Running ‘runTests.R’ [13s/21s]
Running the tests in ‘tests/runTests.R’ failed.
Complete output:
  > BiocGenerics:::testPackage("MetaIntegrator")
  Converting probes:genes for gene list for all discovery GEMsError in FUN(X[[i]], ...) : 
    only defined on a data frame with all numeric-alike variables
  Error in FUN(newX[, i], ...) : 
    argument is not numeric or logical: returning NA
  Error in FUN(newX[, i], ...) : 
    argument is not numeric or logical: returning NA
  Found common probes in 3 
  Computing effect sizes...
  Computing summary effect sizes...
  Computing Fisher's output...Found common probes in 2 
  Computing effect sizes...
  Computing summary effect sizes...
  Computing Fisher's output...Computing effect sizes...
  Computing summary effect sizes...
  Computing Fisher's output...Computing effect sizes...
  Computing summary effect sizes...
  Computing Fisher's output...Error in filterGenes(wrongTinyMetaObject, isLeaveOneOut = FALSE) : 
    Error in the input object!
  In addition: There were 50 or more warnings (use warnings() to see the first 50)
  Error in filterGenes(wrongTinyMetaObject, isLeaveOneOut = TRUE) : 
    Error in the input object!
  In addition: Warning message:
  In .metaCheckAll(object, objectStage) : $metaAnalysis is null.
  Error in forestPlot(tinyMetaObject, geneName = "12341546576877564534") : 
    No gene named '12341546576877564534' in this metaObject. No plot generated
  [1] "character"
  [1] "character"
  Converting probes:genes for gene list for all discovery GEMsError in FUN(X[[i]], ...) : 
    only defined on a data frame with all numeric-alike variables
  In addition: Warning message:
  In getPackageName(topenv(parent.frame())) :
    Created a package name, '2021-12-02 11:27:41', when none found
  Error in getMostRecentFilter(wrongTinyMetaObject) : 
    Error in the input object!
  In addition: Warning messages:
  1: In getPackageName(topenv(parent.frame())) :
    Created a package name, '2021-12-02 11:27:43', when none found
  2: In .metaCheckAll(object, objectStage) : $filterResults is null.
  Error in checkEquals(sampleResults["Gene27", "Sample.1"], 7.016342, tolerance = 0.001) : 
    target is NULL, current is numeric
  
  Error in FUN(newX[, i], ...) : 
    argument is not numeric or logical: returning NA
  Found common probes in 3 
  Computing effect sizes...
  Computing summary effect sizes...
  Computing Fisher's output...Found common probes in 3 
  Computing effect sizes...
  Computing summary effect sizes...
  Computing Fisher's output...Found common probes in 2 
  Computing effect sizes...
  Computing summary effect sizes...
  Computing Fisher's output...Computing effect sizes...
  Computing summary effect sizes...
  Computing Fisher's output...Computing effect sizes...
  Computing summary effect sizes...
  Computing Fisher's output...Error in runMetaAnalysis(wrongTinyMetaObject, runLeaveOneOutAnalysis = FALSE) : 
    In  Whole.Blood.Study.1  there are not @ least two cases and/or two controls
  In addition: Warning message:
  In getPackageName(topenv(parent.frame())) :
    Created a package name, '2021-12-02 11:27:46', when none found
  Error in runMetaAnalysis(wrongTinyMetaObject, runLeaveOneOutAnalysis = TRUE) : 
    In  Whole.Blood.Study.1  there are not @ least two cases and/or two controls
  Error in summarizeFilterResults(tinyMetaObject, "BIGFAKELABEL") : 
    Error! The input label does not match any filter run
  In addition: Warning message:
  In getPackageName(topenv(parent.frame())) :
    Created a package name, '2021-12-02 11:27:48', when none found
  Error in FUN(newX[, i], ...) : 
    argument is not numeric or logical: returning NA
  Error in checkTrue(!is(tt, "try-error")) : Test not TRUE
  
  
  
  RUNIT TEST PROTOCOL -- Thu Dec  2 11:27:49 2021 
  *********************************************** 
  Number of test functions: 7 
  Number of errors: 7 
  Number of failures: 0 
  
