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BioC 3.4: CHECK report for CNPBayes on moscato1

This page was generated on 2016-09-21 03:47:44 -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: rm -rf CNPBayes.buildbin-libdir CNPBayes.Rcheck && mkdir CNPBayes.buildbin-libdir CNPBayes.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CNPBayes.buildbin-libdir CNPBayes_1.3.2.tar.gz >CNPBayes.Rcheck\00install.out 2>&1 && cp CNPBayes.Rcheck\00install.out CNPBayes-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=CNPBayes.buildbin-libdir --install="check:CNPBayes-install.out" --force-multiarch --no-vignettes --timings CNPBayes_1.3.2.tar.gz
StartedAt: 2016-09-20 06:03:26 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 06:19:24 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 958.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: CNPBayes.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CNPBayes.buildbin-libdir CNPBayes.Rcheck && mkdir CNPBayes.buildbin-libdir CNPBayes.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CNPBayes.buildbin-libdir CNPBayes_1.3.2.tar.gz >CNPBayes.Rcheck\00install.out 2>&1 && cp CNPBayes.Rcheck\00install.out CNPBayes-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=CNPBayes.buildbin-libdir --install="check:CNPBayes-install.out" --force-multiarch --no-vignettes --timings CNPBayes_1.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/CNPBayes.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'CNPBayes' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.0Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.4-bioc/meat/CNPBayes.buildbin-libdir/CNPBayes/libs/i386/CNPBayes.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
     user system elapsed
plot 5.38      0    5.38
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'D:/biocbld/bbs-3.4-bioc/meat/CNPBayes.Rcheck/00check.log'
for details.

CNPBayes.Rcheck/00install.out:


install for i386

* installing *source* package 'CNPBayes' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c miscfunctions.cpp -o miscfunctions.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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() ;
       ^
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c singlebatch_pooledvar.cpp -o singlebatch_pooledvar.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c update.cpp -o update.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c updates_batch.cpp -o updates_batch.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c updates_marginal.cpp -o updates_marginal.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c updates_reduced_batch.cpp -o updates_reduced_batch.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c updates_reduced_marginal.cpp -o updates_reduced_marginal.o
Loading required package: Rcpp
Loading required package: Rcpp
Loading required package: Rcpp
Loading required package: Rcpp
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o CNPBayes.dll tmp.def 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 -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lRlapack -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/CNPBayes.buildbin-libdir/CNPBayes/libs/i386
** 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

install for x64

* installing *source* package 'CNPBayes' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c miscfunctions.cpp -o miscfunctions.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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() ;
       ^
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c singlebatch_pooledvar.cpp -o singlebatch_pooledvar.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c update.cpp -o update.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c updates_batch.cpp -o updates_batch.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c updates_marginal.cpp -o updates_marginal.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c updates_reduced_batch.cpp -o updates_reduced_batch.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c updates_reduced_marginal.cpp -o updates_reduced_marginal.o
Loading required package: Rcpp
Loading required package: Rcpp
Loading required package: Rcpp
Loading required package: Rcpp
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o CNPBayes.dll tmp.def 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 -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lRlapack -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/CNPBayes.buildbin-libdir/CNPBayes/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNPBayes' as CNPBayes_1.3.2.zip
* DONE (CNPBayes)

CNPBayes.Rcheck/examples_i386/CNPBayes-Ex.timings:

nameusersystemelapsed
BatchModel0.040.000.04
DensityModel-class0.50.00.5
DensityModel0.020.000.02
Hyperparameters000
HyperparametersBatch000
HyperparametersMarginal000
MarginalModel0.010.000.02
McmcParams-class000
McmcParams000
batch-method0.020.000.01
bic-method0.010.000.02
burnin-method000
chains-method000
chromosome0.020.000.01
clusters-method0.20.00.2
collapseBatch-method0.030.000.04
consensusCNP0.990.000.98
eta.0-method000
hyperParams-method000
iter-method000
k-method0.010.000.01
labelSwitching-method0.020.000.02
logPrior-method000
log_lik-method000
m2.0-method000
map0.060.000.06
marginalLikelihood-method0.090.000.10
mcmcParams-method000
modes-method000
mu-method000
muMean000
muc000
nStarts-method000
nu.0-method0.020.000.01
p000
pic000
plot5.380.005.38
posterior_cases0.020.000.02
probz-method0.030.000.03
qInverseTau20.010.000.02
sigma000
sigma2-method000
sigma2.0-method000
sigmac000
simulateBatchData0.050.000.04
simulateData0.050.000.05
tau000
tau2-method0.010.000.02
tauMean000
tauc000
theta-method0.020.000.01
thin-method000
tracePlot-method0.030.000.03
y-method0.020.000.02
z-method0.000.010.01
zfreq-method000

CNPBayes.Rcheck/examples_x64/CNPBayes-Ex.timings:

nameusersystemelapsed
BatchModel0.030.000.03
DensityModel-class0.680.000.68
DensityModel000
Hyperparameters000
HyperparametersBatch000
HyperparametersMarginal000
MarginalModel0.010.000.01
McmcParams-class000
McmcParams000
batch-method0.020.000.02
bic-method000
burnin-method000
chains-method000
chromosome000
clusters-method0.290.000.29
collapseBatch-method0.030.000.03
consensusCNP1.220.001.22
eta.0-method000
hyperParams-method0.010.000.01
iter-method000
k-method0.020.000.02
labelSwitching-method0.020.000.02
logPrior-method000
log_lik-method000
m2.0-method000
map0.060.000.06
marginalLikelihood-method0.090.000.11
mcmcParams-method000
modes-method000
mu-method000
muMean000
muc000
nStarts-method0.020.000.01
nu.0-method000
p000
pic000
plot4.820.004.82
posterior_cases0.010.000.02
probz-method0.030.000.03
qInverseTau20.020.000.02
sigma000
sigma2-method000
sigma2.0-method000
sigmac000
simulateBatchData0.050.000.04
simulateData0.030.000.03
tau000
tau2-method000
tauMean000
tauc000
theta-method000
thin-method000
tracePlot-method0.030.000.04
y-method0.020.000.01
z-method0.000.020.02
zfreq-method000