BioC 3.5: CHECK report for CNPBayes on malbec2

Package: CNPBayes

Version: 1.6.1

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings CNPBayes_1.6.1.tar.gz

StartedAt: 2017-10-17 22:09:02 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 22:15:38 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 396.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: CNPBayes.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings CNPBayes_1.6.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/CNPBayes.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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 ‘1.6.1’
* 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 ... NOTE
  installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
* 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 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/CNPBayes.Rcheck/00check.log’
for details.

* installing *source* package ‘CNPBayes’ ...
** libs
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c miscfunctions.cpp -o miscfunctions.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c reduced_pooledvariance.cpp -o reduced_pooledvariance.o
reduced_pooledvariance.cpp: In function ‘Rcpp::NumericVector full_theta_pooled(Rcpp::S4)’:
reduced_pooledvariance.cpp:46:10: warning: unused variable ‘prod’ [-Wunused-variable]
   double prod ;
          ^
reduced_pooledvariance.cpp: In function ‘Rcpp::S4 reduced_sigma_pooled(Rcpp::S4)’:
reduced_pooledvariance.cpp:86:7: warning: unused variable ‘K’ [-Wunused-variable]
   int K = thetastar.size() ;
       ^
reduced_pooledvariance.cpp: In function ‘Rcpp::S4 reduced_mu_pooled(Rcpp::S4)’:
reduced_pooledvariance.cpp:330:7: warning: unused variable ‘K’ [-Wunused-variable]
   int K = thetastar.size() ;
       ^
reduced_pooledvariance.cpp: In function ‘Rcpp::NumericVector p_nu0_reduced_pooled(Rcpp::S4)’:
reduced_pooledvariance.cpp:617:7: warning: unused variable ‘N’ [-Wunused-variable]
   int N = x.size() ;
       ^
reduced_pooledvariance.cpp: In function ‘Rcpp::S4 reduced_s20_pooled(Rcpp::S4)’:
reduced_pooledvariance.cpp:682:7: warning: unused variable ‘K’ [-Wunused-variable]
   int K = thetastar.size() ;
       ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c singlebatch_pooledvar.cpp -o singlebatch_pooledvar.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c update.cpp -o update.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c updates_batch.cpp -o updates_batch.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c updates_marginal.cpp -o updates_marginal.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c updates_reduced_batch.cpp -o updates_reduced_batch.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c updates_reduced_marginal.cpp -o updates_reduced_marginal.o
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/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/home/biocbuild/bbs-3.5-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.5-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/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	0.048	0.000	0.046
DensityModel-class	1.148	0.028	1.176
DensityModel	0.300	0.000	0.301
Hyperparameters	0.000	0.000	0.001
HyperparametersBatch	0.000	0.000	0.001
HyperparametersMarginal	0.000	0.000	0.002
MarginalModel	0.064	0.000	0.061
McmcParams-class	0.004	0.000	0.004
McmcParams	0.000	0.000	0.001
batch-method	0.008	0.004	0.010
bic-method	0.016	0.000	0.016
burnin-method	0.000	0.000	0.002
chains-method	0.004	0.000	0.005
chromosome	0	0	0
clusters-method	0.052	0.000	0.049
collapseBatch-method	0.044	0.000	0.045
consensusCNP	2.100	0.000	2.101
eta.0-method	0.000	0.000	0.001
hyperParams-method	0.000	0.000	0.002
iter-method	0.000	0.000	0.001
k-method	0.008	0.000	0.009
labelSwitching-method	0.032	0.000	0.031
logPrior-method	0	0	0
log_lik-method	0.000	0.000	0.001
m2.0-method	0	0	0
map	0.032	0.004	0.034
marginalLikelihood-method	0.076	0.000	0.077
mcmcParams-method	0.004	0.000	0.002
modes-method	0.000	0.000	0.001
mu-method	0	0	0
muMean	0	0	0
muc	0	0	0
nStarts-method	0.000	0.000	0.002
nu.0-method	0.000	0.000	0.001
p	0.000	0.000	0.001
pic	0	0	0
plot	2.644	0.008	2.656
posterior_cases	0.008	0.000	0.011
probz-method	0.012	0.008	0.017
qInverseTau2	0.02	0.00	0.02
sigma	0	0	0
sigma2-method	0.000	0.000	0.001
sigma2.0-method	0.000	0.000	0.001
sigmac	0.000	0.000	0.001
simulateBatchData	0.056	0.008	0.064
simulateData	0.028	0.000	0.029
tau	0	0	0
tau2-method	0.008	0.000	0.007
tauMean	0	0	0
tauc	0.004	0.000	0.000
theta-method	0.008	0.000	0.008
thin-method	0.000	0.000	0.001
tracePlot-method	0.036	0.000	0.036
y-method	0.008	0.000	0.006
z-method	0.004	0.000	0.004
zfreq-method	0.004	0.000	0.000