[Bioc-devel] NanoStringDiff package update

Fri Jan 26 12:50:36 CET 2018

If you have successfully pushed to the git.bioconductor.org server (which I do see your changes) with a valid version bump (which the last was),  the changes will become available to the user on the next build of the system.  We do nightly builds so it should appear on the daily build report with the updated version within the next 24 hours

http://bioconductor.org/checkResults/3.7/bioc-LATEST/

Cheers,

Thank you for your efforts!

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Zhai, Tingting <tingting.zhai at uky.edu>
Sent: Thursday, January 25, 2018 6:00:57 PM
To: Shepherd, Lori
Cc: Martin Morgan; Turaga, Nitesh
Subject: Re: [Bioc-devel] NanoStringDiff package update

I think I have successfully pushed my package files with version 1.9.1 to both Bioconductor and GitHub repositories, and repeated for the release branch with version 1.8.1. So what next I should do to make my updated package available to users?  Thank you again for all your help!

Best wishes,
Tingting

On Thu, Jan 25, 2018 at 1:58 PM, Shepherd, Lori <Lori.Shepherd at roswellpark.org<mailto:Lori.Shepherd at roswellpark.org>> wrote:

So you are missing the upstream remote.  I'm not exactly sure how it got deleted and how you have been able to push to master.

It looks like you have created a github repository for your package and should be following

Create a new GitHub repository tutorial:

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

using origin will push/pull to your github repository

using upstream (once it is added) will push/pull to our git.bioconductor.org<http://git.bioconductor.org> server

You'll want to pick up the above page at step 6 for adding the upstream remote.

Cheers,

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Zhai, Tingting <tingting.zhai at uky.edu<mailto:tingting.zhai at uky.edu>>
Sent: Thursday, January 25, 2018 1:47:51 PM
To: Shepherd, Lori
Cc: Martin Morgan; Turaga, Nitesh

Subject: Re: [Bioc-devel] NanoStringDiff package update

the results of

git remote -v :

origin git at github.com:tingtina/NanoStringDiff.git (fetch)

origin git at github.com:tingtina/NanoStringDiff.git (push)

I'm trying to change the version on the master branch to 1.9.1.

Thanks,

Tingting

On Thu, Jan 25, 2018 at 1:26 PM, Shepherd, Lori <Lori.Shepherd at roswellpark.org<mailto:Lori.Shepherd at roswellpark.org>> wrote:

Can you please send the results of

git remote -v

Also please note:

The version on the master branch (devel) should be 1.9.1

The 1.8.1 will be for RELEASE_3_6

Versions are package_x.y.z   the y in devel is always odd,  y in release is always even, and devel y >  release y

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Zhai, Tingting <tingting.zhai at uky.edu<mailto:tingting.zhai at uky.edu>>
Sent: Thursday, January 25, 2018 1:17:22 PM

To: Shepherd, Lori
Cc: Martin Morgan
Subject: Re: [Bioc-devel] NanoStringDiff package update

Hi Lori,
Sorry to bother you again. Now I have successfully pushed my package files with version 1.8.1 to both Bioconductor and GitHub repositories. But when I repeat for the release branch with "git push upstream RELEASE_3_6", I get following error:

fatal: 'upstream' does not appear to be a git repository

fatal: Could not read from remote repository.

Please make sure you have the correct access rights

and the repository exists.

Could you help me fix this out?

Thanks,
Tingting

On Thu, Jan 25, 2018 at 11:50 AM, Shepherd, Lori <Lori.Shepherd at roswellpark.org<mailto:Lori.Shepherd at roswellpark.org>> wrote:

The current release branch is RELEASE_3_6

So the bottom section instructions would use that as the release branch:

http://bioconductor.org/developers/how-to/git/maintain-bioc-only/

I do see the changes on the git.bioconductor.org<http://git.bioconductor.org> so your push was successful however this is one issue:

Please pay attention to version numbers. I just did a quick glance at the changes that were uploaded and the version number committed is less than the current devel version :

http://bioconductor.org/checkResults/3.7/bioc-LATEST/NanoStringDiff/malbec2-buildsrc.html

The current devel version we have is 1.9.0 and you submitted changes with 1.7.1

Please see the section on versioning

http://bioconductor.org/developers/how-to/version-numbering/

and the recent devel post

https://stat.ethz.ch/pipermail/bioc-devel/2018-January/012657.html

While your changes are on the git server the package won't be rebuild because of the lower Description version number. It needs to be corrected on the master branch to 1.9.1.

