* installing *source* package ‘fdasrvf’ ...
** this is package ‘fdasrvf’ version ‘2.4.0’
** package ‘fdasrvf’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/fdasrvf/src'
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -Ifdaqmap/incl/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -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++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -Ifdaqmap/incl/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -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 wrapperSRSF.cpp -o wrapperSRSF.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -Ifdaqmap/incl/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -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 wrapperQMAP.cpp -o wrapperQMAP.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -Ifdaqmap/incl/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -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 bayesian.cpp -o bayesian.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -Ifdaqmap/incl/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -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 pair_align_functions_expomap.cpp -o pair_align_functions_expomap.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -Ifdaqmap/incl/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -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 fdasrsf/DP.cpp -o fdasrsf/DP.o
fdasrsf/DP.cpp: In function ‘double CostFn2(const double*, const double*, int, int, int, int, int, int, double, int)’:
fdasrsf/DP.cpp:228:44: warning: ‘tmp_pen’ may be used uninitialized [-Wmaybe-uninitialized]
  228 |                         E += (tmp*tmp + lam*tmp_pen);
      |                                         ~~~^~~~~~~~
fdasrsf/DP.cpp:194:73: note: ‘tmp_pen’ was declared here
  194 |         double m = (j-l)/(double)(i-k), sqrtm = sqrt(m), E = 0, y, tmp, tmp_pen, ip, fp, q1dotq2;
      |                                                                         ^~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -Ifdaqmap/incl/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -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 fdasrsf/dp_grid.cpp -o fdasrsf/dp_grid.o
fdasrsf/dp_grid.cpp: In function ‘double dp_costs(double*, double*, int, double*, double*, int, int, double*, int*, int, double*, int*, int, double*, int*, double, size_t, int (*)[2])’:
fdasrsf/dp_grid.cpp:32:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   32 |             for ( i=0; i<dp_nbhd_count; ++i )
      |                        ~^~~~~~~~~~~~~~
pair_align_functions_expomap.cpp: In function ‘arma::vec calcY(double, arma::vec)’:
pair_align_functions_expomap.cpp:9:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
    9 |     for (unsigned int i = 0; i < len; i++) {
      |                              ~~^~~~~
pair_align_functions_expomap.cpp:14:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   14 |     for (unsigned int i = 0; i < len; i++) {
      |                              ~~^~~~~
pair_align_functions_expomap.cpp: In function ‘Rcpp::NumericVector cuL2norm2(arma::vec, arma::vec)’:
pair_align_functions_expomap.cpp:27:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   27 |   for (unsigned int i = 0; i < n; i++) {
      |                            ~~^~~
pair_align_functions_expomap.cpp:34:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   34 |   for (unsigned int i = 0; i < n; i++) {
      |                            ~~^~~
pair_align_functions_expomap.cpp:41:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   41 |   for (unsigned int i = 0; i < (n - 1); i++) {
      |                            ~~^~~~~~~~~
pair_align_functions_expomap.cpp:46:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   46 |   for (unsigned int i = 0; i < (n - 1); i++) {
      |                            ~~^~~~~~~~~
pair_align_functions_expomap.cpp: In function ‘double order_l2norm(arma::vec, arma::vec)’:
pair_align_functions_expomap.cpp:70:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   70 |   for (unsigned int i = 0; i < n; i++) {
      |                            ~~^~~
pair_align_functions_expomap.cpp:77:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   77 |   for (unsigned int i = 0; i < n; i++) {
      |                            ~~^~~
pair_align_functions_expomap.cpp:84:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   84 |   for (unsigned int i = 0; i < (n - 1); i++) {
      |                            ~~^~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -Ifdaqmap/incl/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -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 fdasrsf/dp_nbhd.cpp -o fdasrsf/dp_nbhd.o
In function ‘size_t compute_nbhd_count_rec(size_t, int*)’,
    inlined from ‘size_t compute_nbhd_count(size_t)’ at fdasrsf/dp_nbhd.cpp:101:37,
    inlined from ‘int (* dp_generate_nbhd(size_t, size_t*))[2]’ at fdasrsf/dp_nbhd.cpp:120:35:
fdasrsf/dp_nbhd.cpp:62:15: warning: ‘states[4611686018427387903]’ may be used uninitialized [-Wmaybe-uninitialized]
   62 |   if (states[n] != -1) {
      |       ~~~~~~~~^
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -Ifdaqmap/incl/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -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 fdasrsf/DynamicProgrammingQ2.cpp -o fdasrsf/DynamicProgrammingQ2.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -Ifdaqmap/incl/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -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 fdasrsf/misc_funcs.cpp -o fdasrsf/misc_funcs.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -Ifdaqmap/incl/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -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 fdasrsf/mlogit_warp_grad.cpp -o fdasrsf/mlogit_warp_grad.o
fdasrsf/mlogit_warp_grad.cpp: In function ‘void mlogit_warp_grad(int*, int*, double*, double*, double*, double*, double*, int*, int*, double*, double*, int*, double*)’:
fdasrsf/mlogit_warp_grad.cpp:16:16: warning: unused variable ‘t’ [-Wunused-variable]
   16 |         double t = *ti;
      |                ^
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -Ifdaqmap/incl/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -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 fdaqmap/src/myVector.cpp -o fdaqmap/src/myVector.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -Ifdaqmap/incl/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -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 fdaqmap/src/UnitSquareImage.cpp -o fdaqmap/src/UnitSquareImage.o
fdaqmap/src/UnitSquareImage.cpp: In function ‘void findgrad(double*, double*, const double*, int, int)’:
fdaqmap/src/UnitSquareImage.cpp:9:18: warning: unused variable ‘N’ [-Wunused-variable]
    9 |     int i, j, k, N = n*t;
      |                  ^
fdaqmap/src/UnitSquareImage.cpp: In function ‘void findgrad2D(double*, double*, double*, int, int, int)’:
fdaqmap/src/UnitSquareImage.cpp:64:18: warning: unused variable ‘N’ [-Wunused-variable]
   64 |     int i, j, k, N = n*t;
      |                  ^
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o fdasrvf.so RcppExports.o wrapperSRSF.o wrapperQMAP.o bayesian.o pair_align_functions_expomap.o fdasrsf/DP.o fdasrsf/dp_grid.o fdasrsf/dp_nbhd.o fdasrsf/DynamicProgrammingQ2.o fdasrsf/misc_funcs.o fdasrsf/mlogit_warp_grad.o fdaqmap/src/myVector.o fdaqmap/src/UnitSquareImage.o -fopenmp -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/fdasrvf/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/fdasrvf/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/fdasrvf/src'
installing to /data/gannet/ripley/R/packages/tests-devel/fdasrvf.Rcheck/00LOCK-fdasrvf/00new/fdasrvf/libs
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (fdasrvf)