<mailto:g...@git.bioconductor.org>:packages/DMCHMM.git
fatal: remote upstream already exists.
MacBook-Pro:DMCHMM Farhad$ git fetch --all
Fetching origin
Fetching upstream
MacBook-Pro:DMCHMM Farhad$ git checkout master
Switched to branch 'master'
Your branch is up-to-date with 'origin/master'.
MacBook-Pro:DMCHMM Farhad$
MacBook-Pro:DMCHMM Farhad$ git merge origin/master
Already up-to-date.
MacBook-Pro:DMCHMM Farhad$ git merge upstream/master
Already up-to-date.
MacBook-Pro:DMCHMM Farhad$ git push upstream master
Everything up-to-date
MacBook-Pro:DMCHMM Farhad$ git push origin master
Everything up-to-date



���
Farhad Shokoohi,
Ph.D. in Statistics
shoko...@icloud.com<mailto:shoko...@icloud.com>

On Sep 5, 2018, at 9:33 AM, Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>> wrote:

If you didn't set up your remotes  this link may be useful

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



Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263

From: Shepherd, Lori
Sent: Wednesday, September 5, 2018 9:32:08 AM
To: Obenchain, Valerie; Farhad Shokoohi
Subject: Re: [Bioc-devel] DMCHMM package new dev release

You need to commit changes to git.bioconductor.org<http://git.bioconductor.org> 
.  There are no changes pushed to our Bioconductor server.

Please ensure you have followed the instructions for setting up your remotes 
and pushed to the correct location
https://bioconductor.org/developers/how-to/git/push-to-github-bioc/

I would keep track of the commands you try and if you get any ERRORs please 
post the commands with full output as a reply all.


Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263

From: Bioc-devel 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Farhad Shokoohi via Bioc-devel 
mailto:bioc-devel@r-project.org>>
Sent: Wednesday, September 5, 2018 9:26:58 AM
To: Obenchain, Valerie
Cc: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>
Subject: Re: [Bioc-devel] DMCHMM package new dev release

Hello,

I did everything mentioned in the link.
I am also using Sourcetree app on Mac to commit changes but noting changes.

Best,
���
Farhad Shokoohi,
Ph.D. in Statistics
shoko...@icloud.com<mailto:shoko...@icloud.com>

> On Sep 4, 2018, at 11:59 AM, Obenchain, Valerie 
>  wrote:
>
> The builds start ~5pm EST daily. Commits made before that time will be 
> included in the nightly builds. The build report posts the following day (see 
> time at top of page):
>
> https://www.bioconductor.org/checkResults/release/bioc-LATEST/ 
> <https://www.bioconductor.org/checkResults/release/bioc-LATEST/>
> https://www.bioconductor.org/checkResults/devel/bioc-LATEST/ 
> <https://www.bioconductor.org/checkResults/devel/bioc-LATEST/>
>
> If you don't see the package version you expected it's likely you missed the 
> cutoff or didn't push to the git.bioconductor.org server. See git 
> documentation here:
>
> https://www.bioconductor.org/developers/how-to/git/ 
> <https://www.bioconductor.org/developers/how-to/git/>
>
> Valerie
>
>
> On 09/04/2018 07:58 AM, Farhad Shokoohi via Bioc-devel wrote:
>> Hello,
>>
>> I have made some changes and updated my package DMCHMM and pushed it to 
>> GitHub.
>> When the new update appears on bioconductor?
>>
>> Best,
>>
>> ���
>> Farhad Shokoohi,
>> Ph.D. in Statistics
>>
>>   [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel 
>> <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

Re: [Bioc-devel] DMCHMM package new dev release

2018-09-05 Thread Shepherd, Lori 
If you didn't set up your remotes  this link may be useful


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




Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Shepherd, Lori
Sent: Wednesday, September 5, 2018 9:32:08 AM
To: Obenchain, Valerie; Farhad Shokoohi
Subject: Re: [Bioc-devel] DMCHMM package new dev release


You need to commit changes to git.bioconductor.org .  There are no changes 
pushed to our Bioconductor server.


Please ensure you have followed the instructions for setting up your remotes 
and pushed to the correct location

https://bioconductor.org/developers/how-to/git/push-to-github-bioc/


I would keep track of the commands you try and if you get any ERRORs please 
post the commands with full output as a reply all.



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 Farhad 
Shokoohi via Bioc-devel 
Sent: Wednesday, September 5, 2018 9:26:58 AM
To: Obenchain, Valerie
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] DMCHMM package new dev release

Hello,

I did everything mentioned in the link.
I am also using Sourcetree app on Mac to commit changes but noting changes.

