Running ‘testthat.R’ [80s/101s]
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
  Gene get/setId --- Pass
  Gene get/setDescription --- Pass
  Gene get/setSequence --- Pass
  Gene init/get/setRFPCount --- Pass
  Gene init/get/setSumRFPCount --- Pass
  Gene getSequenceSummary --- Pass
  Gene get/setObservedSynthesisRateValues --- Pass
  Gene getNumObservedSynthesisSets --- Pass
  Gene getObservedSynthesisRate --- Pass
  Gene getNucleotideAt --- Pass
  Gene length --- Pass
  Gene reverseComplement --- Pass
  Gene toAASequence --- Pass
  Gene clear --- Pass
  Invalid string given. Returning 0.
  Invalid string given. Returning 0.
  Invalid codon given. Returning 0.
  Invalid codon given. Returning 0.
  Invalid codon given. Returning 0.
  Invalid codon given. Returning 0.
  Invalid codon given. Returning empty vector.
  Invalid codon given. Returning empty vector.
  Genome get/addGene --- Pass
  Genome getGenes --- Pass
  Genome get/setNumGenesWithPhi --- Pass
  Genome getNumGenesWithPhiForIndex --- Pass
  Genome getGenomeSize --- Pass
  Genome getCodonCountsPerGene --- Pass
  Genome get/addRFPCountColumnNames --- Pass
  Genome clear --- Pass
  Genome getGenomeForGeneIndices --- Pass
  Genome readFasta --- Pass
  Genome writeFasta --- Pass
  Genome readRFPData --- Pass
  Genome writeRFPData --- Pass
  Genome readSimulatedGenomeFromPAModel --- 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
  ERROR: 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.
  Error in Genome::getGenomeForGeneIndices. An index specified is out of bounds for the genome!Returning empty Genome.Error in Genome::getGenomeForGeneIndices. An index specified is out of bounds for the genome!Returning empty Genome.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] -827733 - -1651751 == 824018
  
  ── 2. Failure: identical MCMC-ROC input without Phi, same log posterior (@testMC
  `knownLogPosterior` not equal to `testLogPosterior`.
  1/1 mismatches
  [1] -831329 - -1661012 == 829683
  
  ERROR: Error in Genome::readFasta: Can not open Fasta file /Users/hollisbui/RibModelDev/data/twoMixtures/simulatedAllUniqueR.fasta
  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 getRFPValue(string) / setRFPValue --- Pass
  Sequence Summary getRFPValue(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: 147 SKIPPED: 1 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