[Bioc-devel] Forking out modules from existing packages as new packages

Shian Su @u@@ @end|ng |rom weh|@edu@@u
Sat Aug 24 05:31:49 CEST 2019

Hi Koustav,

My opinion on this is to split the visualisations out into a separate package but keep the functions in the existing package. Then when the new visualisation package is released, depend on it from the existing package.

It’s worth asking: Is the package actually worth splitting up? If the two packages are interdependent as a workflow, i.e. if the visualisations apply only to data produced by the specific methods, then there’s no reason to split them up.

This happens quite often in package development. The goal is to not let users of your existing package lose any functionality when installing new versions of your package because those functions went to another package.

Kind regards,
Shian Su
PhD Student, Ritchie Lab, Epigenetics and Development
Walter & Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville VIC 3052, Australia

On 23 Aug 2019, at 10:08 pm, Koustav Pal <koustav.pal using ifom.eu<mailto:koustav.pal using ifom.eu>> wrote:


I have a curious scenario, I have a package which has some visualisation modules. But, as package development progresses, I think that possibly the visualisation modules themselves might deserve a package for themselves. This would imply,

1. Removing the aforementioned modules from the first package
2. Making a new package for these modules and submitting a new package to Bioconductor.

Has this been done before? What are the best practices? To remove the modules entirely? Or to preserve the old ones in the package while continuing development of the new package?

Is it then possible to create a suite-like package, similar to tidyverse, where users say BiocManager::install(“Set_of_bla_bla_packages”)?

Koustav Pal, PhD
Post-Doctoral Fellow in Genome Architecture,
Computational Genomics Group,
IFOM - The FIRC Institute of Molecular Oncology,
Via Adamello 16,
20139 Milano, Italy.
Phone: +393441130157
E-mail: koustav.pal using ifom.eu<mailto:koustav.pal using ifom.eu>

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