[Bioc-devel] new package for accessing some chemical and biological databases
No we do not allow such submodules currently in Bioconductor. How big is the object? I assume putting the data object in the package increases the package size over the limit? If this is the case, We would recommend storing the data in the ExperimentHub. See [Creating An ExperimentHub package](https://bioconductor.org/packages/devel/bioc/vignettes/ExperimentHub/inst/doc/CreateAnExperimentHubPackage.html) Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Pierrick Roger <pierrick.roger at cea.fr>
Sent: Wednesday, September 11, 2019 5:04 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] new package for accessing some chemical and biological databases
Sent: Wednesday, September 11, 2019 5:04 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] new package for accessing some chemical and biological databases
Dear all, I'd like to submit by package biodb (https://github.com/pkrog/biodb) in the near future. The aim of this package is to present a unified access to diverse databases (ChEBI, KEGG databases, Uniprot, ...). For running examples, building vignettes and running tests, I use a cache that is stored in another GitHub repository (https://github.com/pkrog/biodb-cache), and registered as a Git submodule of biodb. This cache is currently necessary, since accessing the databases during "R CMD check" would lead to some connection errors and would take too much time. I would like to know if this scheme is acceptable for Bioconductor. Best regards, -- Research engineer Pierrick Roger http://www.cea-tech.fr | http://workflow4metabolomics.org | http://www.metabohub.fr https://fr.linkedin.com/in/pkrog | https://github.com/pkrog In varietate concordia. _______________________________________________ Bioc-devel at 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.