[Bioc-devel] Access UnitTests Log-File

Dan Tenenbaum dtenenba at fhcrc.org
Fri Jan 25 20:59:49 CET 2013


On Thu, Jan 24, 2013 at 3:04 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> Hi Anita,
>
> On Thu, Jan 24, 2013 at 2:33 PM, Anita Lerch <lerch.anita at gmail.com> wrote:
>> Hi,
>>
>> is there a way to access the log file of the unit-tests
>> (e.g. QuasR.Rcheck/tests/QuasR_unit_tests.Rout.fail) on the build system?
>> Currently I have failing test on george2, which I can't reproduce on my
>> system.
>> The 13 line output e.g.
>>
>> * checking tests ...
>>   Running ‘QuasR_unit_tests.R’
>>  ERROR
>> Running the tests in ‘tests/QuasR_unit_tests.R’ failed.
>> Last 13 lines of output:
>>   Test full-methylated directed, mode=allC
>>
>>   Test files with failing tests
>>
>>      test_qAlign.R
>>        test_bisulfit_single
>>
>>      test_qMeth.R
>>        test_full_meth_paired
>>
>>
>>   Error in QuasR:::test() : unit tests failed for package QuasR
>>
>> of the check report
>>
>> http://bioconductor.org/checkResults/devel/bioc-LATEST/QuasR/george2-checksrc.html
>>
>> is not very informative, especially if the failing test can't be reproduce.
>> It would be a great help if the log file (e.g.
>> QuasR.Rcheck/tests/QuasR_unit_tests.Rout.fail)
>> could be copied to (e.g.
>> http://bioconductor.org/checkResults/devel/bioc-LATEST/QuasR/) somehow.
>>
>
> At present that log file is not accessible through the build report.
>


But this is a good idea and I will work on adding this to the build
system over the next few weeks.
Dan


> In your case the relevant excerpt is:
>
>
>
> RUNIT TEST PROTOCOL -- Thu Jan 24 03:18:17 2013
> ***********************************************
> Number of test functions: 59
> Number of errors: 0
> Number of failures: 2
>
>
> 1 Test Suite :
> QuasR RUnit Tests - 59 test functions, 0 errors, 2 failures
> FAILURE in test_bisulfit_single: Error in checkTrue(all(ifelse(readInfo[, 8] ==
> "l", readInfo[, 3], readInfo[,  :
>   Test not TRUE
> Test left read position: l 1 145 1
> FAILURE in test_full_meth_paired: Error in checkTrue(all(mcols(meth)[, 1] == mco
> ls(meth)[, 2]), "Test full-methylated directed, mode=allC") :
>   Test not TRUE
> Test full-methylated directed, mode=allC
>
> Test files with failing tests
>
>    test_qAlign.R
>      test_bisulfit_single
>
>    test_qMeth.R
>      test_full_meth_paired
>
> I cannot reproduce this either, even on george2. It seems to happen
> only in the context of the build system's nightly runs. I think it has
> something to do with the parallelization in the code and may have to
> do with the fact that the builds are already parallelized. I'll look
> into it some more.
>
> Thanks
> Dan
>
>
>
>
>> Sorry, if I missed something on the devel webpage.
>> Greetings
>> Anita
>>
>>         [[alternative HTML version deleted]]
>>
>>
>> _______________________________________________
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>>



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