[Bioc-devel] Activating account

[Lan Huong Nguyen]

Thank you very much!

All is clear now. Sorry for a lot of confusion.

Best,
Lan

On Wed, Oct 31, 2018 at 2:53 PM Martin Morgan <mtmorgan.bioc using gmail.com>
wrote:

> ‘We’ (bioc-gitadmin) do not have write permissions to your github
> repository.
>
>
>
> Likely what you did was fetch and merge (i.e., pull) from upstream/master,
> and then push to origin/master (assuming upstream is git.bioconductor.org:packages/TimeSeriesExperiment
> and origin is github.com:nlhuong/TimeSeriesExperiment).
>
>
>
> The fetch / merge from upstream brings the ‘version bump’ commit that we
> made at git.bioconductor.org to your local repository. The push to origin
> sends the version bump commit from your local repository to github.
>
>
>
> Martin
>
>
>
> *From: *Lan Huong Nguyen <nlhuong90 using gmail.com>
> *Date: *Wednesday, October 31, 2018 at 5:29 PM
> *To: *"mtmorgan.bioc using gmail.com" <mtmorgan.bioc using gmail.com>
> *Cc: *"bioc-devel using r-project.org" <bioc-devel using r-project.org>
>
>
> *Subject: *Re: [Bioc-devel] Activating account
>
>
>
> Hi!
>
>
>
> Thank you very much for a detailed response!
>
>
>
> I will check tomorrow for the build whether the files downloaded from the
> server and the vignette rendering completed.
>
>
>
> Thank you for clarification on the versioning. Now I understand that:
>
> 1. Bug fixes for the current release RELEASE_3_8, should be done by
> bumping the version to 1.0.1, 1.0.2 etc. and pushing to upstream/RELEASE_3_8
>
> 2. New features/bug fixes for the development, i.e. master branch (future
> RELEASE_3_9) should be done by bumping
>
> version to 1.1.1, 1.1.2 etc. and pushing to upstream/master
>
>
>
> I have another question on my user github repository. I noticed that a
>  'bioc-gitadmin' <https://github.com/bioc-gitadmin> user changed
>
> my DESCRIPTION file to 1.0.0 and then to 1.1.0 on my user github
> repository at:
>
> https://github.com/nlhuong/TimeSeriesExperiment
>
> which seems odd, as all other packages have the version changes only on
> the
>
> bioconductor repository and not on their own user github repo. Was this
> done due to my package build
>
> error caused by the vignette?
>
>
>
> Best,
>
> Lan
>
>
>
>
>
>
>
>
>
> On Wed, Oct 31, 2018 at 2:04 PM Martin Morgan <mtmorgan.bioc using gmail.com>
> wrote:
>
> Please always include bioc-devel in your email, so that other developers
> with similar questions can help, or others with knowledge can help.
>
>
>
> Remember that there are two branches in Bioconductor, the ‘release’ branch
> and the ‘devel’ branch.
>
>
>
> Your package was added to the devel branch prior to the release, with a
> version number 0.99.x (I’m not sure what ‘x’ was…)
>
>
>
> At release, we made a new branch RELEASE_3_8 in your package at
> git.bioconductor.org and bumped the version to 1.0.0. If you make bug
> fixes in this branch, you will need to make version bumps to 1.0.1, 1.0.2, …
>
>
>
> At the same time, we incremented the master branch to 1.1.0, so that the
> master (devel) branch has a version number that is greater than release. If
> you introduce new features or bug fixes here, then the versions will be
> 1.1.1, 1.1.2, 1.1.3, …
>
>
>
> At the next release, the process will repeat – we will create a new branch
> RELEASE_3_9 and change the version to 1.2.0; master will have version
> change to 1.3.0. Release versions are always even in the second position.
> Devel versions are always odd (and one more than release).
>
>
>
> This is explained at
> http://bioconductor.org/developers/how-to/version-numbering/
>
>
>
> The release version of your package did not build on linux (note that this
> is version 1.0.0, not the devel version 1.1.0), so it did not ‘propagate’
> to the public web site and repository. It looks like it failed at this
> point in the vignette:
>
>
>
> trying to add rname '
> https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE114762&format=file&file=GSE114762_sample_info.csv.gz'
> produced error:
>
>   Empty reply from server
>
>
>
> And it looks like your package failed because the geo server did not
> respond. It is not clear why the server did not respond, but that seems to
> be the nature of internet connectivity. What will happen is, likely,
> tonight your package will retrieve the file from the server and build
> successfully. The package will then propagate and be available in release
> as version 1.0.0. Since you are using BiocFileCache, it is likely that any
> future problems with the server will not be catastrophic like this – the
> file will already be available locally.
>
>
>
> Martin
>
>
>
>
>
> *From: *Lan Huong Nguyen <nlhuong90 using gmail.com>
> *Date: *Wednesday, October 31, 2018 at 4:43 PM
> *To: *"mtmorgan.bioc using gmail.com" <mtmorgan.bioc using gmail.com>
> *Subject: *Re: [Bioc-devel] Activating account
>
>
>
> In addition to why the package seem to why the package seem to return
> error on Linux at https://bioconductor.org/checkResults/3.8/bioc-LATEST/
>
>
>
> I am also curious why my package version is now 1.1.0 instead of 1.0.0.
>
>
>
> Thank you,
>
> Lan
>
>
>
> On Wed, Oct 31, 2018 at 12:48 PM Martin Morgan <mtmorgan.bioc using gmail.com>
> wrote:
>
> Thanks for your patience; the account information has been updated,
> including with your github ssh keys.
>
> Martin
>
> On 10/31/18, 1:58 PM, "Bioc-devel on behalf of Lan Huong Nguyen" <
> bioc-devel-bounces using r-project.org on behalf of nlhuong90 using gmail.com> wrote:
>
>     Hi!
>
>     My package TimeSeriesExperiment has been accepted, but I can't
> activate my
>     account on the following website.
>
>     https://git.bioconductor.org/BiocCredentials/account_activation/
>
>     I receive the following message:
>
>     "my using email.com is not associated with a maintainer of a Bioconductor
>     package. Please check the spelling or contact bioc-devel using r-project.org
> for
>     help."
>
>     I have had my public keys available on the github account before.
>
>     Please let me know if you can check what is wrong and if my package has
>     been added to the build.
>
>     Best,
>     Lan
>
>         [[alternative HTML version deleted]]
>
>     _______________________________________________
>     Bioc-devel using r-project.org mailing list
>     https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
>
> --
>
> -Lan
>
>
>
>
> --
>
> -Lan
>
-- 
-Lan

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