   
  1 Test Suite : 
  MetaIntegrator RUnit Tests - 7 test functions, 7 errors, 0 failures
  ERROR in /home/hornik/tmp/scratch/RtmpNcnLrF/RLIBS_1443d6877fe62/MetaIntegrator/unitTests/test_backwardSearch.R: Error while sourcing  /home/hornik/tmp/scratch/RtmpNcnLrF/RLIBS_1443d6877fe62/MetaIntegrator/unitTests/test_backwardSearch.R : Error in FUN(X[[i]], ...) : 
    only defined on a data frame with all numeric-alike variables
  ERROR in /home/hornik/tmp/scratch/RtmpNcnLrF/RLIBS_1443d6877fe62/MetaIntegrator/unitTests/test_calculateROC.R: Error while sourcing  /home/hornik/tmp/scratch/RtmpNcnLrF/RLIBS_1443d6877fe62/MetaIntegrator/unitTests/test_calculateROC.R : Error in FUN(newX[, i], ...) : 
    argument is not numeric or logical: returning NA
  ERROR in /home/hornik/tmp/scratch/RtmpNcnLrF/RLIBS_1443d6877fe62/MetaIntegrator/unitTests/test_calculateScore.R: Error while sourcing  /home/hornik/tmp/scratch/RtmpNcnLrF/RLIBS_1443d6877fe62/MetaIntegrator/unitTests/test_calculateScore.R : Error in FUN(newX[, i], ...) : 
    argument is not numeric or logical: returning NA
  ERROR in /home/hornik/tmp/scratch/RtmpNcnLrF/RLIBS_1443d6877fe62/MetaIntegrator/unitTests/test_forwardSearch.R: Error while sourcing  /home/hornik/tmp/scratch/RtmpNcnLrF/RLIBS_1443d6877fe62/MetaIntegrator/unitTests/test_forwardSearch.R : Error in FUN(X[[i]], ...) : 
    only defined on a data frame with all numeric-alike variables
  ERROR in /home/hornik/tmp/scratch/RtmpNcnLrF/RLIBS_1443d6877fe62/MetaIntegrator/unitTests/test_getSampleLevelGeneData.R: Error while sourcing  /home/hornik/tmp/scratch/RtmpNcnLrF/RLIBS_1443d6877fe62/MetaIntegrator/unitTests/test_getSampleLevelGeneData.R : Error in checkEquals(sampleResults["Gene27", "Sample.1"], 7.016342, tolerance = 0.001) : 
    target is NULL, current is numeric
  
  ERROR in /home/hornik/tmp/scratch/RtmpNcnLrF/RLIBS_1443d6877fe62/MetaIntegrator/unitTests/test_rocPlot.R: Error while sourcing  /home/hornik/tmp/scratch/RtmpNcnLrF/RLIBS_1443d6877fe62/MetaIntegrator/unitTests/test_rocPlot.R : Error in FUN(newX[, i], ...) : 
    argument is not numeric or logical: returning NA
  ERROR in /home/hornik/tmp/scratch/RtmpNcnLrF/RLIBS_1443d6877fe62/MetaIntegrator/unitTests/test_violinPlot.R: Error while sourcing  /home/hornik/tmp/scratch/RtmpNcnLrF/RLIBS_1443d6877fe62/MetaIntegrator/unitTests/test_violinPlot.R : Error in checkTrue(!is(tt, "try-error")) : Test not TRUE
  
  
  Test files with failing tests
  
     test_backwardSearch.R 
       /home/hornik/tmp/scratch/RtmpNcnLrF/RLIBS_1443d6877fe62/MetaIntegrator/unitTests/test_backwardSearch.R 
  
     test_calculateROC.R 
       /home/hornik/tmp/scratch/RtmpNcnLrF/RLIBS_1443d6877fe62/MetaIntegrator/unitTests/test_calculateROC.R 
  
     test_calculateScore.R 
       /home/hornik/tmp/scratch/RtmpNcnLrF/RLIBS_1443d6877fe62/MetaIntegrator/unitTests/test_calculateScore.R 
  
     test_forwardSearch.R 
       /home/hornik/tmp/scratch/RtmpNcnLrF/RLIBS_1443d6877fe62/MetaIntegrator/unitTests/test_forwardSearch.R 
  
     test_getSampleLevelGeneData.R 
       /home/hornik/tmp/scratch/RtmpNcnLrF/RLIBS_1443d6877fe62/MetaIntegrator/unitTests/test_getSampleLevelGeneData.R 
  
     test_rocPlot.R 
       /home/hornik/tmp/scratch/RtmpNcnLrF/RLIBS_1443d6877fe62/MetaIntegrator/unitTests/test_rocPlot.R 
  
     test_violinPlot.R 
       /home/hornik/tmp/scratch/RtmpNcnLrF/RLIBS_1443d6877fe62/MetaIntegrator/unitTests/test_violinPlot.R 
  
  
  Error in BiocGenerics:::testPackage("MetaIntegrator") : 
    unit tests failed for package MetaIntegrator
  Execution halted