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CHECK report for CNPBayes on merida2

This page was generated on 2019-04-09 13:32:21 -0400 (Tue, 09 Apr 2019).

Package 302/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNPBayes 1.13.5
Jacob Carey
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/CNPBayes
Branch: master
Last Commit: 1e9cdbb
Last Changed Date: 2019-01-03 09:20:51 -0400 (Thu, 03 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  ERROR  skipped  skipped 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ ERROR ] OK 

Summary

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: 2019-04-09 00:00:51 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 00:16:03 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 912.0 seconds
RetCode: 1
Status:  ERROR 
CheckDir: CNPBayes.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CNPBayes.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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  70.160  1.740  72.539
ggplot-functions 45.456  7.759  56.456
MBP              13.865  0.595  14.616
gibbs            10.321  0.278  10.800
upSample2         5.248  0.331   5.828
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
         p.bb = unique(p.bb), gt = simulateGt(n, p.aa, p.ab, p.bb, true.model), baf = simulateBaf(gt, 
             true.model))
  10: summarise.tbl_df(., n = n(), p.b = unique(p.b), p.aa = unique(p.aa), p.ab = unique(p.ab), 
         p.bb = unique(p.bb), gt = simulateGt(n, p.aa, p.ab, p.bb, true.model), baf = simulateBaf(gt, 
             true.model))
  11: summarise_impl(.data, dots, environment(), caller_env())
  12: simulateBaf(gt, true.model)
  13: rbeta(freq[2], ab[1], ab[2]) at testthat/test_baf_likelihood.R:48
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 306 SKIPPED: 3 FAILED: 1
  1. Error: baf likelihood (@test_baf_likelihood.R#55) 
  
  Error: testthat unit tests failed
  Execution halted
* 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: 1 ERROR, 3 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/CNPBayes.Rcheck/00check.log’
for details.

Installation output

CNPBayes.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CNPBayes
###
##############################################################################
##############################################################################


* 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)

Tests output

CNPBayes.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2018-11-27 r75683) -- "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")
── 1. Error: baf likelihood (@test_baf_likelihood.R#55)  ───────────────────────
invalid arguments
1: tibble(snp = rep(1:4, N), p.b = rep(c(0.1, 0.4, 0.8, 0.95), N), p.a = 1 - p.b, p.bb = p.b^2, 
       p.aa = p.a^2, p.ab = 2 * p.a * p.b) %>% group_by(snp) %>% summarize(n = n(), 
       p.b = unique(p.b), p.aa = unique(p.aa), p.ab = unique(p.ab), p.bb = unique(p.bb), 
       gt = simulateGt(n, p.aa, p.ab, p.bb, true.model), baf = simulateBaf(gt, true.model)) at testthat/test_baf_likelihood.R:55
2: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
3: eval(quote(`_fseq`(`_lhs`)), env, env)
4: eval(quote(`_fseq`(`_lhs`)), env, env)
5: `_fseq`(`_lhs`)
6: freduce(value, `_function_list`)
7: withVisible(function_list[[k]](value))
8: function_list[[k]](value)
9: summarize(., n = n(), p.b = unique(p.b), p.aa = unique(p.aa), p.ab = unique(p.ab), 
       p.bb = unique(p.bb), gt = simulateGt(n, p.aa, p.ab, p.bb, true.model), baf = simulateBaf(gt, 
           true.model))
10: summarise.tbl_df(., n = n(), p.b = unique(p.b), p.aa = unique(p.aa), p.ab = unique(p.ab), 
       p.bb = unique(p.bb), gt = simulateGt(n, p.aa, p.ab, p.bb, true.model), baf = simulateBaf(gt, 
           true.model))
11: summarise_impl(.data, dots, environment(), caller_env())
12: simulateBaf(gt, true.model)
13: rbeta(freq[2], ab[1], ab[2]) at testthat/test_baf_likelihood.R:48

══ testthat results  ═══════════════════════════════════════════════════════════
OK: 306 SKIPPED: 3 FAILED: 1
1. Error: baf likelihood (@test_baf_likelihood.R#55) 

Error: testthat unit tests failed
Execution halted

Example timings

CNPBayes.Rcheck/CNPBayes-Ex.timings

nameusersystemelapsed
CopyNumber-methods0.0130.0020.016
Hyperparameters0.0090.0010.011
HyperparametersMultiBatch0.0010.0000.001
HyperparametersSingleBatch0.0050.0010.006
HyperparametersTrios0.0010.0010.002
MBP13.865 0.59514.616
McmcParams-class0.0060.0010.006
McmcParams0.0010.0000.001
MultiBatchModel70.160 1.74072.539
SingleBatchModel0.3560.0180.376
batch-method0.0060.0070.011
bic-method0.8960.0380.941
burnin-method0.0010.0000.001
chains-method0.0090.0010.009
chromosome0.0490.0000.049
collapseBatch-method0.4420.0120.589
consensusCNP0.3250.0020.329
copyNumber0.0080.0000.009
dfr-method0.0030.0010.002
downSample0.0650.0010.069
eta.0-method0.0010.0000.001
ggplot-functions45.456 7.75956.456
gibbs10.321 0.27810.800
hyperParams-method0.0020.0010.002
iter-method0.0000.0000.001
k-method0.0790.0070.086
label_switch0.0000.0000.001
logPrior-method0.0000.0000.001
log_lik-method0.0000.0000.001
m2.0-method0.0010.0000.001
mapParams0.0010.0000.000
map_z0.0010.0000.000
mapping0.0020.0000.002
marginalLikelihood-method0.8190.0790.902
marginal_lik0.0000.0000.001
mcmcParams-method0.0010.0000.001
mlParams0.0010.0000.001
modelName-MixtureModel-method0.0010.0000.001
modes-method0.0000.0000.001
mu-method000
muMean000
muc0.0000.0000.001
nStarts-method0.0010.0000.002
nu.0-method000
numberObs-method000
p-MixtureModel-method000
pic0.0010.0000.000
posteriorPredictive0.0010.0010.000
posteriorSimulation-method0.0370.0020.040
posterior_cases000
pp000
probz-method0.0010.0010.001
probzpar-method000
qInverseTau20.0060.0000.007
sigma0.0000.0010.000
sigma2-method0.0000.0000.001
sigma2.0-method0.0000.0000.001
sigmac0.0120.0110.023
simulateBatchData3.5910.1784.144
simulateData2.6090.4023.194
tau0.0000.0000.001
tau2-method0.0250.0000.028
tauMean000
tauc0.0130.0130.027
theta-method000
thin-method0.0010.0010.002
triodata_lrr-method0.0010.0000.001
upSample25.2480.3315.828
y-method000
z-method000
zfreq-method0.0000.0000.001
zfreqpar-method000