* installing *source* package ‘rliger’ ... ** using staged installation ** libs using C++ compiler: ‘Debian clang version 19.1.2 (1)’ clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-19/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 -O3 -Wall -pedantic -DR_NO_REMAP -c ModularityOptimizer.cpp -o ModularityOptimizer.o ModularityOptimizer.cpp:218:5: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 218 | for (; i <= nNodes; i++) | ^ ModularityOptimizer.cpp:206:3: note: previous statement is here 206 | for (size_t j = 0; j < edge[0].size(); j++) | ^ ModularityOptimizer.cpp:397:11: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 397 | k++; | ^ ModularityOptimizer.cpp:389:9: note: previous statement is here 389 | for (int l = firstNeighborIndex[node[k]]; l < firstNeighborIndex[node[k] + 1]; l++) | ^ ModularityOptimizer.cpp:401:5: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 401 | clustering.orderClustersByNNodes(); | ^ ModularityOptimizer.cpp:379:3: note: previous statement is here 379 | for (int i = 0; i < nNodes; i++) | ^ ModularityOptimizer.cpp:438:9: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 438 | subnetwork.firstNeighborIndex[i + 1] = subnetwork.nEdges; | ^ ModularityOptimizer.cpp:431:7: note: previous statement is here 431 | for (int k = firstNeighborIndex[j]; k < firstNeighborIndex[j + 1]; k++) | ^ ModularityOptimizer.cpp:577:5: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 577 | for (i = 0; i < network->nNodes; i++) | ^ ModularityOptimizer.cpp:571:3: note: previous statement is here 571 | for (i = 0; i < network->nNodes; i++) | ^ ModularityOptimizer.cpp:720:5: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 720 | if (i >= 0) | ^ ModularityOptimizer.cpp:709:3: note: previous statement is here 709 | for (int j = 0; j < clustering->nClusters; j++) | ^ ModularityOptimizer.cpp:725:9: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 725 | if (cluster == clustering->nClusters - 1) | ^ ModularityOptimizer.cpp:722:7: note: previous statement is here 722 | for (int j = 0; j < network->nNodes; j++) | ^ ModularityOptimizer.cpp:746:7: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 746 | if (i >= 0) | ^ ModularityOptimizer.cpp:739:5: note: previous statement is here 739 | for (int k = 0; k < vosClusteringTechnique.clustering->nClusters; k++) | ^ ModularityOptimizer.cpp:771:5: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 771 | IVector firstNeighborIndex(nNodes + 1); | ^ ModularityOptimizer.cpp:764:3: note: previous statement is here 764 | for (size_t i = 0; i < node1.size(); i++) | ^ ModularityOptimizer.cpp:796:7: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 796 | if (modularityFunction == 1) | ^ ModularityOptimizer.cpp:783:5: note: previous statement is here 783 | for (size_t i = 0; i < node1.size(); i++) | ^ 10 warnings generated. clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-19/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 -O3 -Wall -pedantic -DR_NO_REMAP -c RModularityOptimizer.cpp -o RModularityOptimizer.o clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-19/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 -O3 -Wall -pedantic -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-19/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 -O3 -Wall -pedantic -DR_NO_REMAP -c centoidAlign.cpp -o centoidAlign.o clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-19/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 -O3 -Wall -pedantic -DR_NO_REMAP -c data_processing.cpp -o data_processing.o clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-19/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 -O3 -Wall -pedantic -DR_NO_REMAP -c feature_mat.cpp -o feature_mat.o clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-19/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 -O3 -Wall -pedantic -DR_NO_REMAP -c quantile_norm.cpp -o quantile_norm.o clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-19/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 -O3 -Wall -pedantic -DR_NO_REMAP -c snn.cpp -o snn.o clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-19/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 -O3 -Wall -pedantic -DR_NO_REMAP -c wilcoxon.cpp -o wilcoxon.o clang++-19 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-clang-19/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-clang-19/lib -lRblas -L/usr/lib/llvm-19/lib -lFortranRuntime -lFortranDecimal -lm -L/home/hornik/tmp/R-d-clang-19/lib -lR installing to /srv/hornik/tmp/CRAN_pretest/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)