[Bioc-devel] best way to transition users to new version of package
Robert M. Flight
rflight79 at gmail.com
Thu May 28 15:32:40 CEST 2015
Thanks for the feedback Wolfgang. I never thought to look at how many
packages in Bioconductor have a baseName and baseName2 to see how often
this is done. I assume based on the existence of Roxygen2 and ggplot2 that
there were initial versions of those named Roxygen and ggplot.
This also seems like it is probably the easiest way forward for myself and
On Wed, May 27, 2015 at 2:45 PM Wolfgang Huber <whuber at embl.de> wrote:
> with the packages cellHTS, cellHTS2 and DESeq, DESeq2 (and with the
> functions vsn, vsn2 in the vsn package) I three times chose route 1, and am
> generally happy about it. In due time, you can deprecate and then defunct
> the old one.
> Option 2 seems needlessly disruptive (potentially). A large fraction of
> users you never ‘see’ or get in contact with. Not sure how that translates
> into absolute numbers of course.
> With option 3 it seems difficult to implement the exact same (and probably
> unsatisfactory) behaviour that people are used to.
> People also seem used to that from other products (WIndows 3.1, or now
> soon 10; iphone 6; X11; HTML5; …)
> Best wishes
> > On 27 May 2015, at 17:10, Robert M. Flight <rflight79 at gmail.com> wrote:
> > 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
> > 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
> > 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
> > 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
> > functions, warning that old functions are completely gone.
> > 3 - provide wrappers with the same names as old package functions that
> > new functions under the hood, with warning that they will be deprecated
> > next version.
> > I'd appreciate feedback on what the best approach would be in this case.
> > Cheers,
> > -Robert
> > 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 ..." -
> > Asimov
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