Hi, Historically annotation packages were not reviewed in the package tracker. Last year I starting asking authors to upload the package to a S3 bucket and open an issue on the package tracker (with no upload). I reviewed the package and posted comments to the tracker. This kept all communication in one place and gave us a record of approved packages. It doesn't sound like this system will work with the new tracker.
For annotation and large experimental data packages maybe we need an option to create an issue without an associated github repo? Or at least a flag that prevents a commit from kicking off a new build (would fail if data are in S3/dropbox/etc. and only software is in github). This separation of data and software is not a problem with resources contributed to ExperimentHub. Data are permanently stored in S3 and the parent software package submitted to the tracker uses ExperimentHub() to load the data. Kasper, if your package is annotation and not experimental data and you want it as a package instead of in AnnotationHub please upload to this S3 bucket aws --profile username s3 cp dataobject s3://contributed-annotation-experiment/myannotationpackage --acl public-read and I'll start the review from there. If you'd rather put the data in AnnotationHub I can help with that too. Val On 06/15/2016 05:01 AM, Martin Morgan wrote: > On 06/14/2016 10:10 PM, Kasper Daniel Hansen wrote: >> In my case its an annotation package thats >100MB. But I could imagine >> experiment package doing that as well. > very large packages don't play well with SVN or the repository, e.g., > placing storage burden on repository mirrors. ExperimentHub might be a > better, emerging, solution... > > Martin > >> On Tue, Jun 14, 2016 at 10:08 PM, Dan Tenenbaum <dtene...@fredhutch.org> >> wrote: >> >>> Actually, here is the process for experiment packages: >>> >>> >>> https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md#submitting-related-packages >>> >>> Not sure what to do if there is a file > 100MB. There is git/github large >>> file storage but we don't explicitly support it. >>> Maybe it belongs in ExperimentHub instead? >>> >>> Dan >>> >>> >>> ----- Original Message ----- >>>> From: "Dan Tenenbaum" <dtene...@fredhutch.org> >>>> To: "Kasper Daniel Hansen" <kasperdanielhan...@gmail.com> >>>> Cc: "bioc-devel" <bioc-devel@r-project.org> >>>> Sent: Tuesday, June 14, 2016 7:02:25 PM >>>> Subject: Re: [Bioc-devel] submitting annotation and data package >>>> For annotation packages, see this: >>>> >>>> >>> https://bioconductor.org/developers/package-submission/#annotation-packages >>>> For experiment packages, I'm not sure. >>>> >>>> Dan >>>> >>>> >>>> ----- Original Message ----- >>>>> From: "Kasper Daniel Hansen" <kasperdanielhan...@gmail.com> >>>>> To: "bioc-devel" <bioc-devel@r-project.org> >>>>> Sent: Tuesday, June 14, 2016 6:28:06 PM >>>>> Subject: Re: [Bioc-devel] submitting annotation and data package >>>>> Also, just a point, GitHub does not allow files >100MB. That is a >>>>> non-issue (I hope) for software packages, but could be hit by annotation >>>>> packages, including one I maintain >>>>> >>>>> On Tue, Jun 14, 2016 at 8:53 PM, Kasper Daniel Hansen < >>>>> kasperdanielhan...@gmail.com> wrote: >>>>> >>>>>> Should I submit a new annotation and a new data package through the new >>>>>> GitHub interface, or use something differently? >>>>>> >>>>>> Best, >>>>>> Kasper >>>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> Bioc-devel@r-project.org mailing list >>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>> _______________________________________________ >>>> Bioc-devel@r-project.org mailing list >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > This email message may contain legally privileged and/or...{{dropped:2}} > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
