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ccagc / QDNAseq

QDNAseq package for Bioconductor
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Syncing with Bioconductor Git repository #64

Closed HenrikBengtsson closed 5 years ago

HenrikBengtsson commented 5 years ago

Issue

This Git repository is out of sync with the Bioconductor Git repository, e.g. the package version here is 1.11.2 whereas the Bioc release version is 1.20.0 and the Bioc develop version is 1.21.0.

The fact that it's out of sync makes me wary about submitting PRs etc.

Suggestion

https://www.bioconductor.org/developers/how-to/git/

PS. I can help setting this up, and proposing a process of keeping it in sync, but then I'd need permissions to push directly to this GitHub repos.

ilarischeinin commented 5 years ago

I gave you write access.

It would be great if you can help out here. And the timing is actually perfect, as there is one thing* why we'd like to have the package updated before this fall's Bioconductor release. Neither me nor @daoud-sie no longer work in the lab, and I haven't actually being involved with anything Bioconductor for 5 years, so I'm completely out of touch with the current conventions. (Back in my day they still used SVN and the git-svn bridge.)

* That one thing is that currently getBinAnnotations() by default downloads from an S3 bucket (with other options being to load from a local directory or from a Bioconductor annotation package like QDNAseq.hg19). The S3 bucket it points to is my personal one, and because the costs have been pennies per month I haven't bothered with it. But two months ago they jumped to >20€/month because of heavy usage (from Cambridge and Sloan-Kettering). And because of that, I'd like to change the default from my S3 bucket to either a new hosting location, or just local file/annotation package.

ilarischeinin commented 5 years ago

Ha! And perfect timing with that too! #67

HenrikBengtsson commented 5 years ago

Fixed. Due to how the Bioconductor repository moved from SVN to Git the history of our git repository (here) and Bioc git had split histories. Because of this, I had to move the old 'master' branch to 'master-20190830' before I could bring the new 'master' branch in sync with Bioconductor devel. In order to do this, I had to do a git push --force. People with cloned repositories locally will have to re-clone.