CRAN Package Check Results for Package AnaCoDa

Last updated on 2021-01-22 04:47:13 CET.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	0.1.4.4	300.65	235.71	536.36	OK
r-devel-linux-x86_64-debian-gcc	0.1.4.4	219.43	171.06	390.49	OK
r-devel-linux-x86_64-fedora-clang	0.1.4.4			801.75	NOTE
r-devel-linux-x86_64-fedora-gcc	0.1.4.4			742.34	OK
r-devel-windows-ix86+x86_64	0.1.4.4	641.00	457.00	1098.00	NOTE
r-patched-linux-x86_64	0.1.4.4	253.21	228.55	481.76	OK
r-patched-solaris-x86	0.1.4.4			706.80	ERROR
r-release-linux-x86_64	0.1.4.4	246.65	225.25	471.90	OK
r-release-macos-x86_64	0.1.4.4				NOTE
r-release-windows-ix86+x86_64	0.1.4.4	471.00	474.00	945.00	NOTE
r-oldrel-macos-x86_64	0.1.4.4				NOTE
r-oldrel-windows-ix86+x86_64	0.1.4.4	475.00	371.00	846.00	NOTE

Check Details

Version: 0.1.4.4
Check: installed package size
Result: NOTE
     installed size is 30.2Mb
     sub-directories of 1Mb or more:
     libs 28.8Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.1.4.4
Check: tests
Result: ERROR
     Running ‘testthat.R’ [149s/204s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > test_check("AnaCoDa")
     Loading required package: AnaCoDa
     Loading required package: Rcpp
     Loading required package: VGAM
     Loading required package: stats4
     Loading required package: splines
     Loading required package: mvtnorm
     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] -1889714
     [1] -1917942
     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
     ══ Warnings ════════════════════════════════════════════════════════════════════
     ── Warning (testMCMCROC.R:60:1): (code run outside of `test_that()`) ───────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:60:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:60:1): (code run outside of `test_that()`) ───────────
     2 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:60:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:60:1): (code run outside of `test_that()`) ───────────
     2 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:60:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:60:1): (code run outside of `test_that()`) ───────────
     2 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:60:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:60:1): (code run outside of `test_that()`) ───────────
     2 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:60:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:60:1): (code run outside of `test_that()`) ───────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:60:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:60:1): (code run outside of `test_that()`) ───────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:60:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:60:1): (code run outside of `test_that()`) ───────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:60:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:60:1): (code run outside of `test_that()`) ───────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:60:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:60:1): (code run outside of `test_that()`) ───────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:60:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:60:1): (code run outside of `test_that()`) ───────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:60:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:60:1): (code run outside of `test_that()`) ───────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:60:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:60:1): (code run outside of `test_that()`) ───────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:60:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:84:1): (code run outside of `test_that()`) ───────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:84:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:84:1): (code run outside of `test_that()`) ───────────
     2 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:84:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:84:1): (code run outside of `test_that()`) ───────────
     2 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:84:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:84:1): (code run outside of `test_that()`) ───────────
     2 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:84:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:84:1): (code run outside of `test_that()`) ───────────
     2 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:84:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:84:1): (code run outside of `test_that()`) ───────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:84:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:84:1): (code run outside of `test_that()`) ───────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:84:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:84:1): (code run outside of `test_that()`) ───────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:84:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:84:1): (code run outside of `test_that()`) ───────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:84:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:84:1): (code run outside of `test_that()`) ───────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:84:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:84:1): (code run outside of `test_that()`) ───────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:84:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:84:1): (code run outside of `test_that()`) ───────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:84:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:84:1): (code run outside of `test_that()`) ───────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:84:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     2 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     2 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     2 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     2 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     2 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     2 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     2 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     2 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     2 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     2 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     3 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     3 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     3 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     2 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:104:1): (code run outside of `test_that()`) ──────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:104:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:124:1): (code run outside of `test_that()`) ──────────
     2 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:124:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:124:1): (code run outside of `test_that()`) ──────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:124:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:124:1): (code run outside of `test_that()`) ──────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:124:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:124:1): (code run outside of `test_that()`) ──────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:124:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:124:1): (code run outside of `test_that()`) ──────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:124:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:124:1): (code run outside of `test_that()`) ──────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:124:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:124:1): (code run outside of `test_that()`) ──────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:124:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:124:1): (code run outside of `test_that()`) ──────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:124:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:124:1): (code run outside of `test_that()`) ──────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:124:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:124:1): (code run outside of `test_that()`) ──────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:124:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:124:1): (code run outside of `test_that()`) ──────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:124:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:124:1): (code run outside of `test_that()`) ──────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:124:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:156:1): (code run outside of `test_that()`) ──────────
     1 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:156:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:156:1): (code run outside of `test_that()`) ──────────
     4 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:156:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:156:1): (code run outside of `test_that()`) ──────────
     5 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:156:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)
     ── Warning (testMCMCROC.R:156:1): (code run outside of `test_that()`) ──────────
     5 diagonal elements of the working weights variable 'wz' have been replaced by 1.819e-12
     Backtrace:
     1. AnaCoDa::initializeParameterObject(...) testMCMCROC.R:156:0
     2. AnaCoDa:::initializeROCParameterObject(...)
     3. AnaCoDa:::initializeCovarianceMatrices(...)
     4. AnaCoDa:::getCSPbyLogit(codonCounts[idx, ], phi[idx])
     5. VGAM::vglm(...)
     6. VGAM:::vglm.fitter(...)
     7. VGAM::checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon)

     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Failure (testMCMCROC.R:75:3): identical MCMC-ROC input with Phi, same log posterior ──
     `knownLogPosterior` not equal to `testLogPosterior`.
     1/1 mismatches
     [1] -942493 - -1889714 == 947221
     ── Failure (testMCMCROC.R:99:3): identical MCMC-ROC input without Phi, same log posterior ──
     `knownLogPosterior` not equal to `testLogPosterior`.
     1/1 mismatches
     [1] -960298 - -1917942 == 957644

     [ FAIL 2 | WARN 71 | SKIP 0 | PASS 165 ]
     Error: Test failures
     Execution halted
Flavor: r-patched-solaris-x86