Package: CNPBayes

Version: 1.13.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CNPBayes.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CNPBayes_1.13.5.tar.gz

StartedAt: 2019-01-22 00:43:18 -0500 (Tue, 22 Jan 2019)

EndedAt: 2019-01-22 01:03:06 -0500 (Tue, 22 Jan 2019)

EllapsedTime: 1187.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: CNPBayes.Rcheck

Warnings: 3

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CNPBayes.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CNPBayes_1.13.5.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CNPBayes.Rcheck’
* using R Under development (unstable) (2018-12-26 r75909)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNPBayes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNPBayes’ version ‘1.13.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CNPBayes’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘RcppArmadillo’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.simulate_data_multi2: no visible binding for global variable ‘id’
augmentData: no visible binding for global variable ‘medians’
augmentData: no visible binding for global variable ‘nhom’
augmentData: no visible binding for global variable ‘id’
augmentData: no visible binding for global variable ‘batch_index’
bafLikelihood: no visible binding for global variable ‘snpdat’
ci95.wrap: no visible global function definition for ‘t.test’
combineChains: no visible binding for global variable ‘.’
combineModels: no visible binding for global variable ‘.’
combineModels: no visible binding for global variable ‘id’
component_stats: no visible binding for global variable ‘batches’
component_stats: no visible binding for global variable ‘copy_number’
component_stats: no visible binding for global variable ‘log_ratio’
find_surrogates: no visible binding for global variable
  ‘provisional_batch’
gibbs_trios2: no visible binding for global variable ‘maplabel’
gibbs_trios2: no visible binding for global variable ‘mprob’
gibbs_trios3: no visible binding for global variable ‘maplabel’
gibbs_trios3: no visible binding for global variable ‘mprob’
gibbs_trios_K2: no visible binding for global variable
  ‘.gibbs_trios_mcmc2’
gibbs_trios_K3: no visible binding for global variable
  ‘.gibbs_trios_mcmc3’
longFormatK: no visible binding for global variable ‘.’
longFormatK: no visible binding for global variable ‘s’
longFormatKB: no visible binding for global variable ‘.’
longFormatKB: no visible binding for global variable ‘s’
longFormatKB: no visible binding for global variable ‘bk’
longFormatKB2: no visible binding for global variable ‘.’
longFormatKB2: no visible binding for global variable ‘s’
longFormatKB2: no visible binding for global variable ‘bk’
modelSpecs: no visible binding for global variable ‘model’
mprob.matrix: no visible global function definition for ‘:=’
mprob.matrix: no visible binding for global variable ‘parents’
mprob.matrix: no visible binding for global variable ‘father’
mprob.matrix: no visible binding for global variable ‘mother’
posteriorSimulationPooled: possible error in `mcmcParams<-`(object,
  force = TRUE, value = `*tmpv*`): unused argument (force = TRUE)
predictiveTibble: no visible binding for global variable ‘value’
simulate_data_multi2: no visible binding for global variable
  ‘copy_number’
simulate_data_multi3: no visible binding for global variable
  ‘copy_number’
startAtTrueValues2: no visible binding for global variable
  ‘copy_number’
triodata: no visible binding for global variable ‘id’
augmentData2,MultiBatchList: no visible binding for global variable
  ‘model’
augmentData2,MultiBatchList: no visible binding for global variable ‘.’
augmentData2,MultiBatchList: no visible binding for global variable
  ‘id’
batch<-,MultiBatch-numeric: no visible global function definition for
  ‘spec’
batch<-,MultiBatch-numeric: no visible global function definition for
  ‘spec<-’
coerce,McmcChains-list: no visible binding for global variable ‘s’
computePrec,MultiBatch: no visible binding for global variable ‘prec’
findSurrogates,MultiBatch: no visible binding for global variable ‘id’
findSurrogates,MultiBatch: no visible binding for global variable
  ‘provisional_batch’
findSurrogates,MultiBatch: no visible binding for global variable
  ‘batch_labels’
sigma,MultiBatchCopyNumberPooled: no visible binding for global
  variable ‘s2’
Undefined global functions or variables:
  . .gibbs_trios_mcmc2 .gibbs_trios_mcmc3 := batch_index batch_labels
  batches bk copy_number father id log_ratio maplabel medians model
  mother mprob nhom parents prec provisional_batch s s2 snpdat spec
  spec<- t.test value
Consider adding
  importFrom("stats", "t.test")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘TBM’ ‘findSurrogates’ ‘modelName’ ‘p’
Undocumented S4 methods:
  generic '[' and siglist 'MixtureModel,logical,ANY,ANY'
