Install log for 'rliger'

* installing *source* package ‘rliger’ ...
** package ‘rliger’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 19.1.5’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rliger/src'
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DARMA_DONT_USE_OPENMP  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c ModularityOptimizer.cpp -o ModularityOptimizer.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DARMA_DONT_USE_OPENMP  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c RModularityOptimizer.cpp -o RModularityOptimizer.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.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DARMA_DONT_USE_OPENMP  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DARMA_DONT_USE_OPENMP  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c centoidAlign.cpp -o centoidAlign.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DARMA_DONT_USE_OPENMP  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c data_processing.cpp -o data_processing.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DARMA_DONT_USE_OPENMP  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c feature_mat.cpp -o feature_mat.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DARMA_DONT_USE_OPENMP  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c quantile_norm.cpp -o quantile_norm.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DARMA_DONT_USE_OPENMP  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c snn.cpp -o snn.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DARMA_DONT_USE_OPENMP  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c wilcoxon.cpp -o wilcoxon.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang19/lib -L/usr/local/clang19/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o rliger.so ModularityOptimizer.o RModularityOptimizer.o RcppExports.o centoidAlign.o data_processing.o feature_mat.o quantile_norm.o snn.o wilcoxon.o -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortranRuntime -lFortranDecimal -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/rliger/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rliger/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/rliger/src'
installing to /data/gannet/ripley/R/packages/tests-clang/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)