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.hes...@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 <h...@biostat.ucsf.edu> > > > wrote: > > > > > > > On Wed, Mar 4, 2015 at 2:29 PM, Michael Lawrence > > > > <lawrence.mich...@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 < > > mtmor...@fredhutch.org> > > > > > wrote: > > > > > > > > > >> Let me take this belated opportunity to introduce Jim Hester < > > > > >> jhes...@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@r-project.org mailing list > > > > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > >> > > > > > > > > > > [[alternative HTML version deleted]] > > > > > > > > > > _______________________________________________ > > > > > Bioc-devel@r-project.org mailing list > > > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > > > _______________________________________________ > > > > Bioc-devel@r-project.org mailing list > > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
