Re: [Bioc-devel] BFG clean-up and reset for compartmap

2021-05-11 Thread Nitesh Turaga 
cc-ing bioc-devel

From: Nitesh Turaga 
Date: Tuesday, May 11, 2021 at 10:13 AM
To: Johnson, Ben 
Subject: Re: BFG clean-up and reset for compartmap
That is exactly right.

I would also delete/archive non-bioconductor feature branches like dev, hg38 
etc. Only master and RELEASE_X_Y branches should be available.

Best,

Nitesh

From: Johnson, Ben 
Date: Tuesday, May 11, 2021 at 10:11 AM
To: Nitesh Turaga 
Subject: Re: BFG clean-up and reset for compartmap
Hi Nitesh,

Apologies for not having the github in the state it should be in. Just to 
clarify, I need to follow the steps outlined here 
(https://bioconductor.org/developers/how-to/git/sync-existing-repositories/) 
through the merges, run the BFG, and contact you again for the force reset?

Again, my apologies if these are all naïve. Thanks for your time!

Best,
Ben K Johnson

Postdoctoral Fellow
Department of Epigenetics
Van Andel Institute
333 Bostwick Ave. NE
Grand Rapids, MI 49503


From: Nitesh Turaga 
Date: Tuesday, May 11, 2021 at 2:06 PM
To: Johnson, Ben , bioc-devel@r-project.org 

Subject: [External] Re: BFG clean-up and reset for compartmap
Hi,

Thanks for sending the github repo.

I noticed that the repo is missing the RELEASE branches. You’ll have to sync 
this from the Bioconductor repo. I cannot merge just a orphan devel branch into 
what exists on git.bioconductor.org.

You’ll have to have sync your github repo, sync all the branches and run BFG.

Best,

Nitesh

From: Johnson, Ben 
Date: Tuesday, May 11, 2021 at 8:02 AM
To: Nitesh Turaga , bioc-devel@r-project.org 

Subject: Re: BFG clean-up and reset for compartmap
Hi Nitesh,

It would be https://github.com/biobenkj/compartmap. Thanks!

Best,
Ben K Johnson

Postdoctoral Fellow
Department of Epigenetics
Van Andel Institute
333 Bostwick Ave. NE
Grand Rapids, MI 49503


From: Nitesh Turaga 
Date: Tuesday, May 11, 2021 at 2:01 PM
To: Johnson, Ben , bioc-devel@r-project.org 

Subject: [External] Re: BFG clean-up and reset for compartmap
Hi,

What exactly is the github repo we have to pull from?

Nitesh

From: Bioc-devel  on behalf of Johnson, Ben 

Date: Monday, May 10, 2021 at 3:11 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] BFG clean-up and reset for compartmap
Hi all,

We had a couple manifest files that were needing to be cleaned out to pass 
BiocCheck and were removed using the BFG. I�d like to request a reset/force 
pull upstream into the BioC devel git server repo 
(g...@git.bioconductor.org:packages/compartmap<mailto:g...@git.bioconductor.org:packages/compartmap>)
 to commit various bugfixes and API changes for compartmap.

Thanks so much!

Best,
Ben K Johnson

Postdoctoral Fellow
Department of Epigenetics
Van Andel Institute
333 Bostwick Ave. NE
Grand Rapids, MI 49503


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Re: [Bioc-devel] BFG clean-up and reset for compartmap

2021-05-11 Thread Nitesh Turaga 
Hi,

Thanks for sending the github repo.

I noticed that the repo is missing the RELEASE branches. You’ll have to sync 
this from the Bioconductor repo. I cannot merge just a orphan devel branch into 
what exists on git.bioconductor.org.

You’ll have to have sync your github repo, sync all the branches and run BFG.

Best,

Nitesh

From: Johnson, Ben 
Date: Tuesday, May 11, 2021 at 8:02 AM
To: Nitesh Turaga , bioc-devel@r-project.org 

Subject: Re: BFG clean-up and reset for compartmap
Hi Nitesh,

It would be https://github.com/biobenkj/compartmap. Thanks!

