[Bioc-devel] Activating account

[Lan Huong Nguyen]

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

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