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

[Leonardo Collado Torres]

Welcome Jim! I'm a fan of your knitrBootstrap
https://github.com/jimhester/knitrBootstrap and rex
https://github.com/kevinushey/rex packages! Plus gmailR
https://github.com/jimhester/gmailr

I look forward to your future work at BioC!

Cheers,
Leo

On Fri, Mar 6, 2015 at 3:11 PM, Jim Hester <james.f.hester at gmail.com> wrote:

> 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
> > > > >>
> > > > >
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> > > > >
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> > > >
> > > > _______________________________________________
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> > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > > >
> >
>
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