Last updated on 2020-08-07 01:50:15 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| AnaCoDa | 1 | 6 | 5 |
Current CRAN status: ERROR: 1, NOTE: 6, OK: 5
Version: 0.1.3.0
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: 0.1.3.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [74s/90s]
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: 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] -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: 85 | SKIPPED: 0 | WARNINGS: 26 | 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