  generic '[' and siglist 'MixtureModel,numeric,ANY,ANY'
  generic '[' and siglist 'MultiBatchList,ANY,ANY,ANY'
  generic '[<-' and siglist 'MultiBatchList,ANY,ANY,ANY'
  generic '[[' and siglist 'MultiBatchList,character,ANY'
  generic '[[' and siglist 'MultiBatchList,numeric,ANY'
  generic '[[<-' and siglist 'MultiBatchList,ANY,ANY'
  generic 'batch' and siglist 'MultiBatch'
  generic 'batch' and siglist 'MultiBatchList'
  generic 'burnin' and siglist 'MultiBatch'
  generic 'burnin' and siglist 'MultiBatchList'
  generic 'burnin<-' and siglist 'MultiBatch,numeric'
  generic 'burnin<-' and siglist 'MultiBatchList,numeric'
  generic 'chains' and siglist 'MultiBatch'
  generic 'chains' and siglist 'MultiBatchList'
  generic 'dfr' and siglist 'MultiBatch'
  generic 'dfr' and siglist 'MultiBatchList'
  generic 'hyperParams' and siglist 'MultiBatch'
  generic 'hyperParams' and siglist 'MultiBatchList'
  generic 'hyperParams<-' and siglist 'MultiBatch,Hyperparameters'
  generic 'hyperParams<-' and siglist 'MultiBatchList,Hyperparameters'
  generic 'iter' and siglist 'McmcChains'
  generic 'iter' and siglist 'MultiBatch'
  generic 'iter' and siglist 'MultiBatchList'
  generic 'iter<-' and siglist 'McmcChains,ANY'
  generic 'iter<-' and siglist 'MultiBatch,numeric'
  generic 'iter<-' and siglist 'MultiBatchList,numeric'
  generic 'k' and siglist 'McmcChains'
  generic 'k' and siglist 'MultiBatch'
  generic 'k' and siglist 'MultiBatchList'
  generic 'k<-' and siglist 'McmcChains'
  generic 'label_switch' and siglist 'MultiBatch'
  generic 'length' and siglist 'MultiBatchList'
  generic 'logPrior' and siglist 'MultiBatch'
  generic 'log_lik' and siglist 'MultiBatch'
  generic 'marginal_lik' and siglist 'MultiBatch'
  generic 'marginal_lik' and siglist 'MultiBatchList'
  generic 'marginal_lik<-' and siglist 'MultiBatch,numeric'
  generic 'mcmcParams' and siglist 'MultiBatch'
  generic 'mcmcParams' and siglist 'MultiBatchList'
  generic 'mcmcParams<-' and siglist 'MultiBatch,McmcParams'
  generic 'mcmcParams<-' and siglist 'MultiBatchList,McmcParams'
  generic 'modelName' and siglist 'MultiBatch'
  generic 'modelName' and siglist 'MultiBatchList'
  generic 'modes' and siglist 'MultiBatch'
  generic 'modes' and siglist 'MultiBatchList'
  generic 'modes<-' and siglist 'MultiBatch'
  generic 'mu' and siglist 'MultiBatch'
  generic 'nStarts' and siglist 'MultiBatch'
  generic 'nStarts' and siglist 'MultiBatchList'
  generic 'nStarts<-' and siglist 'MultiBatch,integer'
  generic 'nStarts<-' and siglist 'MultiBatch,numeric'
  generic 'nStarts<-' and siglist 'MultiBatchList,integer'
  generic 'nStarts<-' and siglist 'MultiBatchList,numeric'
  generic 'names' and siglist 'MultiBatchList'
  generic 'nu.0' and siglist 'MultiBatch'
  generic 'oned' and siglist 'MultiBatch'
  generic 'oned' and siglist 'MultiBatchList'
  generic 'p' and siglist 'McmcChains'
  generic 'p' and siglist 'MultiBatch'
  generic 'posteriorSimulation' and siglist 'MultiBatch'
  generic 'posteriorSimulation' and siglist 'MultiBatchList'
  generic 'posteriorSimulation' and siglist 'MultiBatchP'
  generic 'posteriorSimulation' and siglist 'list'
  generic 'probz' and siglist 'MultiBatch'
  generic 'sigma2.0' and siglist 'MultiBatch'
  generic 'sigma2' and siglist 'MultiBatch'
  generic 'sigma' and siglist 'MultiBatchPooled'
  generic 'sigma<-' and siglist 'MixtureModel'
  generic 'sigma<-' and siglist 'MultiBatchPooled'
  generic 'tau2' and siglist 'MultiBatch'
  generic 'theta' and siglist 'MultiBatch'
  generic 'theta<-' and siglist 'McmcChains,ANY'
  generic 'theta<-' and siglist 'MixtureModel,ANY'
  generic 'theta<-' and siglist 'MultiBatch,matrix'
  generic 'theta<-' and siglist 'MultiBatchModel,ANY'
  generic 'thin' and siglist 'MultiBatch'
  generic 'thin' and siglist 'MultiBatchList'
  generic 'thin<-' and siglist 'McmcParams,numeric'
  generic 'thin<-' and siglist 'MultiBatch,numeric'
  generic 'thin<-' and siglist 'MultiBatchList,numeric'
  generic 'triodata_lrr' and siglist 'TrioBatchModel'
  generic 'z' and siglist 'MultiBatch'
  generic 'zFreq' and siglist 'MultiBatch'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
S4 class codoc mismatches from documentation object 'MixtureModel-class':
Slots for class 'MixtureModel'
  Code: .internal.constraint .internal.counter batch batchElements data
        data.mean data.prec hyperparams k label_switch loglik logprior
        marginal_lik mcmc.chains mcmc.params modes mu nu.0 pi
        predictive probz sigma2 sigma2.0 tau2 theta u z zfreq zstar
  Docs: .internal.constraint .internal.counter batch batchElements data
        data.mean data.prec hyperparams k label_switch loglik logprior
        marginal_lik marginal_lik mcmc.chains mcmc.params modes mu nu.0
        pi probz sigma2 sigma2.0 tau2 theta u z zfreq

