[Bioc-devel] Activating account

[Martin Morgan]

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<mailto: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<mailto:bioc-devel-bounces using r-project.org> on behalf of nlhuong90 using gmail.com<mailto: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<mailto: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<mailto: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

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--
-Lan

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