----- Original Message ----- > From: "Elena Grassi" <grass...@gmail.com> > To: bioc-devel@r-project.org > Sent: Monday, January 26, 2015 1:14:59 AM > Subject: [Bioc-devel] unit tests for C code inside a package > > Hi, > > I'm writing a package that calculates total affinity (see PMID > 21335606 and 16873464 if transcription factors are your thing): > up until now in our lab we've used a pure C tool that needs fasta and > tabular formatted PFM-PWM files but we are willing to produce > something more comfortable that stems from some related Bioc packages > (TFBSTools and JASPAR2014 basically). > The package has two simple R methods that call a C entry point and > then all the calculations are performed by the C code. > I'd like to write extended unit tests but I am not sure how to do it: > I've some tests for the R portions (that obviously depends > also on the C calculation in some parts) but I would like to test in > a > more fine grained way the C code therefore RUnit and BiocGenerics > seems to solve only a portion of my problem. I would like to use a > C-based library for unit testing and link it to the automatic > check done for the package thanks to BiocGenerics: is this > reasonable? > I've looked at some other packages without being able to find > something similar to this. > I've read > http://stackoverflow.com/questions/26322135/unit-testing-rcpp-code-in-a-package, > but I think > that it would be nice to test the C code with the whole package. >
Choose a C-based unit-testing library, include it with your package, write a C function that calls your test suite, register that function to be callable from R, and call it from an R unit test? Dan > Thanks, > E. > ps. the source code right now is here: > https://github.com/vodkatad/MatrixRider (the vignette is on its way, > the nodevel branch is the one active now and it works with R version > 3.1.2 and Bioconductor 3.0 for our internal use). > > -- > $ pom > > _______________________________________________ > 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
