On Thu, Jan 24, 2013 at 3:04 PM, Dan Tenenbaum <dtene...@fhcrc.org> wrote: > Hi Anita, > > On Thu, Jan 24, 2013 at 2:33 PM, Anita Lerch <lerch.an...@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]] >> >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
