* installing *source* package ‘redist’ ...
** package ‘redist’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 19.1.3’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/redist/src'
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -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 -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c adj_reduce.cpp -o adj_reduce.o
In file included from RcppExports.cpp:6:
In file included from /data/gannet/ripley/R/test-clang/RcppThread/include/RcppThread.h:9:
/data/gannet/ripley/R/test-clang/RcppThread/include/RcppThread/RMonitor.hpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:3:9: note: previous definition is here
3 | #define R_NO_REMAP 1
| ^
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c check_contiguity.cpp -o check_contiguity.o
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c coarsen.cpp -o coarsen.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c coloring.cpp -o coloring.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c compact_vectorized.cpp -o compact_vectorized.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c constraint_calc_helper.cpp -o constraint_calc_helper.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c contiguity.cpp -o contiguity.o
constraint_calc_helper.cpp:124:22: warning: variable 'match' set but not used [-Wunused-but-set-variable]
124 | int i; int j; bool match; arma::uvec store_in(vec1.n_elem);
| ^
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c cores.cpp -o cores.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c crsg.cpp -o crsg.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c distance_helpers.cpp -o distance_helpers.o
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c kirchhoff.cpp -o kirchhoff.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c labeling.cpp -o labeling.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c make_swaps_helper.cpp -o make_swaps_helper.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c map_calc.cpp -o map_calc.o
In file included from map_calc.cpp:2:
In file included from ./map_calc.h:3:
In file included from /data/gannet/ripley/R/test-clang/RcppThread/include/RcppThread.h:9:
/data/gannet/ripley/R/test-clang/RcppThread/include/RcppThread/RMonitor.hpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:3:9: note: previous definition is here
3 | #define R_NO_REMAP 1
| ^
In file included from kirchhoff.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/redistmetrics/include/redistmetrics.h:7:
In file included from /data/gannet/ripley/R/test-clang/redistmetrics/include/redistmetrics_RcppExports.h:9:
In file included from /data/gannet/ripley/R/test-clang/RcppThread/include/RcppThread.h:9:
/data/gannet/ripley/R/test-clang/RcppThread/include/RcppThread/RMonitor.hpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:3:9: note: previous definition is here
3 | #define R_NO_REMAP 1
| ^
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c mcmc_gibbs.cpp -o mcmc_gibbs.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c merge_split.cpp -o merge_split.o
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c pareto.cpp -o pareto.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c pop_helpers.cpp -o pop_helpers.o
In file included from merge_split.cpp:9:
In file included from ./merge_split.h:13:
In file included from ./map_calc.h:3:
In file included from /data/gannet/ripley/R/test-clang/RcppThread/include/RcppThread.h:9:
/data/gannet/ripley/R/test-clang/RcppThread/include/RcppThread/RMonitor.hpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:3:9: note: previous definition is here
3 | #define R_NO_REMAP 1
| ^
In file included from mcmc_gibbs.cpp:1:
In file included from ./mcmc_gibbs.h:7:
In file included from ./map_calc.h:3:
In file included from /data/gannet/ripley/R/test-clang/RcppThread/include/RcppThread.h:9:
/data/gannet/ripley/R/test-clang/RcppThread/include/RcppThread/RMonitor.hpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:3:9: note: previous definition is here
3 | #define R_NO_REMAP 1
| ^
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c random.cpp -o random.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c renumber.cpp -o renumber.o
1 warning generated.
1 warning generated.
