* 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 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpfsJpet/R.INSTALL37f33a3f3e72ae/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/RtmpfsJpet/R.INSTALL37f33a3f3e72ae/NAIR/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpfsJpet/R.INSTALL37f33a3f3e72ae/NAIR/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpfsJpet/R.INSTALL37f33a3f3e72ae/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)