* installing *source* package ‘intcensROC’ ...
** package ‘intcensROC’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
using C++11
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/intcensROC/src'
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c fPos.cpp -o fPos.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c sieve.cpp -o sieve.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c tPos.cpp -o tPos.o
In file included from jointDis.h:6,
from fPos.cpp:6:
Ispline.h: In function 'double Ispline_3(int, double, Eigen::VectorXd&)':
Ispline.h:41:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (t<knot[m+3] && t>knot[m+2])
| ^~
Ispline.h:46:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
46 | if (t>=knot[m+3])
| ^~
In file included from jointDis.h:7:
Mspline.h: In function 'double Mspline_3(int, double, Eigen::VectorXd&)':
Mspline.h:13:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
13 | if (t<=knot[m+1] && t>knot[m])
| ^~
Mspline.h:18:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
18 | if (t<=knot[m+2] &&t>knot[m+1])
| ^~
Mspline.h: In function 'Eigen::MatrixXd Mspline(int, Eigen::VectorXd&, Eigen::VectorXd&)':
Mspline.h:42:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
42 | for(int i = 1; i < qn; i++)
| ^~~
Mspline.h:46:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
46 | return res2;
| ^~~~~~
jointDis.h: In function 'double jointDis(Eigen::VectorXd&, double, double, Eigen::VectorXd&, Eigen::VectorXd&)':
jointDis.h:23:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
23 | for(int i = 0; i < pn; i++)
| ^~~
jointDis.h:28:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
28 | return sum;
| ^~~~~~
Mspline.h: At global scope:
Mspline.h:50:17: warning: 'Eigen::VectorXd MsplineX(int, double, Eigen::VectorXd&)' defined but not used [-Wunused-function]
50 | static VectorXd MsplineX(int qn, double x, VectorXd &knot)
| ^~~~~~~~
Mspline.h:38:17: warning: 'Eigen::MatrixXd Mspline(int, Eigen::VectorXd&, Eigen::VectorXd&)' defined but not used [-Wunused-function]
38 | static MatrixXd Mspline(int qn, VectorXd &x, VectorXd &knot)
| ^~~~~~~
Ispline.h:52:17: warning: 'Eigen::MatrixXd Ispline(int, Eigen::VectorXd&, Eigen::VectorXd&)' defined but not used [-Wunused-function]
52 | static MatrixXd Ispline(int pn, VectorXd &x, VectorXd &knot)
| ^~~~~~~
In file included from gradient.h:20,
from sieve.cpp:19:
sumterms.h: In function 'double sumterms1(Eigen::VectorXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, int)':
sumterms.h:25:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
25 | for(int i = 0; i < pn; i++)
| ^~~
sumterms.h:30:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
30 | return sum;
| ^~~~~~
In file included from sieve.cpp:22:
step2.h: In function 'double conGamma(Eigen::VectorXd&, Eigen::VectorXd&)':
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: In function 'void updateTheta(Eigen::VectorXd&, double, Eigen::VectorXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::VectorXd&, int, int)':
step3.h:60:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
60 | if(theta(i*col) < threadHold)
| ^~
step3.h:62:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
62 | if(theta(size-col+i) < threadHold)
| ^~
In file included from sieve.cpp:25:
step5.h: In function 'void updateX_step5(Eigen::VectorXd&, Eigen::MatrixXd&, std::unordered_set<int>&)':
step5.h:55:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
55 | for(int i = 0; i < X.cols(); i++)
| ^~~
step5.h:58:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
58 | removeRow(X,jStar);
| ^~~~~~~~~
In file included from sieve.cpp:27:
Ispline.h: In function 'double Ispline_3(int, double, Eigen::VectorXd&)':
Ispline.h:41:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (t<knot[m+3] && t>knot[m+2])
| ^~
