[Bioc-devel] Access UnitTests Log-File

[Dan Tenenbaum]

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.

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
>
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>
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