
Hi all, here is  my followup:

The output of flowFit.Rcheck/tests/runTests.Rout is:

RUNIT TEST PROTOCOL -- Mon Jan 21 11:22:51 2013 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

1 Test Suite : 
flowFit RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

No test run …. :-(

RESTARTING FROM SCRATCH with a package skeleton:
require(stats)
## two functions and two "data sets" :
f <- function(x, y) x+y
g <- function(x, y) x-y
d <- data.frame(a = 1, b = 2)
e <- rnorm(1000)
package.skeleton(list = c("f","g","d","e"), name = "RUnitTest")
And inside the package dir:

mkdir tests

mkdir -p inst/unitTests

touch inst/unitTests/test_iWantToFail.R

more inst/unitTests/test_iWantToFail.R 

test_f <- function()
{
  checkTrue(FALSE)
}


OUTPUT is OK:

RUnitTest RUnit Tests - 1 test function, 0 errors, 1 failure
  FAILURE in test_f: Error in checkTrue(FALSE) : Test not TRUE


So where is the problem in my library? 

After a session of "find the differences" game I finally got the problem:

Problem is in the .Rinstignore file. 

here is my .Rinstignore in the ROOT directory of the package:

inst/doc/.*[.]bib$
inst/doc/Makefile
test/*
TODO
README
.DS_Store
.git/*
.project
.Rapp.history
.Rhistory


The problematic line is:

test/*

If I remove the line, the test runs and fail when need to fail with R CMD check:

R CMD check flowFit 

[…]

Last 13 lines of output:
  flowFit RUnit Tests - 1 test function, 0 errors, 1 failure
  FAILURE in test_failing: Error in checkTrue(FALSE) : Test not TRUE
  
  
  Test files with failing tests
  
     test_iWantToFail.R 
       test_failing 
  
  
  Error in BiocGenerics:::testPackage("flowFit") : 
    unit tests failed for package flowFit
  Execution halted


Strange thing: i put test/* in .Rinstignore, but R is ignoring the directory inst/unitTests/* is this the expected behavior?

Anyway, I can test now and I am happy :-)

As soon as I get some feedback about this error,  I will post an answer to my own question in stackoverflow: 

http://stackoverflow.com/questions/14403181/r-developing-a-bioconductor-package-with-tdd-runit


Thanks for help. 

If you need more info about my setup, here is the sessionInfo()

R version 2.15.2 (2012-10-26)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] flowFit_0.3.1

loaded via a namespace (and not attached):
 [1] Biobase_2.18.0     BiocGenerics_0.4.0 feature_1.2.8      flowCore_1.24.0   
 [5] gdata_2.12.0       gplots_2.11.0      graph_1.36.1       gtools_2.7.0      
 [9] ks_1.8.11          kza_2.01           MASS_7.3-23        minpack.lm_1.1-6  
[13] rrcov_1.3-02       stats4_2.15.2      tools_2.15.2  


Regards

Davide Rambaldi







On Jan 18, 2013, at 6:43 PM, Martin Morgan wrote:

> On 01/18/2013 08:26 AM, Davide Rambaldi wrote:
>> Hello, I am trying to follow the bioconductor RUnit guidelines (http://www.bioconductor.org/developers/unitTesting-guidelines/#duringDevelopment)
>> 
>> I have followed the the minimal setup so I have:
>> 
>> Suggests: RUnit, BiocGenerics in DESCRIPTION
>> 
>> BiocGenerics:::testPackage("MyPackage") in MyPackage/tests/runTests.R
>> 
>> and some test_XXX.R files in MyPackage/inst/unitTests/
>> 
>> If I run a single test files with:
>> 
>> library(RUnit)
>> source("LIBRARY FILES")
>> source("MyPackage/inst/unitTests/test_getKeywordValue.R")
>> test_getKeywordValue()
> 
> To me this looks ok. Are you using R-devel and current packages (output of sessionInfo())? After installing your package, does
> 
> R --vanilla -e " BiocGenerics:::testPackage('MyPackage')"
> 
> do the right thing? After running R CMD check, are there any hints in the file
> 
>  MyPackage.Rcheck/tests/runTests.Rout
> 
> ?
> 
>> 
>> The test run (and fails when need to fail), but if I run
>> 
>> R CMD check MyPackage
>> 
>> The command say:
>> 
>> * checking tests ...
>>   Running ‘runTests.R’
>>  OK
>> 
>> But don't run my tests in MyPackage/inst/unitTests directory...
>> 
>> What I missing?
>> 
>> Platform: x86_64-apple-darwin9.8.0
>> R version 2.15.2 (2012-10-26)
>> 
>> Best Regards and thanks in Advance
>> 
>> 
>> -----------------------------------------------------------
>> PLEASE NOTE MY NEW EMAIL ADDRESS
>> -----------------------------------------------------------
>> 
>> -----------------------------------------------------
>> Davide Rambaldi, PhD.
>> -----------------------------------------------------
>> IEO ~ MolMed
>> [e] davide.rambaldi@ieo.eu
>> [e] davide.rambaldi@gmail.com
>> 
>> _______________________________________________
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> 
> 
> 
> -- 
> 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


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