[Bioc-devel] NanoStringDiff package update

Fri Jan 26 00:00:57 CET 2018

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> 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 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>
> *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> 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>
> *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> 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 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/NanoStr
> ingDiff/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>
> *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> 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>
> *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> 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
>
>
> 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 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/1CCwUhjtG82rnmcTWYqY43WcmBx5
> YyQm5UD4pcs1dhEs/viewform?edit_requested=true
>
>
> You will need to enter your email -  because you had an svn account your
> 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> on behalf of Zhai,
> Tingting <tingting.zhai at uky.edu>
> *Sent:* Wednesday, January 24, 2018 2:17:17 PM
> *To:* 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
>
>
> 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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>
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