Re: [Bioc-devel] New(ish!) Seattle Bioconductor team member
Aha! On Fri, Mar 6, 2015 at 4:16 PM, Leonardo Collado Torres lcoll...@jhu.edu wrote: Welcome Jim! I'm a fan of your knitrBootstrap I knew I recognized the name from somewhere, but wasn't able to recall until now. Welcome to Bioc! -steve -- Steve Lianoglou Computational Biologist Genentech ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] New(ish!) Seattle Bioconductor team member
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
[Bioc-devel] New(ish!) Seattle Bioconductor team member
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
Re: [Bioc-devel] New(ish!) Seattle Bioconductor team member
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