Best,
���
Farhad Shokoohi,
Ph.D. in Statistics
shoko...@icloud.com

> On Sep 4, 2018, at 11:59 AM, Obenchain, Valerie 
>  wrote:
>
> The builds start ~5pm EST daily. Commits made before that time will be 
> included in the nightly builds. The build report posts the following day (see 
> time at top of page):
>
> https://www.bioconductor.org/checkResults/release/bioc-LATEST/ 
> <https://www.bioconductor.org/checkResults/release/bioc-LATEST/>
> https://www.bioconductor.org/checkResults/devel/bioc-LATEST/ 
> <https://www.bioconductor.org/checkResults/devel/bioc-LATEST/>
>
> If you don't see the package version you expected it's likely you missed the 
> cutoff or didn't push to the git.bioconductor.org server. See git 
> documentation here:
>
> https://www.bioconductor.org/developers/how-to/git/ 
> <https://www.bioconductor.org/developers/how-to/git/>
>
> Valerie
>
>
> On 09/04/2018 07:58 AM, Farhad Shokoohi via Bioc-devel wrote:
>> Hello,
>>
>> I have made some changes and updated my package DMCHMM and pushed it to 
>> GitHub.
>> When the new update appears on bioconductor?
>>
>> Best,
>>
>> ���
>> Farhad Shokoohi,
>> Ph.D. in Statistics
>>
>>   [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel 
>> <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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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 
delete this email message from your computer. Thank you.
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Re: [Bioc-devel] DMCHMM package new dev release

2018-09-05 Thread Farhad Shokoohi via Bioc-devel 
Hello,

I followed every command. 
Everything is up to date. 



MacBook-Pro:DMCHMM Farhad$ git remote add upstream 
g...@git.bioconductor.org:packages/DMCHMM.git
fatal: remote upstream already exists.
MacBook-Pro:DMCHMM Farhad$ git fetch --all
Fetching origin
Fetching upstream
MacBook-Pro:DMCHMM Farhad$ git checkout master
Switched to branch 'master'
Your branch is up-to-date with 'origin/master'.
MacBook-Pro:DMCHMM Farhad$ 
MacBook-Pro:DMCHMM Farhad$ git merge origin/master
Already up-to-date.
MacBook-Pro:DMCHMM Farhad$ git merge upstream/master
Already up-to-date.
MacBook-Pro:DMCHMM Farhad$ git push upstream master
Everything up-to-date
MacBook-Pro:DMCHMM Farhad$ git push origin master
Everything up-to-date



———
Farhad Shokoohi, 
Ph.D. in Statistics
shoko...@icloud.com

> On Sep 5, 2018, at 9:33 AM, Shepherd, Lori  
> wrote:
> 
> If you didn't set up your remotes  this link may be useful
> 
> https://bioconductor.org/developers/how-to/git/sync-existing-repositories/ 
> <https://bioconductor.org/developers/how-to/git/sync-existing-repositories/>
> 
> 
> 
> Lori Shepherd
> Bioconductor Core Team
> Roswell Park Cancer Institute
> Department of Biostatistics & Bioinformatics
> Elm & Carlton Streets
> Buffalo, New York 14263
> From: Shepherd, Lori
> Sent: Wednesday, September 5, 2018 9:32:08 AM
> To: Obenchain, Valerie; Farhad Shokoohi
> Subject: Re: [Bioc-devel] DMCHMM package new dev release
>  
> You need to commit changes to git.bioconductor.org .  There are no changes 
> pushed to our Bioconductor server. 
> 
> Please ensure you have followed the instructions for setting up your remotes 
> and pushed to the correct location
> https://bioconductor.org/developers/how-to/git/push-to-github-bioc/ 
> <https://bioconductor.org/developers/how-to/git/push-to-github-bioc/>
> 
> I would keep track of the commands you try and if you get any ERRORs please 
> post the commands with full output as a reply all. 
> 
> 
> 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 Farhad 
> Shokoohi via Bioc-devel 
> Sent: Wednesday, September 5, 2018 9:26:58 AM
> To: Obenchain, Valerie
> Cc: bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] DMCHMM package new dev release
>  
> Hello,
> 
> I did everything mentioned in the link. 
> I am also using Sourcetree app on Mac to commit changes but noting changes. 
> 
> Best,
> ———
> Farhad Shokoohi, 
> Ph.D. in Statistics
> shoko...@icloud.com
> 
> > On Sep 4, 2018, at 11:59 AM, Obenchain, Valerie 
> >  wrote:
> > 
> > The builds start ~5pm EST daily. Commits made before that time will be 
> > included in the nightly builds. The build report posts the following day 
> > (see time at top of page):
> > 
> > https://www.bioconductor.org/checkResults/release/bioc-LATEST/ 
> > <https://www.bioconductor.org/checkResults/release/bioc-LATEST/> 
> > <https://www.bioconductor.org/checkResults/release/bioc-LATEST/ 
> > <https://www.bioconductor.org/checkResults/release/bioc-LATEST/>>
> > https://www.bioconductor.org/checkResults/devel/bioc-LATEST/ 
> > <https://www.bioconductor.org/checkResults/devel/bioc-LATEST/> 
> > <https://www.bioconductor.org/checkResults/devel/bioc-LATEST/ 
> > <https://www.bioconductor.org/checkResults/devel/bioc-LATEST/>>
> > 
> > If you don't see the package version you expected it's likely you missed 
> > the cutoff or didn't push to the git.bioconductor.org server. See git 
> > documentation here:
> > 
> > https://www.bioconductor.org/developers/how-to/git/ 
> > <https://www.bioconductor.org/developers/how-to/git/> 
> > <https://www.bioconductor.org/developers/how-to/git/ 
> > <https://www.bioconductor.org/developers/how-to/git/>>
> > 
> > Valerie
> > 
> > 
> > On 09/04/2018 07:58 AM, Farhad Shokoohi via Bioc-devel wrote:
> >> Hello,
> >> 
> >> I have made some changes and updated my package DMCHMM and pushed it to 
> >> GitHub. 
> >> When the new update appears on bioconductor?
> >> 
> >> Best,
> >> 
> >> ———
> >> Farhad Shokoohi, 
> >> Ph.D. in Statistics
> >> 
> >>   [[alternative HTML version deleted]]
> >> 
> >> ___
> >> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org 
> >> <mailto:Bioc-devel@r-project.org>> mailing list
> >> https://stat.ethz.ch/mailman/listi

