BioC 3.3: CHECK report for CNPBayes on linux2.bioconductor.org

Package: CNPBayes

Version: 1.1.2

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings CNPBayes_1.1.2.tar.gz

StartedAt: 2015-10-27 02:46:03 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:52:28 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 385.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: CNPBayes.Rcheck

Warnings: 2

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings CNPBayes_1.1.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/CNPBayes.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.1.2’
* 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 ... [81s/81s] OK
* checking installed package size ... NOTE
  installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
* 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 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
coerce,MixtureModel-SummarizedExperiment: no visible global function
  definition for ‘Rle’
Undefined global functions or variables:
  Rle
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'labelSwitching' and siglist 'MixtureModel'
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
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 ... [20s/20s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
marginalLikelihood-method 9.859  0.047   9.915
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [167s/170s]
 [167s/171s] 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: 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/CNPBayes.Rcheck/00check.log’
for details.

* installing *source* package ‘CNPBayes’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c miscfunctions.cpp -o miscfunctions.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c reduced_pooledvariance.cpp -o reduced_pooledvariance.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c singlebatch_pooledvar.cpp -o singlebatch_pooledvar.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c update.cpp -o update.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c updates_batch.cpp -o updates_batch.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c updates_marginal.cpp -o updates_marginal.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c updates_reduced_batch.cpp -o updates_reduced_batch.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c updates_reduced_marginal.cpp -o updates_reduced_marginal.o
g++ -shared -L/home/biocbuild/bbs-3.3-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-3.3-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.3-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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	0.029
DensityModel-class	0.503	0.012	0.515
DensityModel	0.004	0.000	0.004
Hyperparameters	0.001	0.000	0.001
HyperparametersBatch	0.002	0.000	0.002
HyperparametersMarginal	0.002	0.000	0.002
MarginalModel	0.007	0.000	0.007
McmcParams-class	0.003	0.000	0.003
McmcParams	0.001	0.000	0.001
batch-method	0.008	0.003	0.012
bic-method	0.003	0.000	0.003
burnin-method	0.001	0.001	0.001
chains-method	0.004	0.000	0.004
chromosome	0	0	0
clusters-method	0.227	0.004	0.231
collapseBatch-method	0.021	0.000	0.021
consensusCNP	0.837	0.036	0.873
eta.0-method	0.001	0.000	0.001
hyperParams-method	0.001	0.000	0.001
iter-method	0.001	0.000	0.001
k-method	0.01	0.00	0.01
labelSwitching-method	0.008	0.000	0.009
logPrior-method	0.001	0.000	0.001
log_lik-method	0	0	0
m2.0-method	0.001	0.000	0.001
map	0.02	0.00	0.02
marginalLikelihood-method	9.859	0.047	9.915
mcmcParams-method	0.000	0.000	0.001
modes-method	0	0	0
mu-method	0.001	0.000	0.000
muMean	0.000	0.000	0.001
muc	0.000	0.000	0.001
nStarts-method	0.002	0.000	0.002
nu.0-method	0.001	0.000	0.000
p	0.001	0.000	0.000
pic	0.000	0.000	0.001
plot	3.158	0.004	3.164
probz-method	0.02	0.00	0.02
qInverseTau2	0.007	0.000	0.008
sigma	0	0	0
sigma2-method	0	0	0
sigma2.0-method	0	0	0
sigmac	0.001	0.000	0.001
simulateBatchData	0.027	0.000	0.027
simulateData	0.031	0.000	0.031
tau	0.001	0.000	0.000
tau2-method	0.006	0.000	0.006
tauMean	0.001	0.000	0.000
tauc	0.001	0.000	0.001
theta-method	0.007	0.000	0.007
thin-method	0.001	0.000	0.000
tracePlot-method	0.064	0.000	0.064
y-method	0.008	0.004	0.012
z-method	0.008	0.000	0.007
zfreq-method	0.001	0.000	0.001