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BUILD BIN report for STAN on tokay1

This page was generated on 2020-04-15 12:23:22 -0400 (Wed, 15 Apr 2020).

Package 1669/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
STAN 2.14.0
Rafael Campos-Martin
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/STAN
Branch: RELEASE_3_10
Last Commit: 2d374bb
Last Changed Date: 2019-10-29 13:09:02 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: STAN
Version: 2.14.0
Command: rm -rf STAN.buildbin-libdir && mkdir STAN.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=STAN.buildbin-libdir STAN_2.14.0.tar.gz
StartedAt: 2020-04-15 09:46:04 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 09:47:34 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 89.7 seconds
RetCode: 0
Status:  OK  
PackageFile: STAN_2.14.0.zip
PackageFileSize: 1.535 MiB

Command output

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###
### Running command:
###
###   rm -rf STAN.buildbin-libdir && mkdir STAN.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=STAN.buildbin-libdir STAN_2.14.0.tar.gz
###
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install for i386

* installing *source* package 'STAN' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c Bernoulli.cpp -o Bernoulli.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c EmissionFactory.cpp -o EmissionFactory.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c EmissionFunction.cpp -o EmissionFunction.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c HMM.cpp -o HMM.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c InitialProbability.cpp -o InitialProbability.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c JointlyIndependent.cpp -o JointlyIndependent.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c MemoryAllocation.cpp -o MemoryAllocation.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c Multinomial.cpp -o Multinomial.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c MultivariateGaussian.cpp -o MultivariateGaussian.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c NegativeBinomial.cpp -o NegativeBinomial.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c Poisson.cpp -o Poisson.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c PoissonLogNormal.cpp -o PoissonLogNormal.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c RAccessUtils.cpp -o RAccessUtils.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c RWrapper.cpp -o RWrapper.o
RWrapper.cpp: In function 'EmissionFunction** RGETEMISSION(SEXP, int, SEXP, int*, const char*, double***, int*, int, SEXP, int*, int*, int*)':
RWrapper.cpp:350:16: warning: 'HMMEmissionFunctions' may be used uninitialized in this function [-Wmaybe-uninitialized]
         return HMMEmissionFunctions;
                ^
RWrapper.cpp: In function 'SEXPREC* prepareEmission(const char*, SEXP, SEXP, EmissionFunction**, int)':
RWrapper.cpp:1157:16: warning: 'sexpemissionParam' may be used uninitialized in this function [-Wmaybe-uninitialized]
         return sexpemissionParam;
                ^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c TransitionMatrix.cpp -o TransitionMatrix.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c matUtils.cpp -o matUtils.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o STAN.dll tmp.def Bernoulli.o EmissionFactory.o EmissionFunction.o HMM.o InitialProbability.o JointlyIndependent.o MemoryAllocation.o Multinomial.o MultivariateGaussian.o NegativeBinomial.o ParamContainerEmissions.o Poisson.o PoissonLogNormal.o RAccessUtils.o RWrapper.o TransitionMatrix.o matUtils.o -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -fopenmp -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/STAN.buildbin-libdir/00LOCK-STAN/00new/STAN/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'STAN'
    finding HTML links ... done
    DimNames                                html  
    DirScore                                html  
    Emission                                html  
    EmissionParams                          html  
    HMM-class                               html  
    HMM                                     html  
    HMMEmission-class                       html  
    HMMEmission                             html  
    InitProb                                html  
    LogLik                                  html  
    STAN-package                            html  
    StateNames                              html  
    Transitions                             html  
    bdHMM-class                             html  
    bdHMM                                   html  
    binarizeData                            html  
    c2optimize                              html  
    call_dpoilog                            html  
    data2Gviz                               html  
    example                                 html  
    fitBdClust                              html  
    fitHMM                                  html  
    flags                                   html  
    getAvgSignal                            html  
    getLogLik                               html  
    getPosterior                            html  
    getSizeFactors                          html  
    getViterbi                              html  
    initBdClust                             html  
    initBdHMM                               html  
    initHMM                                 html  
    observations                            html  
    pilot.hg19                              html  
    runningMean                             html  
    sub-HMM-ANY-ANY-ANY-method              html  
    sub-bdHMM-ANY-ANY-ANY-method            html  
    trainRegions                            html  
    ucscGenes                               html  
    viterbi2GRanges                         html  
    viterbi2Gviz                            html  
    yeastTF_SGDGenes                        html  
    yeastTF_databychrom_ex                  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 'STAN' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c Bernoulli.cpp -o Bernoulli.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c EmissionFactory.cpp -o EmissionFactory.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c EmissionFunction.cpp -o EmissionFunction.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c HMM.cpp -o HMM.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c InitialProbability.cpp -o InitialProbability.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c JointlyIndependent.cpp -o JointlyIndependent.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c MemoryAllocation.cpp -o MemoryAllocation.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c Multinomial.cpp -o Multinomial.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c MultivariateGaussian.cpp -o MultivariateGaussian.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c NegativeBinomial.cpp -o NegativeBinomial.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c Poisson.cpp -o Poisson.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c PoissonLogNormal.cpp -o PoissonLogNormal.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c RAccessUtils.cpp -o RAccessUtils.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c RWrapper.cpp -o RWrapper.o
RWrapper.cpp: In function 'EmissionFunction** RGETEMISSION(SEXP, int, SEXP, int*, const char*, double***, int*, int, SEXP, int*, int*, int*)':
RWrapper.cpp:350:16: warning: 'HMMEmissionFunctions' may be used uninitialized in this function [-Wmaybe-uninitialized]
         return HMMEmissionFunctions;
                ^
RWrapper.cpp: In function 'SEXPREC* prepareEmission(const char*, SEXP, SEXP, EmissionFunction**, int)':
RWrapper.cpp:1157:16: warning: 'sexpemissionParam' may be used uninitialized in this function [-Wmaybe-uninitialized]
         return sexpemissionParam;
                ^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c TransitionMatrix.cpp -o TransitionMatrix.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c matUtils.cpp -o matUtils.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o STAN.dll tmp.def Bernoulli.o EmissionFactory.o EmissionFunction.o HMM.o InitialProbability.o JointlyIndependent.o MemoryAllocation.o Multinomial.o MultivariateGaussian.o NegativeBinomial.o ParamContainerEmissions.o Poisson.o PoissonLogNormal.o RAccessUtils.o RWrapper.o TransitionMatrix.o matUtils.o -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -fopenmp -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/STAN.buildbin-libdir/STAN/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'STAN' as STAN_2.14.0.zip
* DONE (STAN)