* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘NAIR’ ...
** package ‘NAIR’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-6) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpFfw3XZ/R.INSTALL2c035c7a8e5abb/NAIR/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c dropDegreeZero.cpp -o dropDegreeZero.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c hamAdjacencyMatSparse.cpp -o hamAdjacencyMatSparse.o
In file included from hamAdjacencyMatSparse.cpp:20:
dropDegreeZero.h:4:9: warning: "ARMA_64BIT_WORD" redefined
    4 | #define ARMA_64BIT_WORD 1
      |         ^~~~~~~~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo:96,
                 from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58,
                 from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29,
                 from hamAdjacencyMatSparse.cpp:18:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:88:11: note: this is the location of the previous definition
   88 |   #define ARMA_64BIT_WORD
      |           ^~~~~~~~~~~~~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c hamDistBounded.cpp -o hamDistBounded.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c levAdjacencyMatSparse.cpp -o levAdjacencyMatSparse.o
In file included from levAdjacencyMatSparse.cpp:20:
dropDegreeZero.h:4:9: warning: "ARMA_64BIT_WORD" redefined
    4 | #define ARMA_64BIT_WORD 1
      |         ^~~~~~~~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo:96,
                 from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58,
                 from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29,
                 from levAdjacencyMatSparse.cpp:18:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:88:11: note: this is the location of the previous definition
   88 |   #define ARMA_64BIT_WORD
      |           ^~~~~~~~~~~~~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c levDistBounded.cpp -o levDistBounded.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c patternAdjacencyMatSparse.cpp -o patternAdjacencyMatSparse.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c sortAdjacencyMatSparse.cpp -o sortAdjacencyMatSparse.o
In file included from sortAdjacencyMatSparse.cpp:24:
dropDegreeZero.h:4:9: warning: "ARMA_64BIT_WORD" redefined
    4 | #define ARMA_64BIT_WORD 1
      |         ^~~~~~~~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo:96,
                 from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58,
                 from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29,
                 from sortAdjacencyMatSparse.cpp:18:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:88:11: note: this is the location of the previous definition
   88 |   #define ARMA_64BIT_WORD
      |           ^~~~~~~~~~~~~~~
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o NAIR.so RcppExports.o dropDegreeZero.o hamAdjacencyMatSparse.o hamDistBounded.o levAdjacencyMatSparse.o levDistBounded.o patternAdjacencyMatSparse.o sortAdjacencyMatSparse.o -fopenmp -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpFfw3XZ/R.INSTALL2c035c7a8e5abb/NAIR/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpFfw3XZ/R.INSTALL2c035c7a8e5abb/NAIR/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpFfw3XZ/R.INSTALL2c035c7a8e5abb/NAIR/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-NAIR/00new/NAIR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘NAIR’
    finding HTML links ... done
    NAIR-package                            html  
    addClusterLabels                        html  
    addClusterMembership                    html  
    addClusterStats                         html  
    addGraphLabels                          html  
    addNodeNetworkStats                     html  
    addNodeStats                            html  
    addPlots                                html  
    aggregateIdenticalClones                html  
    buildAssociatedClusterNetwork           html  
    buildPublicClusterNetwork               html  
    buildPublicClusterNetworkByRepresentative
                                            html  
    buildRepSeqNetwork                      html  
    chooseNodeStats                         html  
    combineSamples                          html  
    extractLayout                           html  
    filterInputData                         html  
    findAssociatedClones                    html  
    findAssociatedSeqs                      html  
    findPublicClusters                      html  
    generateAdjacencyMatrix                 html  
    generateNetworkGraph                    html  
    generateNetworkObjects                  html  
    getClusterStats                         html  
    getNeighborhood                         html  
    hamDistBounded                          html  
    levDistBounded                          html  
    plotNetworkGraph                        html  
    saveNetwork                             html  
    saveNetworkPlots                        html  
    simulateToyData                         html  
*** 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 (NAIR)