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CHECK report for CNPBayes on merida2

This page was generated on 2018-10-17 08:55:36 -0400 (Wed, 17 Oct 2018).

Package 276/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNPBayes 1.10.0
Jacob Carey
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/CNPBayes
Branch: RELEASE_3_7
Last Commit: 103b6b1
Last Changed Date: 2018-04-30 10:35:39 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CNPBayes
Version: 1.10.0
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_1.10.0.tar.gz
StartedAt: 2018-10-16 20:35:39 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:43:00 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 441.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: CNPBayes.Rcheck
Warnings: 1

Command output

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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_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/CNPBayes.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.10.0’
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
copyNumber,SingleBatchCopyNumber: no visible binding for global
  variable ‘theta.star’
Undefined global functions or variables:
  theta.star
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'marginal_lik'
  ‘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
ggplot-functions 6.852  0.215   7.134
ggPredictive     6.259  0.115   6.422
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/CNPBayes.Rcheck/00check.log’
for details.



Installation output

CNPBayes.Rcheck/00install.out

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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/3.5/Resources/library’
* installing *source* package ‘CNPBayes’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c miscfunctions.cpp -o miscfunctions.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c multibatch.cpp -o multibatch.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c multibatch_pooledvar.cpp -o multibatch_pooledvar.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c multibatch_pooledvar_reduced.cpp -o multibatch_pooledvar_reduced.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c multibatch_reduced.cpp -o multibatch_reduced.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c singlebatch.cpp -o singlebatch.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c singlebatch_pooledvar.cpp -o singlebatch_pooledvar.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c singlebatch_pooledvar_reduced.cpp -o singlebatch_pooledvar_reduced.o
singlebatch_pooledvar_reduced.cpp:46:10: warning: unused variable 'prod' [-Wunused-variable]
  double prod ;
         ^
singlebatch_pooledvar_reduced.cpp:86:7: warning: unused variable 'K' [-Wunused-variable]
  int K = thetastar.size() ;
      ^
singlebatch_pooledvar_reduced.cpp:330:7: warning: unused variable 'K' [-Wunused-variable]
  int K = thetastar.size() ;
      ^
singlebatch_pooledvar_reduced.cpp:617:7: warning: unused variable 'N' [-Wunused-variable]
  int N = x.size() ;
      ^
singlebatch_pooledvar_reduced.cpp:682:7: warning: unused variable 'K' [-Wunused-variable]
  int K = thetastar.size() ;
      ^
5 warnings generated.
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c singlebatch_reduced.cpp -o singlebatch_reduced.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c update.cpp -o update.o
clang++ -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_pooledvar_reduced.o multibatch_reduced.o singlebatch.o singlebatch_pooledvar.o singlebatch_pooledvar_reduced.o singlebatch_reduced.o update.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/3.5/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’
Creating a generic function from function ‘sigma’ in package ‘CNPBayes’
** 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


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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, lengths, 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. Failure: extdata is current (@test_currentExtData.R#9)  ──────────────────
`grl` not identical to `grl2`.
Attributes: < Component "class": 1 string mismatch >
Attributes: < Component "partitioning": Attributes: < Component "elementType": 1 string mismatch > >
Attributes: < Component "unlistData": Attributes: < Names: 5 string mismatches > >
Attributes: < Component "unlistData": Attributes: < Length mismatch: comparison on first 7 components > >
Attributes: < Component "unlistData": Attributes: < Component 3: Modes: list, character > >
Attributes: < Component "unlistData": Attributes: < Component 3: Length mismatch: comparison on first 0 components > >
Attributes: < Component "unlistData": Attributes: < Component 4: Modes: S4, list > >
Attributes: < Component "unlistData": Attributes: < Component 4: Lengths: 25, 0 > >
Attributes: < Component "unlistData": Attributes: < Component 4: Attributes: < Modes: list, NULL > > >
...

══ testthat results  ═══════════════════════════════════════════════════════════
OK: 168 SKIPPED: 1 FAILED: 1
1. Failure: extdata is current (@test_currentExtData.R#9) 

Error: testthat unit tests failed
recover called non-interactively; frames dumped, use debugger() to view
> 
> proc.time()
   user  system elapsed 
189.786   8.978 204.453 

Example timings

CNPBayes.Rcheck/CNPBayes-Ex.timings

nameusersystemelapsed
CopyNumber-methods0.0720.0080.081
Hyperparameters0.0090.0010.010
HyperparametersMultiBatch0.0020.0000.002
HyperparametersSingleBatch0.0040.0000.005
McmcParams-class0.0110.0010.012
McmcParams0.0030.0000.003
MultiBatchModel20.5560.0190.584
SingleBatchModel20.0650.0020.068
batch-method0.0160.0100.025
bic-method1.1000.0311.138
burnin-method0.0020.0000.003
chains-method0.0070.0000.007
chromosome0.0010.0000.001
collapseBatch-method0.0150.0000.015
combinePlates-method0.0150.0010.015
consensusCNP0.3000.0100.312
copyNumber0.4110.0870.502
eta.0-method0.0020.0000.003
ggPredictive6.2590.1156.422
ggplot-functions6.8520.2157.134
gibbs0.0380.0060.045
gibbs_all0.0250.0030.028
gibbs_pooled0.0290.0020.032
hyperParams-method0.0040.0000.005
iter-method0.0010.0000.002
k-method0.0630.0010.064
label_switch0.0010.0000.002
logPrior-method0.0010.0000.001
log_lik-method0.0010.0000.001
m2.0-method0.0020.0000.001
mapComponents0.1550.0030.159
mapParams0.0020.0000.002
map_z0.0080.0080.016
mapping0.0350.0010.037
marginalLikelihood-method0.5080.0350.556
marginal_lik0.0010.0000.001
mcmcParams-method0.0010.0000.002
mlParams0.0010.0010.001
modes-method0.0010.0000.001
mu-method0.0010.0000.001
muMean0.0010.0000.001
muc0.0000.0000.001
nStarts-method0.0020.0000.002
nu.0-method0.0010.0000.001
numberObs-method0.0010.0010.001
p0.0020.0000.001
pic0.0010.0000.001
posteriorPredictive2.5230.1252.672
posteriorSimulation-method0.0470.0070.054
posterior_cases0.0110.0010.011
probz-method0.0300.0310.062
qInverseTau20.0090.0010.010
sigma0.0010.0000.002
sigma2-method0.0020.0010.002
sigma2.0-method0.0020.0000.002
sigmac0.0010.0000.001
simulateBatchData0.0240.0020.027
simulateData0.0330.0060.039
tau0.0010.0000.001
tau2-method0.0430.0010.046
tauMean0.0020.0000.002
tauc0.0020.0000.002
theta-method0.0120.0010.014
thin-method0.0030.0010.003
tile-functions4.7050.0604.811
y-method0.0120.0120.025
z-method0.0080.0100.018
zfreq-method0.0020.0000.001