[Bioc-devel] Help with creating first Bioconductor package

January Weiner january.weiner at gmail.com
Fri Nov 14 22:11:32 CET 2014

Dear all,

thanks for your input, it was very helpful. I have some other specific
questions, though:

> You'll want to develop your package on Bioc- and R-devel, as this
> is the environment in which your package will be introduced to
> the Bioc community.

Specifically, I won't want to; I will have to. This is the last
obstacle and I am aware of it. There is no way that I do my research
on development version of R (not only for scientific reasons,
unfortunately), so I need two versions running concurrently. There are
means and ways to do it (I guess from the fact that it all runs on svn
and that one can set up scripts setting environmental variables; there
is no real guide on that, am I right?), but from my experience, for
someone who is not a full time developer it will be horrible, and
keeping it up to date -- without automata and apt-get -- will sooner
or later lead to a disaster.

> If you want to check it beforehand, have a look at
> e.g. http://win-builder.r-project.org/.

I use it regularly to check my CRAN packages (pca3d, riverplot and
tagcloud), but I assumed that it does not have org.Hs.eg.db and GO.db
which I need for my vignette.

True, most likely there will not be any problems -- but I have had at
least once troubles with a package that did not build correctly on
Windows only (well, it did include C code).

Tim Triche, Jr:
> "S3 objects as far as the eye can see"

Is using S3 a problem? For simple things like to overload a few
standard functions like plot and print? (Also, as a I user, I much
prefer limma's EList than anything that was even lying next to an
ExpressionSet; but then, I like Perl much more than Python).

Nathaniel Hayden:
> Yihui's formatR ( http://cran.r-project.org/web/packages/formatR/index.html ) makes formatting R files so simple and painless

That is precisely the package I had in mind when I said that it would
be annoying -- I'd still need to switch (and worse, *remember to
switch*) between the two formatting styles whenever I was to submit a
package :-)

Kind regards,


-------- January Weiner --------------------------------------

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