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.
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
