* installing *source* package ‘rliger’ ...
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -DARMA_DONT_USE_OPENMP  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -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++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -DARMA_DONT_USE_OPENMP  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c RModularityOptimizer.cpp -o RModularityOptimizer.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -DARMA_DONT_USE_OPENMP  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -DARMA_DONT_USE_OPENMP  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c centoidAlign.cpp -o centoidAlign.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -DARMA_DONT_USE_OPENMP  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -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++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -DARMA_DONT_USE_OPENMP  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -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 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 unsigned int’} [-Wsign-compare]
   41 |     for(int j=0; j < associated_barcodes.size(); ++j){
      |                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -DARMA_DONT_USE_OPENMP  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -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++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -DARMA_DONT_USE_OPENMP  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c snn.cpp -o snn.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -DARMA_DONT_USE_OPENMP  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -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 unsigned int’} and ‘int’ [-Wsign-compare]
   19 |     for (size_t i = idx_begin; i <= idx_end; i++) {
      |                                ~~^~~~~~~~~~
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o rliger.so ModularityOptimizer.o RModularityOptimizer.o RcppExports.o centoidAlign.o data_processing.o feature_mat.o quantile_norm.o snn.o wilcoxon.o -llapack -L/home/hornik/tmp/R-d-gcc-14/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR
installing to /home/hornik/tmp/CRAN_special_noSuggests/rliger.Rcheck/00LOCK-rliger/00new/rliger/libs
** 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
** 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 (rliger)