S4 class codoc mismatches from documentation object 'MultiBatch-class':
Slots for class 'MultiBatch'
  Code: chains current_values data down_sample flags parameters specs
        summaries
  Docs: chains current_values data down_sample flags parameters
        summaries

S4 class codoc mismatches from documentation object 'MultiBatchModel-class':
Slots for class 'MultiBatchModel'
  Code: .internal.constraint .internal.counter batch batchElements data
        data.mean data.prec hyperparams k label_switch loglik logprior
        marginal_lik mcmc.chains mcmc.params modes mu nu.0 pi
        predictive probz sigma2 sigma2.0 tau2 theta u z zfreq zstar
  Inherited: k hyperparams theta sigma2 nu.0 sigma2.0 pi mu tau2
        predictive zstar data data.mean data.prec z zfreq probz u
        logprior loglik mcmc.chains batch batchElements modes
        mcmc.params label_switch marginal_lik .internal.constraint
        .internal.counter
  Docs: .internal.constraint batch batchElements data data.mean
        data.prec hyperparams is_mendelian k label_switch loglik
        logprior mcmc.chains mcmc.params modes mu nu.0 pi probz sigma2
        sigma2.0 tau2 theta z zfreq

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'HyperparametersTrios'
  ‘k’ ‘mu.0’ ‘tau2.0’ ‘eta.0’ ‘m2.0’ ‘alpha’ ‘beta’ ‘a’ ‘b’ ‘dfr’

Undocumented arguments in documentation object 'McmcParams'
  ‘min_GR’ ‘min_effsize’ ‘max_burnin’ ‘min_chains’

Duplicated \argument entries in documentation object 'MultiBatchModel2':
  ‘dat’ ‘batches’ ‘hp’ ‘mp’

Undocumented arguments in documentation object 'TrioBatchModel'
  ‘mprob’ ‘maplabel’
Documented arguments not in \usage in documentation object 'TrioBatchModel':
  ‘batches’

Undocumented arguments in documentation object 'gibbs'
  ‘maplabel’ ‘mprob’

Documented arguments not in \usage in documentation object 'iter<-':
  ‘force’

Documented arguments not in \usage in documentation object 'mcmcParams':
  ‘force’

Undocumented arguments in documentation object 'sigma<-'
  ‘value’

Undocumented arguments in documentation object 'singleBatchGuided,MultiBatchList,MultiBatch-method'
  ‘x’ ‘guide’

