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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/chromVAR_1.14.0.tar.gz && rm -rf chromVAR.buildbin-libdir && mkdir chromVAR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chromVAR.buildbin-libdir chromVAR_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL chromVAR_1.14.0.zip && rm chromVAR_1.14.0.tar.gz chromVAR_1.14.0.zip
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install for i386

* installing *source* package 'chromVAR' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pwm_similarity.cpp -o pwm_similarity.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utils.cpp -o utils.o
utils.cpp: In function 'Rcpp::NumericVector row_sds(arma::mat&, bool)':
utils.cpp:12:21: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for( int j=0; j < X.n_rows; j++ ) {
                   ~~^~~~~~~~~~
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o chromVAR.dll tmp.def RcppExports.o pwm_similarity.o utils.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/chromVAR.buildbin-libdir/00LOCK-chromVAR/00new/chromVAR/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'chromVAR'
    finding HTML links ... done
    addGCBias                               html  
    annotationMatches                       html  
    assembleKmers                           html  
    cbind-chromVARDeviations-method         html  
    chromVAR                                html  
    chromVARDeviations-class                html  
    chromVAR_theme                          html  
    computeDeviations                       html  
    computeExpectations                     html  
    computeVariability                      html  
    counts                                  html  
    deviationScores                         html  
    deviations                              html  
    deviationsCovariability                 html  
    deviationsTsne                          html  
    differentialDeviations                  html  
    differentialVariability                 html  
    example_counts                          html  
    filterPeaks                             html  
    filterSamples                           html  
    filterSamplesPlot                       html  
    getAnnotationCorrelation                html  
    getAnnotationSynergy                    html  
    getAnnotations                          html  
    getBackgroundPeaks                      html  
    getCisGroups                            html  
    getCounts                               html  
    getFragmentsPerPeak                     html  
    getFragmentsPerSample                   html  
    getJasparMotifs                         html  
    getPeaks                                html  
    getPermutedData                         html  
    getSampleCorrelation                    html  
    getSampleDepths                         html  
    getSampleDistance                       html  
    getTotalFragments                       html  
    makeBiasBins                            html  
    makePermutedSets                        html  
    matchKmers                              html  
    mini_counts                             html  
    mini_dev                                html  
    mini_ix                                 html  
    plotDeviationsTsne                      html  
    plotKmerMismatch                        html  
    plotVariability                         html  
    pwmDistance                             html  
    rbind-chromVARDeviations-method         html  
    readNarrowpeaks                         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 'chromVAR' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pwm_similarity.cpp -o pwm_similarity.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utils.cpp -o utils.o
utils.cpp: In function 'Rcpp::NumericVector row_sds(arma::mat&, bool)':
utils.cpp:12:21: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for( int j=0; j < X.n_rows; j++ ) {
                   ~~^~~~~~~~~~
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o chromVAR.dll tmp.def RcppExports.o pwm_similarity.o utils.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/chromVAR.buildbin-libdir/chromVAR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'chromVAR' as chromVAR_1.14.0.zip
* DONE (chromVAR)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'chromVAR' successfully unpacked and MD5 sums checked