[Bioc-devel] Activating account

Martin Morgan mtmorg@n@bioc @ending from gm@il@com
Wed Oct 31 22:53:40 CET 2018

‘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.


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


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:
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?


On Wed, Oct 31, 2018 at 2:04 PM Martin Morgan <mtmorgan.bioc using gmail.com<mailto: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<http://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.


From: Lan Huong Nguyen <nlhuong90 using gmail.com<mailto:nlhuong90 using gmail.com>>
Date: Wednesday, October 31, 2018 at 4:43 PM
To: "mtmorgan.bioc using gmail.com<mailto:mtmorgan.bioc using gmail.com>" <mtmorgan.bioc using gmail.com<mailto: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,

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.


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:


    My package TimeSeriesExperiment has been accepted, but I can't activate my
    account on the following website.


    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

    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.


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