I can do that (when Im done in a day or two), but just wanted to add that right now I have my annotation / data packages on Bitbucket which has some of the same advantages as Github but does not have a 100MB limit on files (in effect it has a similar 1-2GB limit on repo size). That would allow review to be done as issues / etc, but there is no integration with the build system.
Best, Kasper On Wed, Jun 15, 2016 at 10:52 AM, Obenchain, Valerie < valerie.obench...@roswellpark.org> wrote: > On 06/15/2016 07:33 AM, Obenchain, Valerie wrote: > > 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 > > Sorry, the 'cp' part was confusing, this should have read: > > aws --profile username s3 cp myannotationpackage > s3://contributed-annotation-experiment/myannotationpackage --acl > public-read > > Val > > > > > > 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 > > > > > > 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. 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