In file included from renumber.cpp:4:
./hungarian.h:177:25: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation]
177 | for (row = 0; row<nOfRows; row++)
| ^
./hungarian.h:169:21: note: previous statement is here
169 | if (fabs(distMatrix[row + nOfRows*col]) < DBL_EPSILON)
| ^
./hungarian.h:258:13: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation]
258 | if (nOfCoveredColumns == minDim)
| ^
./hungarian.h:254:9: note: previous statement is here
254 | for (col = 0; col<nOfColumns; col++)
| ^
./hungarian.h:292:33: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation]
292 | if (starCol == nOfColumns) /* no starred zero found */
| ^
./hungarian.h:288:29: note: previous statement is here
288 | for (starCol = 0; starCol<nOfColumns; starCol++)
| ^
./hungarian.h:330:13: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation]
330 | while (starRow<nOfRows)
| ^
./hungarian.h:326:9: note: previous statement is here
326 | for (starRow = 0; starRow<nOfRows; starRow++)
| ^
./hungarian.h:342:21: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation]
342 | newStarMatrix[primeRow + nOfRows*primeCol] = true;
| ^
./hungarian.h:337:17: note: previous statement is here
337 | for (primeCol = 0; primeCol<nOfColumns; primeCol++)
| ^
./hungarian.h:383:21: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation]
383 | for (row = 0; row<nOfRows; row++)
| ^
./hungarian.h:374:17: note: previous statement is here
374 | for (col = 0; col<nOfColumns; col++)
| ^
./hungarian.h:389:25: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation]
389 | for (col = 0; col<nOfColumns; col++)
| ^
./hungarian.h:383:21: note: previous statement is here
383 | for (row = 0; row<nOfRows; row++)
| ^
./hungarian.h:395:29: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation]
395 | step3(assignment, distMatrix, starMatrix, newStarMatrix, primeMatrix, coveredColumns, coveredRows, nOfRows, nOfColumns, minDim);
| ^
./hungarian.h:389:25: note: previous statement is here
389 | for (col = 0; col<nOfColumns; col++)
| ^
8 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c rsg.cpp -o rsg.o
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c scorer_helpers.cpp -o scorer_helpers.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c shatter_search.cpp -o shatter_search.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c smc.cpp -o smc.o
In file included from rsg.cpp:5:
In file included from ./sw_mh_helper.h:16:
In file included from ./map_calc.h:3:
In file included from /data/gannet/ripley/R/test-clang/RcppThread/include/RcppThread.h:9:
/data/gannet/ripley/R/test-clang/RcppThread/include/RcppThread/RMonitor.hpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:3:9: note: previous definition is here
3 | #define R_NO_REMAP 1
| ^
In file included from smc.cpp:8:
In file included from ./smc.h:13:
In file included from /data/gannet/ripley/R/test-clang/RcppThread/include/RcppThread.h:9:
/data/gannet/ripley/R/test-clang/RcppThread/include/RcppThread/RMonitor.hpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:3:9: note: previous definition is here
3 | #define R_NO_REMAP 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c smc_base.cpp -o smc_base.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c splits.cpp -o splits.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c sw_mh_alg.cpp -o sw_mh_alg.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c sw_mh_helper.cpp -o sw_mh_helper.o
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c tree_op.cpp -o tree_op.o
In file included from splits.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/redistmetrics/include/redistmetrics.h:7:
In file included from /data/gannet/ripley/R/test-clang/redistmetrics/include/redistmetrics_RcppExports.h:9:
In file included from /data/gannet/ripley/R/test-clang/RcppThread/include/RcppThread.h:9:
/data/gannet/ripley/R/test-clang/RcppThread/include/RcppThread/RMonitor.hpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:3:9: note: previous definition is here
3 | #define R_NO_REMAP 1
| ^
In file included from sw_mh_alg.cpp:15:
In file included from ./sw_mh_helper.h:16:
In file included from ./map_calc.h:3:
In file included from /data/gannet/ripley/R/test-clang/RcppThread/include/RcppThread.h:9:
/data/gannet/ripley/R/test-clang/RcppThread/include/RcppThread/RMonitor.hpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:3:9: note: previous definition is here
3 | #define R_NO_REMAP 1
| ^
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c varinfo.cpp -o varinfo.o
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -I'/data/gannet/ripley/R/test-clang/redistmetrics/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD=1 -g0 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c wilson.cpp -o wilson.o
In file included from sw_mh_helper.cpp:10:
In file included from ./sw_mh_helper.h:16:
In file included from ./map_calc.h:3:
In file included from /data/gannet/ripley/R/test-clang/RcppThread/include/RcppThread.h:9:
/data/gannet/ripley/R/test-clang/RcppThread/include/RcppThread/RMonitor.hpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:3:9: note: previous definition is here
3 | #define R_NO_REMAP 1
| ^
1 warning generated.
1 warning generated.
/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 redist.so RcppExports.o adj_reduce.o check_contiguity.o coarsen.o coloring.o compact_vectorized.o constraint_calc_helper.o contiguity.o cores.o crsg.o distance_helpers.o kirchhoff.o labeling.o make_swaps_helper.o map_calc.o mcmc_gibbs.o merge_split.o pareto.o pop_helpers.o random.o renumber.o rsg.o scorer_helpers.o shatter_search.o smc.o smc_base.o splits.o sw_mh_alg.o sw_mh_helper.o tree_op.o varinfo.o wilson.o -latomic -lpthread -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortranRuntime -lFortranDecimal -lm -fopenmp
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/redist/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/redist/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/redist/src'
installing to /data/gannet/ripley/R/packages/tests-clang/redist.Rcheck/00LOCK-redist/00new/redist/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 (redist)