############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL openCyto ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’ * installing *source* package ‘openCyto’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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&)’: cpPmden.cpp:88:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 88 | for (auto i = 0; i < (nsamp-1); i++) { | ~~^~~~~~~~~~~ cpPmden.cpp:100:17: warning: variable ‘newaccx’ set but not used [-Wunused-but-set-variable] 100 | double rhs, newaccx; | ^~~~~~~ cpPmden.cpp:157:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 157 | for (auto i = 0; i < nsamp; i++) { | ~~^~~~~~~ cpPmden.cpp:164:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 164 | for (auto i=0; i < (nsamp-2); i++) { | ~~^~~~~~~~~~~ cpPmden.cpp:193:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 193 | for (auto i = 0; i < nsamp; i++) { | ~~^~~~~~~ cpPmden.cpp:219:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 219 | for (auto i = 0; i < nsamp; i++) { | ~~^~~~~~~ cpPmden.cpp:251:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 251 | for (auto i = 0; i < nsamp; i++) { | ~~^~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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&, std::vector&, const std::vector >&, const std::vector >&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, DISSIMILARITY)’: fill_SMAWK.cpp:80:8: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 80 | if(N >= js.size()) { | ~~^~~~~~~~~~~~ fill_SMAWK.cpp:90:11: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 90 | while(m > N) { // js_reduced has more than N positions / columns | ~~^~~ fill_SMAWK.cpp:121:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 121 | for(int r=(left+1); r < m; ++r) { | ~~^~~ fill_SMAWK.cpp: In function ‘void fill_even_positions(int, int, int, int, const std::vector&, std::vector >&, std::vector >&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, DISSIMILARITY)’: fill_SMAWK.cpp:164:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 164 | for(++ r; r < n && js[r]<=jmax; r++) { | ~~^~~ fill_SMAWK.cpp:164:29: warning: comparison of integer expressions of different signedness: ‘const value_type’ {aka ‘const long unsigned int’} and ‘int’ [-Wsign-compare] 164 | for(++ r; r < n && js[r]<=jmax; r++) { fill_SMAWK.cpp:168:15: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘int’ [-Wsign-compare] 168 | if(jabs > i) break; | ~~~~~^~~ fill_SMAWK.cpp: In function ‘void find_min_from_candidates(int, int, int, int, const std::vector&, std::vector >&, std::vector >&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, DISSIMILARITY)’: fill_SMAWK.cpp:218:16: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘int’ [-Wsign-compare] 218 | if(j_abs > i) break; | ~~~~~~^~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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)’: getTautStringApprox.cpp:32:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 32 | for (int i = 1; i != fullString.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~~ getTautStringApprox.cpp:56:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 56 | for (int i = 0; i != plotSpecs.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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&, 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] 77 | double min, max; | ^~~ kkuiper.cpp: In function ‘void easymax(std::vector&, 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] 64 | *erga=maxi; | ~~~~~^~~~~ kkuiper.cpp:63:10: warning: ‘mini’ may be used uninitialized in this function [-Wmaybe-uninitialized] 63 | *ergb=mini; | ~~~~~^~~~~ kkuiper.cpp: In function ‘void difficultmax(std::vector&, 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] 161 | *erga=minis[maxi]; | ^ kkuiper.cpp: In function ‘std::vector kkuiper(std::vector&, long int, int)’: kkuiper.cpp:176:15: warning: ‘maxi’ may be used uninitialized in this function [-Wmaybe-uninitialized] 176 | long i,mini,maxi,maxa,maxb,newa,newb,einordnen ; | ^~~~ kkuiper.cpp:176:10: warning: ‘mini’ may be used uninitialized in this function [-Wmaybe-uninitialized] 176 | long i,mini,maxi,maxa,maxb,newa,newb,einordnen ; | ^~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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&)’: medianAbsoluteDeviation.cpp:28:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 28 | for (auto i = 0; i != devs.size(); ++i) | ~~^~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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 rQuantile(const std::vector&, std::vector)’: rQuantile.cpp:35:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 35 | for (auto i = 0; i != lowInd.size(); ++i) { | ~~^~~~~~~~~~~~~~~~ rQuantile.cpp:41:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 41 | for (auto i = 0; i != lowInd.size(); ++i) { | ~~^~~~~~~~~~~~~~~~ rQuantile.cpp:47:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 47 | for (auto i = 0; i != offSet.size(); ++i) | ~~^~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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&, const std::vector&, const std::vector&, const std::vector&, double, double, long int, int)’: tautstring.cpp:148:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 148 | for (auto i = 0; i < knotst.size(); i++) { | ~~^~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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 findKmedGates(const std::vector&, const std::vector&, int)’: tsGates.cpp:41:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 41 | for (auto j = 0; j != classVector.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~ tsGates.cpp: In function ‘std::vector tsGates(const std::vector&, int)’: tsGates.cpp:81:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 81 | for (auto i = 1; i != (localMins.size()-1); ++i) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ tsGates.cpp:86:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 86 | for (auto i = 0; i != yvals.size(); ++i) | ~~^~~~~~~~~~~~~~~ tsGates.cpp:96:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 96 | for (auto j = 0; j != cutValues.size(); ++j) { | ~~^~~~~~~~~~~~~~~~~~~ tsGates.cpp:99:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 99 | for (auto i = 0; i != ys.size(); ++i) | ~~^~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-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-3.14-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.14-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)