On 01/21/2013 04:01 AM, Davide Rambaldi wrote:
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 :-)
Glad you sorted that out. RShowDoc("R-exts") says that .Rinstignore does
perl-style regular expression matching. The '/*' part of your pattern says
'match zero or more / characters' whereas you were probably expecting glob-style
matching, '/' followed by anything. The Writing R Extensions manual says, in a
footnote, that the pattern matching is case-insensitive on Windows (probably
this isn't a good design decision, but beside the point), which would NOT
exclude unitTests on your MacOS but would exclude the individual test_.*R files
> grep("test/*", c("inst/unitTests/bar", "inst/unitTests/test_bar.R"),
perl=TRUE)
[1] 2
So yes, it would seem like you were getting what you asked for!
Martin
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
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1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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