* installing *source* package 'rliger' ...
** package 'rliger' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++.exe (GCC) 12.3.0'
make[1]: Entering directory '/d/temp/2024_12_20_01_50_00_19051/RtmpKch8p5/R.INSTALL1d72c18e76ea0/rliger/src'
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -DARMA_DONT_USE_OPENMP -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ModularityOptimizer.cpp -o ModularityOptimizer.o
ModularityOptimizer.cpp: In constructor 'ModularityOptimizer::Network::Network(int, DVector*, std::vector<std::vector<int> >&, DVector*)':
ModularityOptimizer.cpp:206:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
206 | for (size_t j = 0; j < edge[0].size(); j++)
| ^~~
ModularityOptimizer.cpp:218:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
218 | for (; i <= nNodes; i++)
| ^~~
ModularityOptimizer.cpp: In member function 'ModularityOptimizer::Clustering ModularityOptimizer::Network::identifyComponents()':
ModularityOptimizer.cpp:389:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
389 | for (int l = firstNeighborIndex[node[k]]; l < firstNeighborIndex[node[k] + 1]; l++)
| ^~~
ModularityOptimizer.cpp:397:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
397 | k++;
| ^
ModularityOptimizer.cpp:379:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
379 | for (int i = 0; i < nNodes; i++)
| ^~~
ModularityOptimizer.cpp:401:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
401 | clustering.orderClustersByNNodes();
| ^~~~~~~~~~
ModularityOptimizer.cpp: In member function 'ModularityOptimizer::Network ModularityOptimizer::Network::createSubnetwork(const ModularityOptimizer::Clustering&, int, IVector&, IVector&, IVector&, DVector&) const':
ModularityOptimizer.cpp:431:7: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
431 | for (int k = firstNeighborIndex[j]; k < firstNeighborIndex[j + 1]; k++)
| ^~~
ModularityOptimizer.cpp:438:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
438 | subnetwork.firstNeighborIndex[i + 1] = subnetwork.nEdges;
| ^~~~~~~~~~
ModularityOptimizer.cpp: In member function 'bool ModularityOptimizer::VOSClusteringTechnique::runLocalMovingAlgorithm(ModularityOptimizer::JavaRandom&)':
ModularityOptimizer.cpp:571:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
571 | for (i = 0; i < network->nNodes; i++)
| ^~~
ModularityOptimizer.cpp:577:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
577 | for (i = 0; i < network->nNodes; i++)
| ^~~
ModularityOptimizer.cpp: In member function 'int ModularityOptimizer::VOSClusteringTechnique::removeCluster(int)':
ModularityOptimizer.cpp:709:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
709 | for (int j = 0; j < clustering->nClusters; j++)
| ^~~
ModularityOptimizer.cpp:720:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
720 | if (i >= 0)
| ^~
ModularityOptimizer.cpp:722:7: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
722 | for (int j = 0; j < network->nNodes; j++)
| ^~~
ModularityOptimizer.cpp:725:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
725 | if (cluster == clustering->nClusters - 1)
| ^~
ModularityOptimizer.cpp: In member function 'void ModularityOptimizer::VOSClusteringTechnique::removeSmallClusters(int)':
ModularityOptimizer.cpp:739:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
739 | for (int k = 0; k < vosClusteringTechnique.clustering->nClusters; k++)
| ^~~
ModularityOptimizer.cpp:746:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
746 | if (i >= 0)
| ^~
ModularityOptimizer.cpp: In function 'std::shared_ptr<ModularityOptimizer::Network> ModularityOptimizer::matrixToNetwork(IVector&, IVector&, DVector&, int)':
ModularityOptimizer.cpp:764:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
764 | for (size_t i = 0; i < node1.size(); i++)
| ^~~
ModularityOptimizer.cpp:771:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
771 | IVector firstNeighborIndex(nNodes + 1);
| ^~~~~~~
ModularityOptimizer.cpp:783:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
783 | for (size_t i = 0; i < node1.size(); i++)
| ^~~
