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.b...@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 <nlhuon...@gmail.com> > *Date: *Wednesday, October 31, 2018 at 5:29 PM > *To: *"mtmorgan.b...@gmail.com" <mtmorgan.b...@gmail.com> > *Cc: *"bioc-devel@r-project.org" <bioc-devel@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.b...@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 <nlhuon...@gmail.com> > *Date: *Wednesday, October 31, 2018 at 4:43 PM > *To: *"mtmorgan.b...@gmail.com" <mtmorgan.b...@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.b...@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-boun...@r-project.org on behalf of nlhuon...@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: > > "m...@email.com is not associated with a maintainer of a Bioconductor > package. Please check the spelling or contact bioc-devel@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@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > -- > > -Lan > > > > > -- > > -Lan > -- -Lan [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
