BioC 3.5: CHECK report for CNPBayes on oaxaca

Package: CNPBayes

Version: 1.5.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CNPBayes_1.5.0.tar.gz

StartedAt: 2017-03-04 00:51:41 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 00:58:42 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 421.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: CNPBayes.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CNPBayes_1.5.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/CNPBayes.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.5.0’
* 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 ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘GenomicRanges’
A package should be listed in only one of these fields.
* 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 loading without being on the library search path ... 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
consensusRegion: no visible global function definition for
  ‘elementLengths’
Undefined global functions or variables:
  elementLengths
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'labelSwitching':
labelSwitching
  Code: function(object, ...)
  Docs: function(object, merge = TRUE)
  Argument names in code not in docs:
    ...
  Argument names in docs not in code:
    merge
  Mismatches in argument names:
    Position: 2 Code: ... Docs: merge

* checking Rd \usage sections ... OK
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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-3.5-bioc/meat/CNPBayes.Rcheck/00check.log’
for details.

* installing *source* package ‘CNPBayes’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c miscfunctions.cpp -o miscfunctions.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c reduced_pooledvariance.cpp -o reduced_pooledvariance.o
reduced_pooledvariance.cpp:46:10: warning: unused variable 'prod' [-Wunused-variable]
  double prod ;
         ^
reduced_pooledvariance.cpp:86:7: warning: unused variable 'K' [-Wunused-variable]
  int K = thetastar.size() ;
      ^
reduced_pooledvariance.cpp:330:7: warning: unused variable 'K' [-Wunused-variable]
  int K = thetastar.size() ;
      ^
reduced_pooledvariance.cpp:617:7: warning: unused variable 'N' [-Wunused-variable]
  int N = x.size() ;
      ^
reduced_pooledvariance.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/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c update.cpp -o update.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c updates_batch.cpp -o updates_batch.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c updates_marginal.cpp -o updates_marginal.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c updates_reduced_batch.cpp -o updates_reduced_batch.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c updates_reduced_marginal.cpp -o updates_reduced_marginal.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 reduced_pooledvariance.o singlebatch_pooledvar.o update.o updates_batch.o updates_marginal.o updates_reduced_batch.o updates_reduced_marginal.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/CNPBayes.Rcheck/CNPBayes/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CNPBayes)

name	user	system	elapsed
BatchModel	0.029	0.000	0.030
DensityModel-class	1.449	0.054	1.654
DensityModel	0.273	0.005	0.280
Hyperparameters	0.001	0.000	0.001
HyperparametersBatch	0.002	0.000	0.002
HyperparametersMarginal	0.004	0.000	0.003
MarginalModel	0.119	0.000	0.119
McmcParams-class	0.005	0.001	0.006
McmcParams	0.001	0.000	0.001
batch-method	0.007	0.005	0.013
bic-method	0.018	0.000	0.019
burnin-method	0.000	0.000	0.001
chains-method	0.005	0.001	0.005
chromosome	0.001	0.000	0.000
clusters-method	0.081	0.002	0.082
collapseBatch-method	0.063	0.001	0.064
consensusCNP	2.587	0.018	2.606
eta.0-method	0.001	0.001	0.001
hyperParams-method	0.002	0.000	0.002
iter-method	0.001	0.000	0.001
k-method	0.015	0.001	0.015
labelSwitching-method	0.062	0.000	0.061
logPrior-method	0.002	0.000	0.001
log_lik-method	0.001	0.001	0.001
m2.0-method	0.001	0.000	0.001
map	0.057	0.007	0.065
marginalLikelihood-method	0.055	0.005	0.078
mcmcParams-method	0.001	0.000	0.002
modes-method	0.001	0.000	0.001
mu-method	0.001	0.000	0.000
muMean	0.001	0.000	0.001
muc	0.001	0.000	0.001
nStarts-method	0.002	0.000	0.002
nu.0-method	0.001	0.000	0.000
p	0.001	0.001	0.000
pic	0.001	0.000	0.001
plot	3.001	0.136	3.186
posterior_cases	0.016	0.000	0.016
probz-method	0.015	0.018	0.034
qInverseTau2	0.024	0.000	0.025
sigma	0.000	0.000	0.001
sigma2-method	0	0	0
sigma2.0-method	0.001	0.000	0.000
sigmac	0.001	0.000	0.001
simulateBatchData	0.080	0.005	0.084
simulateData	0.036	0.004	0.039
tau	0.000	0.000	0.001
tau2-method	0.005	0.000	0.006
tauMean	0	0	0
tauc	0.001	0.000	0.001
theta-method	0.007	0.002	0.009
thin-method	0.000	0.000	0.001
tracePlot-method	0.053	0.004	0.062
y-method	0.004	0.006	0.010
z-method	0.003	0.004	0.006
zfreq-method	0.000	0.000	0.001