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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL openCyto
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘openCyto’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c cpPmden.cpp -o cpPmden.o
cpPmden.cpp: In function ‘stringInfo cpPmden(const std::vector<double>&)’:
cpPmden.cpp:88:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto i = 0; i < (nsamp-1); i++) {
                    ~~^~~~~~~~~~~
cpPmden.cpp:100:17: warning: variable ‘newaccx’ set but not used [-Wunused-but-set-variable]
     double rhs, newaccx;
                 ^~~~~~~
cpPmden.cpp:157:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto i = 0; i < nsamp; i++) {
                      ~~^~~~~~~
cpPmden.cpp:164:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto i=0; i < (nsamp-2); i++) {
                    ~~^~~~~~~~~~~
cpPmden.cpp:193:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto i = 0; i < nsamp; i++) {
                      ~~^~~~~~~
cpPmden.cpp:219:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (auto i = 0; i < nsamp; i++) {
                        ~~^~~~~~~
cpPmden.cpp:251:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (auto i = 0; i < nsamp; i++) {
                        ~~^~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c cppApprox.cpp -o cppApprox.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c cppdip.cpp -o cppdip.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c dynamic_prog.cpp -o dynamic_prog.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fill_SMAWK.cpp -o fill_SMAWK.o
fill_SMAWK.cpp: In function ‘void reduce_in_place(int, int, int, int, const std::vector<long unsigned int>&, std::vector<long unsigned int>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<long unsigned int> >&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, DISSIMILARITY)’:
fill_SMAWK.cpp:80:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(N >= js.size()) {
      ~~^~~~~~~~~~~~
fill_SMAWK.cpp:90:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while(m > N) { // js_reduced has more than N positions / columns
         ~~^~~
fill_SMAWK.cpp:121:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int r=(left+1); r < m; ++r) {
                       ~~^~~
fill_SMAWK.cpp: In function ‘void fill_even_positions(int, int, int, int, const std::vector<long unsigned int>&, std::vector<std::vector<double> >&, std::vector<std::vector<long unsigned int> >&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, DISSIMILARITY)’:
fill_SMAWK.cpp:164:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(++ r; r < n && js[r]<=jmax; r++) {
               ~~^~~
fill_SMAWK.cpp:164:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(++ r; r < n && js[r]<=jmax; r++) {
fill_SMAWK.cpp:168:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if(jabs > i) break;
          ~~~~~^~~
fill_SMAWK.cpp: In function ‘void find_min_from_candidates(int, int, int, int, const std::vector<long unsigned int>&, std::vector<std::vector<double> >&, std::vector<std::vector<long unsigned int> >&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, DISSIMILARITY)’:
fill_SMAWK.cpp:218:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if(j_abs > i) break;
          ~~~~~~^~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c getTautStringApprox.cpp -o getTautStringApprox.o
getTautStringApprox.cpp: In function ‘Rcpp::List getTautStringApprox(std::vector<double>)’:
getTautStringApprox.cpp:32:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i = 1; i != fullString.size(); ++i) {
                   ~~^~~~~~~~~~~~~~~~~~~~
getTautStringApprox.cpp:56:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i  = 0; i != plotSpecs.size(); ++i) {
                    ~~^~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c kMedDP.cpp -o kMedDP.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c kkuiper.cpp -o kkuiper.o
kkuiper.cpp: In function ‘void difficultmax(std::vector<double>&, long int, long int, long int, long int*, long int*, double*)’:
kkuiper.cpp:77:10: warning: variable ‘min’ set but not used [-Wunused-but-set-variable]
   double min, max;
          ^~~
kkuiper.cpp: In function ‘void easymax(std::vector<double>&, long int, long int, long int, long int*, long int*, double*)’:
kkuiper.cpp:64:10: warning: ‘maxi’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     *erga=maxi;
     ~~~~~^~~~~
kkuiper.cpp:63:10: warning: ‘mini’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     *ergb=mini;
     ~~~~~^~~~~
kkuiper.cpp: In function ‘void difficultmax(std::vector<double>&, long int, long int, long int, long int*, long int*, double*)’:
kkuiper.cpp:161:23: warning: ‘maxi’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       *erga=minis[maxi];
                       ^
kkuiper.cpp: In function ‘std::vector<double> kkuiper(std::vector<double>&, long int, int)’:
kkuiper.cpp:176:15: warning: ‘maxi’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   long i,mini,maxi,maxa,maxb,newa,newb,einordnen ;
               ^~~~
kkuiper.cpp:176:10: warning: ‘mini’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   long i,mini,maxi,maxa,maxb,newa,newb,einordnen ;
          ^~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c local_density.cpp -o local_density.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c medianAbsoluteDeviation.cpp -o medianAbsoluteDeviation.o
medianAbsoluteDeviation.cpp: In function ‘double medianAbsoluteDeviation(const std::vector<double>&)’:
medianAbsoluteDeviation.cpp:28:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto i = 0; i != devs.size(); ++i)
                    ~~^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c misc.cpp -o misc.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c rQuantile.cpp -o rQuantile.o
rQuantile.cpp: In function ‘std::vector<double> rQuantile(const std::vector<double>&, std::vector<double>)’:
rQuantile.cpp:35:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto i = 0; i != lowInd.size(); ++i) {
                    ~~^~~~~~~~~~~~~~~~
rQuantile.cpp:41:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto i = 0; i != lowInd.size(); ++i) {
                    ~~^~~~~~~~~~~~~~~~
rQuantile.cpp:47:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto i = 0; i != offSet.size(); ++i)
                    ~~^~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c singleDip.cpp -o singleDip.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c tautstring.cpp -o tautstring.o
tautstring.cpp: In function ‘stringInfo tautString(const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, double, double, long int, int)’:
tautstring.cpp:148:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto i = 0; i < knotst.size(); i++) {
                    ~~^~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c tsGates.cpp -o tsGates.o
tsGates.cpp: In function ‘std::vector<double> findKmedGates(const std::vector<double>&, const std::vector<int>&, int)’:
tsGates.cpp:41:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto j = 0; j != classVector.size(); j++)
                      ~~^~~~~~~~~~~~~~~~~~~~~
tsGates.cpp: In function ‘std::vector<double> tsGates(const std::vector<double>&, int)’:
tsGates.cpp:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto i = 1; i != (localMins.size()-1); ++i) {
                      ~~^~~~~~~~~~~~~~~~~~~~~~~
tsGates.cpp:86:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto i = 0; i != yvals.size(); ++i)
                      ~~^~~~~~~~~~~~~~~
tsGates.cpp:96:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto j = 0; j != cutValues.size(); ++j) {
                      ~~^~~~~~~~~~~~~~~~~~~
tsGates.cpp:99:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (auto i = 0; i != ys.size(); ++i)
                        ~~^~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c unlockNamespace.c -o unlockNamespace.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o openCyto.so RcppExports.o cpPmden.o cppApprox.o cppdip.o dynamic_prog.o fill_SMAWK.o getTautStringApprox.o kMedDP.o kkuiper.o local_density.o medianAbsoluteDeviation.o misc.o rQuantile.o singleDip.o tautstring.o tsGates.o unlockNamespace.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-openCyto/00new/openCyto/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (openCyto)