Undocumented arguments in documentation object 'theta'
  ‘value’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
MultiBatchModel  77.287  7.764  85.222
ggplot-functions 49.775 18.086  68.341
MBP              15.253  1.851  17.109
gibbs            10.763  1.048  12.083
upSample2         6.516  0.785   7.337
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/CNPBayes.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CNPBayes
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘CNPBayes’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c miscfunctions.cpp -o miscfunctions.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c multibatch.cpp -o multibatch.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c multibatch_pooledvar.cpp -o multibatch_pooledvar.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c multibatch_reduced.cpp -o multibatch_reduced.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c pooledvar_reduced.cpp -o pooledvar_reduced.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c triomodel.cpp -o triomodel.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o CNPBayes.so RcppExports.o miscfunctions.o multibatch.o multibatch_pooledvar.o multibatch_reduced.o pooledvar_reduced.o triomodel.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/CNPBayes/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘alpha’ in package ‘CNPBayes’
in method for ‘convergence’ with signature ‘"MultiBatchList"’: no definition for class “MultiBatchList”
Creating a generic function from function ‘sigma’ in package ‘CNPBayes’
Note: wrong number of arguments to '/' 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CNPBayes)

R Under development (unstable) (2018-12-26 r75909) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> Sys.setenv("R_TESTS"="")
> library(testthat)
> library(CNPBayes)
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb

Attaching package: 'CNPBayes'

The following object is masked from 'package:stats':

    sigma

> test_check("CNPBayes")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 312 SKIPPED: 3 FAILED: 0
> 
> proc.time()
   user  system elapsed 
532.947 155.506 682.001 

name	user	system	elapsed
CopyNumber-methods	0.012	0.004	0.015
Hyperparameters	0.011	0.003	0.014
HyperparametersMultiBatch	0.001	0.001	0.002
HyperparametersSingleBatch	0.004	0.001	0.005
HyperparametersTrios	0.001	0.000	0.001
MBP	15.253	1.851	17.109
McmcParams-class	0.005	0.000	0.005
McmcParams	0.001	0.000	0.001
MultiBatchModel	77.287	7.764	85.222
SingleBatchModel	0.354	0.046	0.400
batch-method	0.008	0.012	0.019
bic-method	1.005	0.114	1.119
burnin-method	0.002	0.000	0.002
chains-method	0.012	0.001	0.012
chromosome	0.057	0.002	0.058
collapseBatch-method	0.474	0.044	0.519
consensusCNP	0.249	0.002	0.251
copyNumber	0.011	0.001	0.012
dfr-method	0.003	0.001	0.004
downSample	0.095	0.002	0.096
eta.0-method	0.002	0.000	0.002
ggplot-functions	49.775	18.086	68.341
gibbs	10.763	1.048	12.083
hyperParams-method	0.002	0.000	0.003
iter-method	0.000	0.000	0.001
k-method	0.053	0.001	0.053
label_switch	0.001	0.000	0.000
logPrior-method	0	0	0
log_lik-method	0.002	0.001	0.002
m2.0-method	0.001	0.000	0.002
mapParams	0.001	0.001	0.001
map_z	0.001	0.000	0.001
mapping	0.002	0.000	0.003
marginalLikelihood-method	0.877	0.179	1.058
marginal_lik	0.000	0.001	0.001
mcmcParams-method	0.001	0.000	0.001
mlParams	0.000	0.001	0.001
modelName-MixtureModel-method	0.001	0.000	0.001
modes-method	0.000	0.001	0.001
mu-method	0.000	0.000	0.001
muMean	0.001	0.000	0.000
muc	0.001	0.000	0.001
nStarts-method	0.002	0.000	0.002
nu.0-method	0	0	0
numberObs-method	0.000	0.000	0.001
p-MixtureModel-method	0.000	0.000	0.001
pic	0.001	0.001	0.000
posteriorPredictive	0	0	0
posteriorSimulation-method	0.039	0.003	0.043
posterior_cases	0.000	0.001	0.000
pp	0	0	0
probz-method	0.001	0.001	0.000
probzpar-method	0.001	0.000	0.001
qInverseTau2	0.006	0.001	0.005
sigma	0.001	0.000	0.000
sigma2-method	0.000	0.000	0.001
sigma2.0-method	0	0	0
sigmac	0.014	0.019	0.034
simulateBatchData	3.988	0.503	4.492
simulateData	3.873	0.813	4.686
tau	0.001	0.000	0.001
tau2-method	0.026	0.001	0.026
tauMean	0.000	0.000	0.001
tauc	0.014	0.021	0.035
theta-method	0.001	0.000	0.001
thin-method	0.002	0.000	0.002
triodata_lrr-method	0	0	0
upSample2	6.516	0.785	7.337
y-method	0.000	0.000	0.001
z-method	0.001	0.000	0.001
zfreq-method	0	0	0
zfreqpar-method	0.000	0.000	0.001