Re: [Bioc-devel] DMCHMM package new dev release

2018-09-05 Thread Farhad Shokoohi via Bioc-devel 
Hello,

I did everything mentioned in the link. 
I am also using Sourcetree app on Mac to commit changes but noting changes. 

Best,
———
Farhad Shokoohi, 
Ph.D. in Statistics
shoko...@icloud.com

> On Sep 4, 2018, at 11:59 AM, Obenchain, Valerie 
>  wrote:
> 
> The builds start ~5pm EST daily. Commits made before that time will be 
> included in the nightly builds. The build report posts the following day (see 
> time at top of page):
> 
> https://www.bioconductor.org/checkResults/release/bioc-LATEST/ 
> 
> https://www.bioconductor.org/checkResults/devel/bioc-LATEST/ 
> 
> 
> If you don't see the package version you expected it's likely you missed the 
> cutoff or didn't push to the git.bioconductor.org server. See git 
> documentation here:
> 
> https://www.bioconductor.org/developers/how-to/git/ 
> 
> 
> Valerie
> 
> 
> On 09/04/2018 07:58 AM, Farhad Shokoohi via Bioc-devel wrote:
>> Hello,
>> 
>> I have made some changes and updated my package DMCHMM and pushed it to 
>> GitHub. 
>> When the new update appears on bioconductor?
>> 
>> Best,
>> 
>> ———
>> Farhad Shokoohi, 
>> Ph.D. in Statistics
>> 
>>  [[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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Re: [Bioc-devel] DMCHMM package new dev release

2018-09-04 Thread Obenchain, Valerie 
The builds start ~5pm EST daily. Commits made before that time will be included 
in the nightly builds. The build report posts the following day (see time at 
top of page):

https://www.bioconductor.org/checkResults/release/bioc-LATEST/
https://www.bioconductor.org/checkResults/devel/bioc-LATEST/

If you don't see the package version you expected it's likely you missed the 
cutoff or didn't push to the git.bioconductor.org server. See git documentation 
here:

https://www.bioconductor.org/developers/how-to/git/

Valerie


On 09/04/2018 07:58 AM, Farhad Shokoohi via Bioc-devel wrote:

Hello,

I have made some changes and updated my package DMCHMM and pushed it to GitHub.
When the new update appears on bioconductor?

Best,

���
Farhad Shokoohi,
Ph.D. in Statistics

[[alternative HTML version deleted]]

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This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
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[Bioc-devel] DMCHMM package new dev release

2018-09-04 Thread Farhad Shokoohi via Bioc-devel 
Hello,

I have made some changes and updated my package DMCHMM and pushed it to GitHub. 
When the new update appears on bioconductor?

Best,

———
Farhad Shokoohi, 
Ph.D. in Statistics

[[alternative HTML version deleted]]

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