Ispline.h:46:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
46 | if (t>=knot[m+3])
| ^~
In file included from sieve.cpp:28:
Mspline.h: In function 'double Mspline_3(int, double, Eigen::VectorXd&)':
Mspline.h:13:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
13 | if (t<=knot[m+1] && t>knot[m])
| ^~
Mspline.h:18:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
18 | if (t<=knot[m+2] &&t>knot[m+1])
| ^~
Mspline.h: In function 'Eigen::MatrixXd Mspline(int, Eigen::VectorXd&, Eigen::VectorXd&)':
Mspline.h:42:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
42 | for(int i = 1; i < qn; i++)
| ^~~
Mspline.h:46:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
46 | return res2;
| ^~~~~~
sieve.cpp: In function 'Rcpp::NumericVector sieve(Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, int)':
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 jointDis.h:6,
from tPos.cpp:3:
Ispline.h: In function 'double Ispline_3(int, double, Eigen::VectorXd&)':
Ispline.h:41:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (t<knot[m+3] && t>knot[m+2])
| ^~
Ispline.h:46:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
46 | if (t>=knot[m+3])
| ^~
In file included from jointDis.h:7:
Mspline.h: In function 'double Mspline_3(int, double, Eigen::VectorXd&)':
Mspline.h:13:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
13 | if (t<=knot[m+1] && t>knot[m])
| ^~
Mspline.h:18:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
18 | if (t<=knot[m+2] &&t>knot[m+1])
| ^~
Mspline.h: In function 'Eigen::MatrixXd Mspline(int, Eigen::VectorXd&, Eigen::VectorXd&)':
Mspline.h:42:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
42 | for(int i = 1; i < qn; i++)
| ^~~
Mspline.h:46:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
46 | return res2;
| ^~~~~~
jointDis.h: In function 'double jointDis(Eigen::VectorXd&, double, double, Eigen::VectorXd&, Eigen::VectorXd&)':
jointDis.h:23:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
23 | for(int i = 0; i < pn; i++)
| ^~~
jointDis.h:28:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
28 | return sum;
| ^~~~~~
jointDis.h: At global scope:
jointDis.h:31:15: warning: 'double margM(Eigen::VectorXd&, double, Eigen::VectorXd&)' defined but not used [-Wunused-function]
31 | static double margM(VectorXd &theta, double m, VectorXd &knot2 )
| ^~~~~
Mspline.h:50:17: warning: 'Eigen::VectorXd MsplineX(int, double, Eigen::VectorXd&)' defined but not used [-Wunused-function]
50 | static VectorXd MsplineX(int qn, double x, VectorXd &knot)
| ^~~~~~~~
Mspline.h:38:17: warning: 'Eigen::MatrixXd Mspline(int, Eigen::VectorXd&, Eigen::VectorXd&)' defined but not used [-Wunused-function]
38 | static MatrixXd Mspline(int qn, VectorXd &x, VectorXd &knot)
| ^~~~~~~
Ispline.h:52:17: warning: 'Eigen::MatrixXd Ispline(int, Eigen::VectorXd&, Eigen::VectorXd&)' defined but not used [-Wunused-function]
52 | static MatrixXd Ispline(int pn, VectorXd &x, VectorXd &knot)
| ^~~~~~~
Mspline.h: At global scope:
Mspline.h:50:17: warning: 'Eigen::VectorXd MsplineX(int, double, Eigen::VectorXd&)' defined but not used [-Wunused-function]
50 | static VectorXd MsplineX(int qn, double x, VectorXd &knot)
| ^~~~~~~~
Ispline.h:65:17: warning: 'Eigen::VectorXd IsplineX(int, double, Eigen::VectorXd&)' defined but not used [-Wunused-function]
65 | static VectorXd IsplineX(int pn, double x, VectorXd &knot)
| ^~~~~~~~
g++-13 -std=gnu++11 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o intcensROC.so RcppExports.o fPos.o sieve.o tPos.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/intcensROC/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/intcensROC/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/intcensROC/src'
installing to /data/gannet/ripley/R/packages/tests-devel/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)