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INSTALL report for CNPBayes on tokay2

This page was generated on 2019-04-09 12:25:15 -0400 (Tue, 09 Apr 2019).

Package 302/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNPBayes 1.13.5
Jacob Carey
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/CNPBayes
Branch: master
Last Commit: 1e9cdbb
Last Changed Date: 2019-01-03 09:20:51 -0400 (Thu, 03 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] ERROR  skipped  skipped 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  ERROR  skipped  skipped 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 

Summary

Package: CNPBayes
Version: 1.13.5
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/CNPBayes_1.13.5.tar.gz && rm -rf CNPBayes.buildbin-libdir && mkdir CNPBayes.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNPBayes.buildbin-libdir CNPBayes_1.13.5.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL CNPBayes_1.13.5.zip && rm CNPBayes_1.13.5.tar.gz CNPBayes_1.13.5.zip
StartedAt: 2019-04-08 19:48:19 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 19:52:50 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 271.1 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/CNPBayes_1.13.5.tar.gz && rm -rf CNPBayes.buildbin-libdir && mkdir CNPBayes.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNPBayes.buildbin-libdir CNPBayes_1.13.5.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL CNPBayes_1.13.5.zip && rm CNPBayes_1.13.5.tar.gz CNPBayes_1.13.5.zip
###
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install for i386

* installing *source* package 'CNPBayes' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c miscfunctions.cpp -o miscfunctions.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c multibatch.cpp -o multibatch.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c multibatch_pooledvar.cpp -o multibatch_pooledvar.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c multibatch_reduced.cpp -o multibatch_reduced.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pooledvar_reduced.cpp -o pooledvar_reduced.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c triomodel.cpp -o triomodel.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 multibatch.o multibatch_pooledvar.o multibatch_reduced.o pooledvar_reduced.o triomodel.o -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/CNPBayes.buildbin-libdir/00LOCK-CNPBayes/00new/CNPBayes/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'alpha' in package 'CNPBayes'
in method for 'convergence' with signature '"MultiBatchList"': no definition for class "MultiBatchList"
Creating a generic function from function 'sigma' in package 'CNPBayes'
Note: wrong number of arguments to '/' 
** help
*** installing help indices
  converting help for package 'CNPBayes'
    finding HTML links ... done
    BatchModelExample                       html  
    CNPBayes                                html  
    CopyNumber-classes                      html  
    CopyNumber-methods                      html  
    Defunct-classes                         html  
    Hyperparameters-class                   html  
    Hyperparameters                         html  
    HyperparametersBatch-class              html  
    HyperparametersMarginal-class           html  
    HyperparametersMultiBatch-class         html  
    HyperparametersMultiBatch               html  
    HyperparametersSingleBatch-class        html  
    HyperparametersSingleBatch              html  
    HyperparametersTrios-class              html  
    HyperparametersTrios                    html  
    MBP                                     html  
    MarginalModelExample                    html  
    McmcChains-class                        html  
    McmcParams-class                        html  
    McmcParams                              html  
    MixtureModel-class                      html  
    MultiBatch-class                        html  
    MultiBatchModel-class                   html  
    MultiBatchModel                         html  
    MultiBatchModelExample                  html  
    MultiBatchPooledExample                 html  
    SingleBatchModel-class                  html  
    SingleBatchModel                        html  
    SingleBatchModelExample                 html  
    TrioBatchModel                          html  
    bafLikelihood                           html  
    batch-method                            html  
    bayesFactor                             html  
    bic-method                              html  
    burnin-method                           html  
    chains-method                           html  
    chromosome                              html  
    collapseBatch-method                    html  
    consensusCNP                            html  
    copyNumber                              html  
    dfr-method                              html  
    downSample                              html  
    eta.0-method                            html  
    extract-methods                         html  
    findSurrogates-MultiBatch-method        html  
    ggplot-functions                        html  
    gibbs                                   html  
    hyperParams-method                      html  
    iter-method                             html  
    k-method                                html  
    label_switch                            html  
    logBayesFactor                          html  
    logPrior-method                         html  
    log_lik-method                          html  
    m2.0-method                             html  
    mapCnProbability                        html  
    mapParams                               html  
    map_z                                   html  
    mapping                                 html  
    marginalLik                             html  
    marginalLikelihood-method               html  
    marginal_lik                            html  
    mcmcParams-method                       html  
    mlParams                                html  
    modelName-MixtureModel-method           html  
    modes-method                            html  
    mu-method                               html  
    muMean                                  html  
    muc                                     html  
    nStarts-method                          html  
    names-methods                           html  
    nu.0-method                             html  
    numberObs-method                        html  
    oned-method                             html  
    orderModels                             html  
    p-MixtureModel-method                   html  
    pic                                     html  
    posteriorPredictive                     html  
    posteriorSimulation-method              html  
    posterior_cases                         html  
    pp                                      html  
    probCopyNumber                          html  
    probz-method                            html  
    probzpar-method                         html  
    qInverseTau2                            html  
    saveBatch                               html  
    sigma                                   html  
    sigma2-method                           html  
    sigma2.0-method                         html  
    sigmac                                  html  
    simulateBatchData                       html  
    simulateData                            html  
    singleBatchGuided-MultiBatchList-MultiBatch-method
                                            html  
    tau                                     html  
    tau2-method                             html  
    tauMean                                 html  
    tauc                                    html  
    theta-method                            html  
    thin-method                             html  
    tile-functions                          html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpwltFHF/R.INSTALL23c4541e6c11/CNPBayes/man/tile-functions.Rd:28: file link 'ntile' in package 'dplyr' does not exist and so has been treated as a topic
    triodata_lrr-method                     html  
    upSample2                               html  
    y-method                                html  
    z-method                                html  
    zfreq-method                            html  
    zfreqpar-method                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'CNPBayes' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c miscfunctions.cpp -o miscfunctions.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c multibatch.cpp -o multibatch.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c multibatch_pooledvar.cpp -o multibatch_pooledvar.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c multibatch_reduced.cpp -o multibatch_reduced.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pooledvar_reduced.cpp -o pooledvar_reduced.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c triomodel.cpp -o triomodel.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 multibatch.o multibatch_pooledvar.o multibatch_reduced.o pooledvar_reduced.o triomodel.o -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/CNPBayes.buildbin-libdir/CNPBayes/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNPBayes' as CNPBayes_1.13.5.zip
* DONE (CNPBayes)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'CNPBayes' successfully unpacked and MD5 sums checked