ModularityOptimizer.cpp:796:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
796 | if (modularityFunction == 1)
| ^~
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -DARMA_DONT_USE_OPENMP -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RModularityOptimizer.cpp -o RModularityOptimizer.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -DARMA_DONT_USE_OPENMP -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -DARMA_DONT_USE_OPENMP -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c centoidAlign.cpp -o centoidAlign.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -DARMA_DONT_USE_OPENMP -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c data_processing.cpp -o data_processing.o
data_processing.cpp: In function 'arma::mat colNormalize_dense_cpp(arma::mat&, arma::uword)':
data_processing.cpp:27:21: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
27 | for (int j = 0; j < x.n_cols; ++j) {
| ~~^~~~~~~~~~
data_processing.cpp:32:23: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
32 | for (int i = 0; i < x.n_rows; ++i) {
| ~~^~~~~~~~~~
data_processing.cpp: In function 'Rcpp::NumericVector SparseRowVarStd(arma::sp_mat, Rcpp::NumericVector, Rcpp::NumericVector, double)':
data_processing.cpp:254:18: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
254 | for (int k=0; k<x.n_cols; ++k) {
| ~^~~~~~~~~
data_processing.cpp: In function 'arma::mat colAggregateMedian_dense_cpp(const arma::mat&, const arma::uvec&, arma::uword)':
data_processing.cpp:290:21: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
290 | for (int i = 0; i < n; ++i) {
| ~~^~~
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -DARMA_DONT_USE_OPENMP -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c feature_mat.cpp -o feature_mat.o
feature_mat.cpp: In function 'Rcpp::NumericMatrix makeFeatureMatrix(Rcpp::DataFrame&, Rcpp::StringVector&)':
feature_mat.cpp:29:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
29 | for(int i = 0; i < barcodes_v.size(); ++i){
| ~~^~~~~~~~~~~~~~~~~~~
feature_mat.cpp:41:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
41 | for(int j=0; j < associated_barcodes.size(); ++j){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -DARMA_DONT_USE_OPENMP -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c quantile_norm.cpp -o quantile_norm.o
quantile_norm.cpp: In function 'Rcpp::IntegerVector cluster_vote_rcpp(const arma::mat&, Rcpp::IntegerVector)':
quantile_norm.cpp:12:19: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
12 | for(int j=0; j<k; ++j) {
| ~^~
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -DARMA_DONT_USE_OPENMP -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c snn.cpp -o snn.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -DARMA_DONT_USE_OPENMP -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c wilcoxon.cpp -o wilcoxon.o
wilcoxon.cpp: In function 'std::__cxx11::list<float> cpp_in_place_rank_mean(arma::vec&, int, int)':
wilcoxon.cpp:19:34: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
19 | for (size_t i = idx_begin; i <= idx_end; i++) {
| ~~^~~~~~~~~~
g++ -std=gnu++17 -shared -s -static-libgcc -o rliger.dll tmp.def ModularityOptimizer.o RModularityOptimizer.o RcppExports.o centoidAlign.o data_processing.o feature_mat.o quantile_norm.o snn.o wilcoxon.o -LD:/RCompile/recent/R-4.3.3/bin/x64 -lRlapack -LD:/RCompile/recent/R-4.3.3/bin/x64 -lRblas -lgfortran -lm -lquadmath -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R-4.3.3/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2024_12_20_01_50_00_19051/RtmpKch8p5/R.INSTALL1d72c18e76ea0/rliger/src'
make[1]: Entering directory '/d/temp/2024_12_20_01_50_00_19051/RtmpKch8p5/R.INSTALL1d72c18e76ea0/rliger/src'
make[1]: Leaving directory '/d/temp/2024_12_20_01_50_00_19051/RtmpKch8p5/R.INSTALL1d72c18e76ea0/rliger/src'
installing to d:/Rcompile/CRANpkg/lib/4.3/00LOCK-rliger/00new/rliger/libs/x64
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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
* MD5 sums
packaged installation of 'rliger' as rliger_2.1.0.zip
* DONE (rliger)