When you submit your changes on the RELEASE_3_6 branch the current version we have is 1.8.0 so the changes should be committed with 1.8.1 ...

The version increases happen at release time.  You should pull from the git repository after a release happens and periodically.

http://bioconductor.org/developers/how-to/git/pull-upstream-changes/

Cheers,

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Zhai, Tingting <tingting.zhai at uky.edu<mailto:tingting.zhai at uky.edu>>
Sent: Thursday, January 25, 2018 11:13:44 AM
To: Shepherd, Lori
Cc: Martin Morgan

Subject: Re: [Bioc-devel] NanoStringDiff package update

Hi Lori and Morgan,
I am taking the "Maintain a Bioconductor-only repository tutorial". I'm done with "Push your local commits to the Bioconductor repository" so far. So what next I should do to make my new package available to the user community?
I guess I need to do the next step "Merge changes to the current release branch", but I don't know my current release branch.
Could you all help me out?

Thank you!
Best wishes,
Tingting

On Thu, Jan 25, 2018 at 9:58 AM, Shepherd, Lori <Lori.Shepherd at roswellpark.org<mailto:Lori.Shepherd at roswellpark.org>> wrote:

Sorry for the delay.  Please try again. We have just processed the keys again and it should be accessible.  If you continue to have issues please reply all so that it stays on the devel mailing list thread and other members of the team can also assist.

Cheers

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Zhai, Tingting <tingting.zhai at uky.edu<mailto:tingting.zhai at uky.edu>>
Sent: Thursday, January 25, 2018 9:49:47 AM
To: Shepherd, Lori
Subject: Re: [Bioc-devel] NanoStringDiff package update

Hi Lori,
You are so helpful! I really appreciate it!
I submitted the form you mentioned above two days ago (Jan. 23). But when I run "git clone git at git.bioconductor.org:packages/NanoStringDiff.git", I still get the error that "Permission denied (publickey).
fatal: Could not read from remote repository." Does it mean that my key has not been added to your system?

Thank you again for your help.

Best wishes,
Tingting

On Thu, Jan 25, 2018 at 7:13 AM, Shepherd, Lori <Lori.Shepherd at roswellpark.org<mailto:Lori.Shepherd at roswellpark.org>> wrote:

Bioconductor has switched from svn to git, and was announced back in August 2017, so you are correct that you are no longer able to use svn to upload changes to the new location for the Bioconductor repository

git.bioconductor.org<http://git.bioconductor.org>

You don't have to use github to maintain your package locally (we do recommend it but not necessary) but we do require git for maintaining the Bioconductor canonical location.  There are lots of scenarios and useful FAQ section on the Bioconductor website

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

Create a new GitHub repository tutorial - will take you through how to convert an existing directory onto github and how to maintain the two locations (local github and bioconductor git location)

Maintain a Bioconductor-only repository  tutorial - will take you through how to link to the Bioconductor git.bioconductor.org<http://git.bioconductor.org> repository without creating a github.

There are many tutorials with how to push changes and how to pull from the Bioconductor repo (after a release happens this is necessary) and how to trouble shoot common issues.

The first step will be to submit an id and ssh-key to the following form to gain access to the package

https://docs.google.com/forms/d/1CCwUhjtG82rnmcTWYqY43WcmBx5YyQm5UD4pcs1dhEs/viewform?edit_requested=true

You will need to enter your email -  because you had an svn account your svn.id<http://svn.id> - and a ssh public key -

Cheers,

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces at r-project.org<mailto:bioc-devel-bounces at r-project.org>> on behalf of Zhai, Tingting <tingting.zhai at uky.edu<mailto:tingting.zhai at uky.edu>>
Sent: Wednesday, January 24, 2018 2:17:17 PM
To: bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>
Subject: [Bioc-devel] NanoStringDiff package update

I’m one of the maintainers of NanoStringDiff package on Bioconductor. Now I
want to update this package and add some useful functions. I’m using SVN,
but when committing, it gives me this error: The new canonical location for
Bioconductor software and

data experiment packages is git.bioconductor.org<http://git.bioconductor.org>

The recommended way to maintain your Bioconductor software

or data experiment package is to use GitHub.

Does this mean I’m not able to use SVN to maintain my package any more? I’m
not familiar with github.

Thank you very much for any help in advance.

Best wishes,

Tingting

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