[Bioc-devel] unit tests for C code inside a package

----- Original Message -----
From: "Elena Grassi" <grassi.e at gmail.com>
To: bioc-devel at 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

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Thank you both for your suggestions.

Peter: Rcpp attributes seem great but right now I would prefer to
avoid changing all the pure C structs of my old codebase in C++
classes and so on. But if in the future we will need to add new
features I will definitely add these two ++ :)
Dan: yep, that was roughly my idea, I wanted to check if that's reasonable/ok.

E.
$ pom