* installing *source* package ‘intcensROC’ ...
** package ‘intcensROC’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 19.1.5’
using C++11
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/intcensROC/src'
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++11 -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/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -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;
| ^
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;
| ^
5 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++11 -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/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c fPos.cpp -o fPos.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++11 -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/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c sieve.cpp -o sieve.o
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 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 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 fPos.cpp:6:
In file included from ./jointDis.h:6:
./Ispline.h:46:7: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation]
46 | if (t>=knot[m+3])
| ^
./Ispline.h:41:5: note: previous statement is here
41 | if (t<knot[m+3] && t>knot[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 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 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 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;
| ^
In file included from fPos.cpp:6:
In file included from ./jointDis.h:6:
./Ispline.h:52:17: warning: unused function 'Ispline' [-Wunused-function]
52 | 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.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++11 -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/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c tPos.cpp -o tPos.o
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:46:7: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation]
46 | if (t>=knot[m+3])
| ^
./Ispline.h:41:5: note: previous statement is here
41 | if (t<knot[m+3] && t>knot[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 tPos.cpp:3:
In file included from ./jointDis.h: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 tPos.cpp:3:
In file included from ./jointDis.h: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 tPos.cpp:3:
In file included from ./jointDis.h: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 tPos.cpp:3:
In file included from ./jointDis.h: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 tPos.cpp:3:
In file included from ./jointDis.h:6:
./Ispline.h:46:7: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation]
46 | if (t>=knot[m+3])
| ^
./Ispline.h:41:5: note: previous statement is here
41 | if (t<knot[m+3] && t>knot[m+2])
| ^
In file included from tPos.cpp:3:
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 tPos.cpp:3:
./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 tPos.cpp:3:
In file included from ./jointDis.h:6:
./Ispline.h:52:17: warning: unused function 'Ispline' [-Wunused-function]
52 | static MatrixXd Ispline(int pn, VectorXd &x, VectorXd &knot)
| ^~~~~~~
In file included from tPos.cpp:3:
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)
| ^~~~~~~~
In file included from tPos.cpp:3:
./jointDis.h:31:15: warning: unused function 'margM' [-Wunused-function]
31 | static double margM(VectorXd &theta, double m, VectorXd &knot2 )
| ^~~~~
13 warnings generated.
In file included from sieve.cpp:27:
./Ispline.h:65:17: warning: unused function 'IsplineX' [-Wunused-function]
65 | 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/clang19/bin/clang++ -stdlib=libc++ -std=gnu++11 -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 intcensROC.so RcppExports.o fPos.o sieve.o tPos.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/intcensROC/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/intcensROC/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/intcensROC/src'
installing to /data/gannet/ripley/R/packages/tests-clang/intcensROC.Rcheck/00LOCK-intcensROC/00new/intcensROC/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (intcensROC)