[Bioc-devel] New(ish!) Seattle Bioconductor team member

[Jim Hester]

I realized I sent this response the first time from the wrong email, so I
don't believe it made it to the mailing list.  Apologies if
you receive this twice.

In regards to using covr with RUnit tests, covr is not dependent on using
any particular testing framework it simply runs any commands found in
tests/.  So assuming `BiocGenerics:::testPackage()` (or whatever you have
in tests/) can properly find the tests to run from the package source root
directory it should work.

The bigger issue seems to be supporting S4 classes as used by
Bioconductor.  I have some support for tracking coverage of S4 classes, but
Bioconductor packages leverage far more S4 features than I have tested so
far, so you are likely to run into cases that break things I have not
encountered.  Currently S4 coverage is experimental at best I would say.

Thank you for all the warm welcome as well!

Jim

> I second the welcomings.  And I am quite interested in covr, but I wonder
> > what we have
> > to do to get it to work with the RUnit-based conventions that we've
> > followed so far,
> > with [basefolder]/tests and [basefolder]/inst/unitTests?
> >
> > On Wed, Mar 4, 2015 at 6:03 PM, Henrik Bengtsson <hb at biostat.ucsf.edu>
> > wrote:
> >
> > > On Wed, Mar 4, 2015 at 2:29 PM, Michael Lawrence
> > > <lawrence.michael at gene.com> wrote:
> > > > Welcome.
> > > >
> > > > For those who don't know, Jim is also the author of the neat "lintr"
> > > > package, which checks your R code as you type, across multiple
> editors.
> > > >
> > > > https://github.com/jimhester/lintr
> > >
> > > Not to mention https://github.com/jimhester/covr - It only took me one
> > > round of 'covr' to become a test-coverage-oholic.
> > >
> > > Jim, great to have you on board.
> > >
> > > /Henrik
> > >
> > > >
> > > > Michael
> > > >
> > > > On Wed, Mar 4, 2015 at 2:20 PM, Martin Morgan <
> mtmorgan at fredhutch.org>
> > > > wrote:
> > > >
> > > >> Let me take this belated opportunity to introduce Jim Hester <
> > > >> jhester at fredhutch.org> to the Bioconductor developer community.
> > > >>
> > > >> Jim is working in the short term on SummarizedExperiment, including
> the
> > > >> refactoring efforts he introduced yesterday as well as coercion
> methods
> > > to
> > > >> and from ExpressionSet (an initial version from ExpressionSet to
> > > >> SummarizedExperiment is available in the development version
> > > GenomicRanges;
> > > >> iterations will include coercion in the reverse direction as well as
> > > >> perhaps more 'clever' mapping between the probeset or gene names of
> > > >> ExpressionSet and relevant range-based notation). Jim will also
> > > contribute
> > > >> to ongoing project activities like new package reviews, package
> > > >> maintenance, and upcoming release activities.
> > > >>
> > > >> Jim brings a lot of interesting biological and software development
> > > >> experience to the project. Say hi when you have a chance!
> > > >>
> > > >> Martin
> > > >> --
> > > >> Computational Biology / Fred Hutchinson Cancer Research Center
> > > >> 1100 Fairview Ave. N.
> > > >> PO Box 19024 Seattle, WA 98109
> > > >>
> > > >> Location: Arnold Building M1 B861
> > > >> Phone: (206) 667-2793
> > > >>
> > > >> _______________________________________________
> > > >> Bioc-devel at r-project.org mailing list
> > > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > > >>
> > > >
> > > >         [[alternative HTML version deleted]]
> > > >
> > > > _______________________________________________
> > > > Bioc-devel at r-project.org mailing list
> > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >
> > > _______________________________________________
> > > Bioc-devel at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >
>

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