Running 'testthat.R' [70s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("AnaCoDa")
  Loading required package: AnaCoDa
  Loading required package: Rcpp
  CovarianceMatrix getCovMatrix & initCovarianceMatrix --- Pass
  CovarianceMatrix setDiag --- Pass
  CovarianceMatrix getCholeskyMatrix & choleskyDecomposition --- Pass
  CovarianceMatrix getNumVariates --- Pass
  CovarianceMatrix == operator --- Pass
  ERROR: Index 11 is out of bounds. Index must be between 3 & 10
  ERROR: Index 5 is out of bounds. Index must be between 6 & 11
  Finished check IndexERROR: Index 2 is out of bounds. Index must be between 1 & 1
  Warning: Invalid index given for simulated genes, returning simulated gene 1.
  ERROR: Index 6 is out of bounds. Index must be between 1 & 4
  Warning: Invalid index given for genes, returning gene 1.
  checked mcmc.isEstimateSynthesisRate(default)
  checked mcmc.isEstimateSynthesisRate(false)
  checked mcmc.isEstimateSynthesisRate(true)
  MCMCAlgorithm is/setEstimateSynthesisRate --- Pass
  MCMCAlgorithm is/setEstimateCodonSpecificParameter --- Pass
  MCMCAlgorithm is/setEstimateHyperParameter --- Pass
  MCMCAlgorithm is/setEstimateMixtureAssignment --- Pass
  ERROR: Cannot set steps - value must be smaller than samples times thinning (maxIterations)
  MCMCAlgorithm get/setStepsToAdapt --- Pass
  MCMCAlgorithm getLogPosteriorTrace --- Pass
  -- 1. Failure: identical MCMC-ROC input with Phi, same log posterior (@testMCMCR
  `knownLogPosterior` not equal to `testLogPosterior`.
  1/1 mismatches
  [1] -828047 - -828638 == 591
  
  -- 2. Failure: identical MCMC-ROC input without Phi, same log posterior (@testMC
  `knownLogPosterior` not equal to `testLogPosterior`.
  1/1 mismatches
  [1] -831329 - -835960 == 4631
  
  Parameter getMixtureAssignment --- Pass
  Parameter setMixtureAssignment --- Pass
  Parameter getMutationSelectionState --- Pass
  Parameter getNumParam --- Pass
  Parameter getNumMixtureElements --- Pass
  Parameter getStdDevSynthesisRate --- Pass
  Parameter setStdDevSynthesisRate --- Pass
  Parameter getCurrentStdDevSynthesisRateProposalWidth --- Pass
  Parameter getNumAcceptForStdDevSynthesisRate --- Pass
  Parameter getStdCspForIndex --- Pass
  Parameter getNumAcceptForCspForIndex --- Pass
  Parameter getNumMutationCategories --- Pass
  Parameter getNumSelectionCategories --- Pass
  Parameter getNumSynthesisRateCategories--- Pass
  Parameter getMutationCategory --- Pass
  Parameter getSelectionCategory --- Pass
  Parameter getMixtureElementsOfMutationCategory --- Pass
  Parameter getMixtureElementsOfSelectionCategory --- Pass
  Parameter getCategoryProbability --- Pass
  Parameter setCategoryProbability --- Pass
  Parameter getSynthesisRate --- Pass
  Parameter setSynthesisRate --- Pass
  Parameter getSynthesisRateCategory --- Pass
  Parameter getNumAcceptForSynthesisRate --- Pass
  Parameter getSynthesisRateProposalWidth --- Pass
  Parameter getCurrentSynthesisRateProposalWidth --- Pass
  Parameter initParameterSet --- Pass
  Parameter get/setGroupList --- Pass
  Parameter getGroupListSize --- Pass
  Parameter getGrouping --- Pass
  Parameter InitializeSynthesisRate --- Pass
  Parameter get/setLastIteration --- Pass
  Parameter get/setNumObservedPhiSets --- Pass
  Sequence Summary clear --- Pass
  Sequence Summary processSequence --- Pass
  Sequence Summary complimentNucleotide --- Pass
  Sequence Summary getAACountForAA(string) --- Pass
  Sequence Summary getAACountForAA(index) --- Pass
  Sequence Summary getCodonCountsForCodon(string) --- Pass
  Sequence Summary getCodonCountsForCodon(index) --- Pass
  Sequence Summary getCodonPositions(string) --- Pass
  Sequence Summary getCodonPositions(index) --- Pass
  Sequence Summary init/get/setRFPCount / getSingleRFPCount --- Pass
  Sequence Summary init/get/setSumRFPCount --- Pass
  Sequence Summary get/setPositionCodonID --- Pass
  Sequence Summary getCodonSpecificSumRFPCount(string) / setCodonSpecificSumRFPCount --- Pass
  Sequence Summary getCodonSpecificSumRFPCount(index) --- Pass
  Testing my_print, no argument.
  Testing my_print, one argument: 0.
  Testing my_print, multiple arguments: String, 0, 0.5.
  
  Utility my_print --- Pass
  Testing my_printError, no argument.
  Testing my_printError, one argument: 0.
  Testing my_printError, multiple arguments: String, 0, 0.5.
  Utility my_printError --- Pass
  == testthat results  ===========================================================
  OK: 107 SKIPPED: 0 FAILED: 2
  1. Failure: identical MCMC-ROC input with Phi, same log posterior (@testMCMCROC.R#56) 
  2. Failure: identical MCMC-ROC input without Phi, same log posterior (@testMCMCROC.R#78) 
  
  Error: testthat unit tests failed
  Execution halted