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BioC 3.4: CHECK report for CNPBayes on zin1

This page was generated on 2016-09-21 03:40:19 -0700 (Wed, 21 Sep 2016).

Package 226/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNPBayes 1.3.2
Jacob Carey
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CNPBayes
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: CNPBayes
Version: 1.3.2
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings CNPBayes_1.3.2.tar.gz
StartedAt: 2016-09-20 04:44:41 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 04:52:22 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 460.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: CNPBayes.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings CNPBayes_1.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/CNPBayes.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.3.2’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   9.5Mb
* 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 ... OK
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/CNPBayes.Rcheck/00check.log’
for details.


CNPBayes.Rcheck/00install.out:

* installing *source* package ‘CNPBayes’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c miscfunctions.cpp -o miscfunctions.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c singlebatch_pooledvar.cpp -o singlebatch_pooledvar.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c update.cpp -o update.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c updates_batch.cpp -o updates_batch.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c updates_marginal.cpp -o updates_marginal.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c updates_reduced_batch.cpp -o updates_reduced_batch.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c updates_reduced_marginal.cpp -o updates_reduced_marginal.o
g++ -shared -L/home/biocbuild/bbs-3.4-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-3.4-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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)

CNPBayes.Rcheck/CNPBayes-Ex.timings:

nameusersystemelapsed
BatchModel0.0280.0000.031
DensityModel-class0.5440.0080.551
DensityModel0.0040.0000.005
Hyperparameters0.0040.0000.001
HyperparametersBatch0.0000.0000.001
HyperparametersMarginal0.0000.0040.002
MarginalModel0.0080.0000.007
McmcParams-class0.0040.0000.003
McmcParams0.0000.0000.001
batch-method0.0040.0080.012
bic-method0.0040.0000.005
burnin-method0.0040.0000.001
chains-method0.0040.0000.004
chromosome0.0000.0000.001
clusters-method0.2280.0000.231
collapseBatch-method0.0240.0000.026
consensusCNP0.8880.0240.910
eta.0-method0.0000.0000.001
hyperParams-method0.0000.0000.001
iter-method0.0000.0000.001
k-method0.0080.0000.011
labelSwitching-method0.0080.0000.011
logPrior-method0.0000.0000.001
log_lik-method0.0000.0000.001
m2.0-method0.0040.0000.001
map0.0440.0040.047
marginalLikelihood-method0.0800.0000.081
mcmcParams-method0.0040.0000.001
modes-method0.0000.0000.001
mu-method000
muMean000
muc000
nStarts-method0.0000.0000.001
nu.0-method0.0000.0000.001
p0.0000.0000.001
pic000
plot4.8600.0044.866
posterior_cases0.0120.0000.012
probz-method0.0080.0200.026
qInverseTau20.0120.0000.012
sigma0.0000.0000.001
sigma2-method0.0000.0000.001
sigma2.0-method000
sigmac000
simulateBatchData0.0320.0000.034
simulateData0.0320.0000.035
tau0.0000.0000.001
tau2-method0.0080.0000.006
tauMean0.0000.0000.001
tauc000
theta-method0.0080.0000.008
thin-method000
tracePlot-method0.0200.0000.021
y-method0.0080.0040.009
z-method0.0040.0000.005
zfreq-method0.0000.0000.001