* installing *source* package ‘cenROC’ ... ** package ‘cenROC’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘clang version 18.1.4’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/cenROC/src' /usr/local/clang18/bin/clang++ -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/RcppEigen/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61: /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 273 | Index count = 0; | ^ In file included from RcppExports.cpp:4: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35: /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] 78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree | ^ /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree | ^ In file included from RcppExports.cpp:4: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 72 | Index replacements = 0; | ^ /usr/local/clang18/bin/clang++ -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/RcppEigen/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c fPos.cpp -o fPos.o /usr/local/clang18/bin/clang++ -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/RcppEigen/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c sieve.cpp -o sieve.o In file included from RcppExports.cpp:4: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] 246 | int count = 0; | ^ In file included from fPos.cpp:4: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61: /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 273 | Index count = 0; | ^ In file included from fPos.cpp:4: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35: /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] 78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree | ^ /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree | ^ In file included from sieve.cpp:18: In file included from ./initialGuess.h:8: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61: /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 273 | Index count = 0; | ^ In file included from fPos.cpp:4: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 72 | Index replacements = 0; | ^ In file included from sieve.cpp:18: In file included from ./initialGuess.h:8: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35: /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] 78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree | ^ /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree | ^ In file included from sieve.cpp:18: In file included from ./initialGuess.h:8: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 72 | Index replacements = 0; | ^ In file included from fPos.cpp:4: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] 246 | int count = 0; | ^ In file included from sieve.cpp:18: In file included from ./initialGuess.h:8: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] 246 | int count = 0; | ^ 5 warnings generated. In file included from sieve.cpp:19: In file included from ./gradient.h:20: ./sumterms.h:30:5: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 30 | return sum; | ^ ./sumterms.h:25:3: note: previous statement is here 25 | for(int i = 0; i < pn; i++) | ^ In file included from sieve.cpp:22: ./step2.h:21:10: warning: unused variable 'threadHold_coverge' [-Wunused-variable] 21 | double threadHold_coverge = 1e-8; | ^~~~~~~~~~~~~~~~~~ In file included from sieve.cpp:23: ./step3.h:62:4: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] 62 | if(theta(size-col+i) < threadHold) | ^ ./step3.h:60:5: note: previous statement is here 60 | if(theta(i*col) < threadHold) | ^ ./step3.h:28:7: warning: variable 'k' set but not used [-Wunused-but-set-variable] 28 | int k = 0; | ^ In file included from sieve.cpp:25: ./step5.h:58:5: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 58 | removeRow(X,jStar); | ^ ./step5.h:55:3: note: previous statement is here 55 | for(int i = 0; i < X.cols(); i++) | ^ In file included from sieve.cpp:27: ./Ispline.h:47:7: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] 47 | if (t>=knot[m+3]) | ^ ./Ispline.h:42:5: note: previous statement is here 42 | if (tknot[m+2]) | ^ In file included from sieve.cpp:28: ./Mspline.h:18:5: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] 18 | if (t<=knot[m+2] &&t>knot[m+1]) | ^ ./Mspline.h:13:3: note: previous statement is here 13 | if (t<=knot[m+1] && t>knot[m]) | ^ ./Mspline.h:46:5: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 46 | return res2; | ^ ./Mspline.h:42:3: note: previous statement is here 42 | for(int i = 1; i < qn; i++) | ^ sieve.cpp:120:16: warning: variable 'start' set but not used [-Wunused-but-set-variable] 120 | std::clock_t start; | ^ sieve.cpp:121:10: warning: unused variable 'duration' [-Wunused-variable] 121 | double duration; | ^~~~~~~~ sieve.cpp:131:11: warning: unused variable 'start0' [-Wunused-variable] 131 | clock_t start0 = clock(); | ^~~~~~ In file included from fPos.cpp:6: In file included from ./jointDis.h:6: ./Ispline.h:47:7: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] 47 | if (t>=knot[m+3]) | ^ ./Ispline.h:42:5: note: previous statement is here 42 | if (tknot[m+2]) | ^ In file included from fPos.cpp:6: In file included from ./jointDis.h:7: ./Mspline.h:18:5: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] 18 | if (t<=knot[m+2] &&t>knot[m+1]) | ^ ./Mspline.h:13:3: note: previous statement is here 13 | if (t<=knot[m+1] && t>knot[m]) | ^ ./Mspline.h:46:5: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 46 | return res2; | ^ ./Mspline.h:42:3: note: previous statement is here 42 | for(int i = 1; i < qn; i++) | ^ In file included from fPos.cpp:6: ./jointDis.h:28:5: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 28 | return sum; | ^ ./jointDis.h:23:3: note: previous statement is here 23 | for(int i = 0; i < pn; i++) | ^ In file included from fPos.cpp:6: In file included from ./jointDis.h:6: ./Ispline.h:53:17: warning: unused function 'Ispline' [-Wunused-function] 53 | static MatrixXd Ispline(int pn, VectorXd &x, VectorXd &knot) | ^~~~~~~ In file included from fPos.cpp:6: In file included from ./jointDis.h:7: ./Mspline.h:38:17: warning: unused function 'Mspline' [-Wunused-function] 38 | static MatrixXd Mspline(int qn, VectorXd &x, VectorXd &knot) | ^~~~~~~ ./Mspline.h:50:17: warning: unused function 'MsplineX' [-Wunused-function] 50 | static VectorXd MsplineX(int qn, double x, VectorXd &knot) | ^~~~~~~~ 12 warnings generated. In file included from sieve.cpp:27: ./Ispline.h:66:17: warning: unused function 'IsplineX' [-Wunused-function] 66 | static VectorXd IsplineX(int pn, double x, VectorXd &knot) | ^~~~~~~~ In file included from sieve.cpp:28: ./Mspline.h:50:17: warning: unused function 'MsplineX' [-Wunused-function] 50 | static VectorXd MsplineX(int qn, double x, VectorXd &knot) | ^~~~~~~~ 18 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o cenROC.so RcppExports.o fPos.o sieve.o make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/cenROC/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/cenROC/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/cenROC/src' installing to /data/gannet/ripley/R/packages/tests-clang/cenROC.Rcheck/00LOCK-cenROC/00new/cenROC/libs ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (cenROC)