[Bioc-devel] Mac build (xcms)

[Hervé Pagès]

Hi Steffen,

Steffen Neumann wrote:
[...]
> 
> If we'd add a unit test to XCMS (which are disabled 
> in the BioC builds ?!)

*Unit* tests are not "standard" tests!

Standard tests are described here:
   http://cran.fhcrc.org/doc/manuals/R-exts.html#Package-subdirectories
and must be put in the tests/ subdir of your package.
By default they are run by 'R CMD check' (unless the --no-tests
option is specified, but our build system doesn't do that).

As you can see here:
http://bioconductor.org/checkResults/2.6/bioc-LATEST/xcms/pitt-checksrc.html
the build system runs 'R CMD check --no-vignettes xcms_1.21.14.tar.gz',
so that won't trigger the execution of the *unit* tests unless you add
some code to your package for that purpose.

See for example the latest CHECK report for the IRanges package:

http://bioconductor.org/checkResults/2.6/bioc-LATEST/IRanges/pitt-checksrc.html

At the bottom of the "Command output" section, you have:

* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking tests ...
   Running ‘runalltests.R’
   Comparing ‘runalltests.Rout’ to ‘runalltests.Rout.save’ ... OK
  OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

The standard tests are run i.e. the *.R files under tests/ are executed.
To have 'R CMD check' run the *unit* tests, the trick is to put code in
those *.R files that will run them. Which is what the IRanges package
does.

Cheers,
H.

-- 
Hervé Pagès

Program in Computational Biology
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