[Bioc-devel] package has been cleaned for large data files and needs to be reset.

Thu Oct 17 17:20:56 CEST 2019

I believe we have reset it.

Please really look at the documentation
http://bioconductor.org/developers/how-to/git/

If you set up remotes to be linked to Bioc, please always remember to pull from bioc before making changes
git pull upstream master

# make changes
# push to both

git push   # your github
git push upstream  master  # bioc

For What Its Worth -  Your changes won't currently be recognized even with the reset because there was no version bump in the DESCRIPTION.   Please try and bump the version of your package following:

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

Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Cuklina Jelena <jelena.chuklina using imsb.biol.ethz.ch>
Sent: Thursday, October 17, 2019 6:26 AM
To: Shepherd, Lori <Lori.Shepherd using RoswellPark.org>; Michael Lawrence via Bioc-devel <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] package has been cleaned for large data files and needs to be reset.

Dear Lori, dear Bioconductor team,

I have re-cleaned the repository, could you please run the tests again and reset the upstream?

Thank you very much for the support.

Best regards,
Jelena Čuklina.
On 16 Oct 2019, 16:01 +0200, Shepherd, Lori <Lori.Shepherd using RoswellPark.org>, wrote:
Hi Jelena,

I was running some checks on your repository before I reset it.  It looks like you cleaned the repository but the the repository you cleaned is not from our git.bioconductor.org.  This is evident as the release commits that occur are missing from your current repo
```
git log --all --grep "RELEASE"
```

Displays nothing but it should be in sync with our git.bioconductor.org repository and have the commits from last release.

Something like
```
Author: Nitesh Turaga <nitesh.turaga using gmail.com>
Date:   Thu May 2 12:14:38 2019 -0400

    bump x.y.z versions to odd y after creation of RELEASE_3_9    branch

```

You will need to merge the master branch from the upstream remote of bioconductor and clean the repo as necessary from there.

The two most relevant help files:

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

Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
Sent: Wednesday, October 16, 2019 7:19 AM
To: Cuklina Jelena <jelena.chuklina using imsb.biol.ethz.ch>; Michael Lawrence via Bioc-devel <bioc-devel using r-project.org>; Jelena Chuklina <chuklina.jelena using gmail.com>
Subject: Re: [Bioc-devel] package has been cleaned for large data files and needs to be reset.

I am working on the reset now.  I will email again when we think it is set.  Sorry for the delay.

Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Cuklina Jelena <jelena.chuklina using imsb.biol.ethz.ch>
Sent: Wednesday, October 16, 2019 5:56 AM
To: Michael Lawrence via Bioc-devel <bioc-devel using r-project.org>; Jelena Chuklina <chuklina.jelena using gmail.com>
Subject: Re: [Bioc-devel] package has been cleaned for large data files and needs to be reset.

Dear Bioconductor team,

May I ask on the process of the package reset? How do I know the Bioconductor upstream of my project has been updated/failed?

Thank you very much for your work.

Best regards,
Jelena �uklina.
On 14 Oct 2019, 18:49 +0200, Jelena Chuklina <chuklina.jelena using gmail.com>, wrote:
Dear Bioconductor team,

We�ve cleaned the updated repository for large files and duplicates and would like to reset the upstream master branch as well as release branch.

Could you please help with that?

GitHub version of the package is: https://github.com/symbioticMe/proBatch

Thank you in advance!

Best regards,
Jelena �uklina.

[[alternative HTML version deleted]]

_______________________________________________
Bioc-devel using r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

        [[alternative HTML version deleted]]

_______________________________________________
Bioc-devel using 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]]

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.
	[[alternative HTML version deleted]]