Hi Hervé, I've made a new package with metadata.csv, as described in CreateAnAnnotationPackage vignette.
The data is located on the public service as a zipped SQLite database. So I've set both SourceType and DispatchClass as 'Zip'. >From AnnotationHub::DispatchClassList() I expect that I should have an unzipped file path. My first question is: how do I get that path? The second question is: what should I put into make-data.R? The database is already created, cleaned and validated. All I need for the package is to download it, unzip and connect. Thank you, Anatoly On Thu, Aug 26, 2021 at 12:59 PM Hervé Pagès <hpages.on.git...@gmail.com> wrote: > Hi Anatoly, > > Let's keep this conversation on the bioc-devel mailing list where it > started. > > On 26/08/2021 02:46, Anatoly Sorokin wrote: > > Hi Hervé, > > > > thank you for your answer. Does this mean that the SQLite file will be > > downloaded separately and kept in some cache? > > Yes. > > > > > And another question: does this mean that there should be two packages, > > one for code and another one for the database? > > Yes. One is what we call the software package and the other one the > accompanying data package. > > Cheers, > H. > > > > > On Wed, Aug 25, 2021 at 6:58 AM Hervé Pagès <hpages.on.git...@gmail.com > > <mailto:hpages.on.git...@gmail.com>> wrote: > > > > Hi Anatoly, > > > > What kind of data is in your SQLite database? The Bioconductor > approach > > for this is to provide the data as a separate data annotation or data > > experiment package. More precisely, the data itself should go on > > AnnotationHub or ExperimentHub. It should be associated with a "Hub > > package", that is, a data package that documents it and explains how > to > > retrieve it from AnnotationHub or ExperimentHub. See vignettes in the > > HubPub package for more information: > > > > http://bioconductor.org/packages/HubPub > > <http://bioconductor.org/packages/HubPub> > > > > Best, > > > > H. > > > > On 24/08/2021 17:53, Nitesh Turaga wrote: > > > Hi, > > > > > > We don’t have LFS support on the Bioconductor git server. > > > > > > I would suggest finding an alternative. > > > > > > Best, > > > > > > > > > > > > > > > Nitesh Turaga > > > Scientist II, Department of Data Science, > > > Bioconductor Core Team Member > > > Dana Farber Cancer Institute > > > > > >> On Aug 24, 2021, at 6:18 PM, Anatoly Sorokin <lpto...@gmail.com > > <mailto:lpto...@gmail.com>> wrote: > > >> > > >> Hi all, > > >> > > >> we have developed a package that provides access to the data in > > the locally > > >> stored SQLite database. The GitHub Action successfully built the > > package, > > >> but in Bioconductor, it got an error. The only reason for the > > error is that > > >> the database itself is stored on GitHub via git-lfs, and the R > > code got an > > >> lfs placeholder instead of the actual database. > > >> > > >> Is it possible to activate lfs within Bioconductor automatic > > building > > >> server? The database is tiny (80 Mb), but I don't want to have > > it as a > > >> regular git object. > > >> > > >> Thank you, > > >> Anatoly > > >> > > >> [[alternative HTML version deleted]] > > >> > > >> _______________________________________________ > > >> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> > > mailing list > > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > <https://stat.ethz.ch/mailman/listinfo/bioc-devel> > > > > > > _______________________________________________ > > > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> > > mailing list > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > <https://stat.ethz.ch/mailman/listinfo/bioc-devel> > > > > > > > -- > > Hervé Pagès > > > > Bioconductor Core Team > > hpages.on.git...@gmail.com <mailto:hpages.on.git...@gmail.com> > > > > -- > Hervé Pagès > > Bioconductor Core Team > hpages.on.git...@gmail.com > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel