[Bioc-devel] new package for accessing some chemical and biological databases

Shepherd, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Wed Sep 11 13:19:41 CEST 2019

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 using r-project.org> on behalf of Pierrick Roger <pierrick.roger using cea.fr>
Sent: Wednesday, September 11, 2019 5:04 AM
To: bioc-devel using r-project.org <bioc-devel using 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
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.

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