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BioC 3.6: CHECK report for CNPBayes on veracruz1

This page was generated on 2017-08-16 13:47:54 -0400 (Wed, 16 Aug 2017).

Package 252/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNPBayes 1.7.1
Jacob Carey
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CNPBayes
Last Changed Rev: 129284 / Revision: 131943
Last Changed Date: 2017-04-29 16:38:57 -0400 (Sat, 29 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CNPBayes
Version: 1.7.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CNPBayes_1.7.1.tar.gz
StartedAt: 2017-08-16 01:23:41 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:31:11 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 449.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: CNPBayes.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CNPBayes_1.7.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/CNPBayes.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.7.1’
* 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 ... 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-3.6-bioc/meat/CNPBayes.Rcheck/00check.log’
for details.


CNPBayes.Rcheck/00install.out:

* 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   -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/3.4/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/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -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   -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/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -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   -fPIC  -Wall -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   -fPIC  -Wall -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   -fPIC  -Wall -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   -fPIC  -Wall -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/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 /Users/biocbuild/bbs-3.6-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
BatchModel0.0370.0000.037
DensityModel-class1.4240.0541.521
DensityModel0.2770.0010.286
Hyperparameters0.0010.0000.002
HyperparametersBatch0.0020.0000.003
HyperparametersMarginal0.0030.0000.003
MarginalModel0.0800.0000.081
McmcParams-class0.0030.0010.003
McmcParams0.0010.0000.002
batch-method0.0090.0060.015
bic-method0.0170.0000.018
burnin-method0.0010.0000.001
chains-method0.0050.0000.005
chromosome0.0000.0000.001
clusters-method0.0560.0010.057
collapseBatch-method0.0600.0000.061
consensusCNP2.1230.0152.177
eta.0-method0.0010.0000.001
hyperParams-method0.0010.0000.002
iter-method0.0010.0000.002
k-method0.010.000.01
labelSwitching-method0.0300.0010.031
logPrior-method0.0010.0000.002
log_lik-method0.0010.0000.001
m2.0-method0.0020.0000.001
map0.0380.0040.042
marginalLikelihood-method0.0490.0050.054
mcmcParams-method0.0010.0000.001
modes-method0.0000.0010.000
mu-method000
muMean0.0010.0000.000
muc000
nStarts-method0.0020.0010.002
nu.0-method0.0010.0000.006
p0.0010.0000.000
pic0.0000.0010.001
plot2.3600.1252.529
posterior_cases0.0140.0000.014
probz-method0.0170.0250.041
qInverseTau20.0210.0000.022
sigma0.0010.0000.001
sigma2-method0.0000.0000.001
sigma2.0-method0.0000.0000.001
sigmac0.0010.0000.001
simulateBatchData0.0740.0040.079
simulateData0.0340.0030.038
tau000
tau2-method0.0050.0010.006
tauMean0.0010.0000.000
tauc0.0010.0000.001
theta-method0.0090.0010.010
thin-method0.0010.0000.002
tracePlot-method0.0430.0020.046
y-method0.0060.0080.014
z-method0.0020.0040.009
zfreq-method0.0010.0000.001