CRAN Package Check Results for Package AnaCoDa

Last updated on 2019-03-19 07:46:50 CET.

Additional issues

clang-ASAN gcc-ASAN valgrind

Check Details

Version: 0.1.2.3
Check: installed package size
Result: NOTE
     installed size is 27.3Mb
     sub-directories of 1Mb or more:
     libs 25.9Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.1.2.3
Check: tests
Result: ERROR
     Running ‘testthat.R’ [84s/108s]
    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] -1889720
     ── 1. Failure: identical MCMC-ROC input with Phi, same log posterior (@testMCMCR
     `knownLogPosterior` not equal to `testLogPosterior`.
     1/1 mismatches
     [1] -942493 - -1889720 == 947227
    
     [1] -1917970
     ── 2. Failure: identical MCMC-ROC input without Phi, same log posterior (@testMC
     `knownLogPosterior` not equal to `testLogPosterior`.
     1/1 mismatches
     [1] -960298 - -1917970 == 957672
    
     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: 111 SKIPPED: 0 FAILED: 2
     1. Failure: identical MCMC-ROC input with Phi, same log posterior (@testMCMCROC.R#75)
     2. Failure: identical MCMC-ROC input without Phi, same log posterior (@testMCMCROC.R#100)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-patched-solaris-x86

Version: 0.1.2.2
Check: installed package size
Result: NOTE
     installed size is 21.3Mb
     sub-directories of 1Mb or more:
     libs 19.9Mb
Flavors: r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64