[Bioc-devel] best way to transition users to new version of package

Robert M. Flight rflight79 at gmail.com
Wed May 27 17:10:22 CEST 2015

I am the author and maintainer of the categoryCompare package on
Bioconductor. As I and others have used it over the years, I am seeing that
there are a lot of design mistakes in the code, and that it was not
extensible in it's current form. Therefore, I decided to do a complete
rewrite starting from scratch. Because of a new logic, I decided on a
completely new function naming scheme, class names, etc.

There are currently no packages on Bioconductor that depend on my package,
and I only know of a handful of other users that are actively using it (I
have no posts on the support forum, and I've only gotten three emails
directly with questions about using it).

I'm trying to figure out how best to transition the few users who may have
analysis code relying on the package. I have three possibilities in mind,
ranging from what I consider most radical to least, and probably least
amount of work on my part to most:

1 - change name of new package to categoryComare2 or something else. May
lose old users who don't find the package. Could be mitigated by adding
startupMessage to the next iteration of the original package, and adding
information to Bioconductor landing page

2 - add startupMessage's pointing users to vignettes with new workflow and
functions, warning that old functions are completely gone.

3 - provide wrappers with the same names as old package functions that use
new functions under the hood, with warning that they will be deprecated in
next version.

I'd appreciate feedback on what the best approach would be in this case.



Robert M Flight, PhD
Bioinformatics Research Associate
Resource Center for Stable Isotope Resolved Metabolomics
Markey Cancer Center
University of Kentucky
Lexington, KY

Twitter: @rmflight
Web: rmflight.github.io
EM rflight79 at gmail.com
PH 502-509-1827

The most exciting phrase to hear in science, the one that heralds new
discoveries, is not "Eureka!" (I found it!) but "That's funny ..." - Isaac

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