##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf sitePath.buildbin-libdir && mkdir sitePath.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sitePath.buildbin-libdir sitePath_1.4.2.tar.gz
###
##############################################################################
##############################################################################



install for i386

* installing *source* package 'sitePath' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c exportFunc.cpp -o exportFunc.o
exportFunc.cpp: In function 'Rcpp::ListOf<Rcpp::Vector<13> > majorSNPtips(const CharacterVector&, int)':
exportFunc.cpp:110:48: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
     for (unsigned int siteIndex = 0; siteIndex < alignedSeqs[0].size(); ++siteIndex) {
                                      ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
exportFunc.cpp: In function 'Rcpp::ListOf<Rcpp::Vector<13> > mergePaths(const Rcpp::ListOf<Rcpp::Vector<13> >&)':
exportFunc.cpp:141:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
     for (unsigned int i = 1; i < paths.size(); ++i) {
                              ~~^~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c fixationSite.cpp -o fixationSite.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c minEntropy.cpp -o minEntropy.o
minEntropy.cpp: In function 'Rcpp::ListOf<Rcpp::Vector<13> > MinEntropy::updatedSegmentation(const Rcpp::ListOf<Rcpp::Vector<13> >&, const segment&)':
minEntropy.cpp:50:40: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
             for (unsigned int j = 0; j < aa.size(); ++j) {
                                      ~~^~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c searchNode.cpp -o searchNode.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c searchTree.cpp -o searchTree.o
searchTree.cpp: In instantiation of 'MinEntropy::SearchTree<T>::SearchTree(unsigned int, unsigned int, const Rcpp::ListOf<Rcpp::Vector<13> >&) [with T = MinEntropy::Segmentor]':
searchTree.cpp:206:28:   required from here
searchTree.cpp:20:36: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
         for (unsigned int j = 0; j < aa.size(); ++j) {
                                  ~~^~~~~~~~~~~
searchTree.cpp: In instantiation of 'MinEntropy::SearchTree<T>::SearchTree(unsigned int, unsigned int, const Rcpp::ListOf<Rcpp::Vector<13> >&) [with T = MinEntropy::Amalgamator]':
searchTree.cpp:207:28:   required from here
searchTree.cpp:20:36: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c treemer.cpp -o treemer.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o sitePath.dll tmp.def RcppExports.o exportFunc.o fixationSite.o minEntropy.o searchNode.o searchTree.o treemer.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/sitePath.buildbin-libdir/00LOCK-sitePath/00new/sitePath/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'sitePath'
    finding HTML links ... done
    addMSA                                  html  
    extractTips                             html  
    findSites                               html  
    h3n2_align                              html  
    h3n2_align_reduced                      html  
    h3n2_tree                               html  
    h3n2_tree_reduced                       html  
    plot.lineagePath                        html  
    plot.sitePath                           html  
    plotSingleSite                          html  
    pre-assessment                          html  
    setSiteNumbering                        html  
    treemer                                 html  
    zikv_align                              html  
    zikv_align_reduced                      html  
    zikv_tree                               html  
    zikv_tree_reduced                       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 'sitePath' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c exportFunc.cpp -o exportFunc.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c fixationSite.cpp -o fixationSite.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c minEntropy.cpp -o minEntropy.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c searchNode.cpp -o searchNode.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c searchTree.cpp -o searchTree.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c treemer.cpp -o treemer.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o sitePath.dll tmp.def RcppExports.o exportFunc.o fixationSite.o minEntropy.o searchNode.o searchTree.o treemer.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/sitePath.buildbin-libdir/sitePath/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sitePath' as sitePath_1.4.2.zip
* DONE (sitePath)