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.ramba...@ieo.eu
>> [e] davide.ramba...@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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