Best,
Ben K Johnson

Postdoctoral Fellow
Department of Epigenetics
Van Andel Institute
333 Bostwick Ave. NE
Grand Rapids, MI 49503


From: Nitesh Turaga 
Date: Tuesday, May 11, 2021 at 2:01 PM
To: Johnson, Ben , bioc-devel@r-project.org 

Subject: [External] Re: BFG clean-up and reset for compartmap
Hi,

What exactly is the github repo we have to pull from?

Nitesh

From: Bioc-devel  on behalf of Johnson, Ben 

Date: Monday, May 10, 2021 at 3:11 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] BFG clean-up and reset for compartmap
Hi all,

We had a couple manifest files that were needing to be cleaned out to pass 
BiocCheck and were removed using the BFG. I�d like to request a reset/force 
pull upstream into the BioC devel git server repo 
(g...@git.bioconductor.org:packages/compartmap<mailto:g...@git.bioconductor.org:packages/compartmap>)
 to commit various bugfixes and API changes for compartmap.

Thanks so much!

Best,
Ben K Johnson

Postdoctoral Fellow
Department of Epigenetics
Van Andel Institute
333 Bostwick Ave. NE
Grand Rapids, MI 49503


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recognize the sender and know the content is safe. If you have any questions, 
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Re: [Bioc-devel] BFG clean-up and reset for compartmap

2021-05-11 Thread Johnson, Ben 
Hi Nitesh,

It would be https://github.com/biobenkj/compartmap. Thanks!

Best,
Ben K Johnson

Postdoctoral Fellow
Department of Epigenetics
Van Andel Institute
333 Bostwick Ave. NE
Grand Rapids, MI 49503


From: Nitesh Turaga 
Date: Tuesday, May 11, 2021 at 2:01 PM
To: Johnson, Ben , bioc-devel@r-project.org 

Subject: [External] Re: BFG clean-up and reset for compartmap
Hi,

What exactly is the github repo we have to pull from?

Nitesh

From: Bioc-devel  on behalf of Johnson, Ben 

Date: Monday, May 10, 2021 at 3:11 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] BFG clean-up and reset for compartmap
Hi all,

We had a couple manifest files that were needing to be cleaned out to pass 
BiocCheck and were removed using the BFG. I�d like to request a reset/force 
pull upstream into the BioC devel git server repo 
(g...@git.bioconductor.org:packages/compartmap<mailto:g...@git.bioconductor.org:packages/compartmap>)
 to commit various bugfixes and API changes for compartmap.

Thanks so much!

Best,
Ben K Johnson

Postdoctoral Fellow
Department of Epigenetics
Van Andel Institute
333 Bostwick Ave. NE
Grand Rapids, MI 49503


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(nturaga.b...@gmail.com). Do not click links or open attachments unless you 
recognize the sender and know the content is safe. If you have any questions, 
please contact serviced...@vai.org<mailto:serviced...@vai.org>.

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Re: [Bioc-devel] BFG clean-up and reset for compartmap

2021-05-11 Thread Nitesh Turaga 
Hi,

What exactly is the github repo we have to pull from?

Nitesh

From: Bioc-devel  on behalf of Johnson, Ben 

Date: Monday, May 10, 2021 at 3:11 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] BFG clean-up and reset for compartmap
Hi all,

We had a couple manifest files that were needing to be cleaned out to pass 
BiocCheck and were removed using the BFG. I�d like to request a reset/force 
pull upstream into the BioC devel git server repo 
(g...@git.bioconductor.org:packages/compartmap<mailto:g...@git.bioconductor.org:packages/compartmap>)
 to commit various bugfixes and API changes for compartmap.

Thanks so much!

Best,
Ben K Johnson

Postdoctoral Fellow
Department of Epigenetics
Van Andel Institute
333 Bostwick Ave. NE
Grand Rapids, MI 49503


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[Bioc-devel] BFG clean-up and reset for compartmap

2021-05-10 Thread Johnson, Ben 
Hi all,

We had a couple manifest files that were needing to be cleaned out to pass 
BiocCheck and were removed using the BFG. I�d like to request a reset/force 
pull upstream into the BioC devel git server repo 
(g...@git.bioconductor.org:packages/compartmap)
 to commit various bugfixes and API changes for compartmap.

Thanks so much!

Best,
Ben K Johnson

Postdoctoral Fellow
Department of Epigenetics
Van Andel Institute
333 Bostwick Ave. NE
Grand Rapids, MI 49503


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