* installing *source* package ‘geoCount’ ...
** package ‘geoCount’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/geoCount/src'
g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I../inst/include -I'/data/gannet/ripley/R/test-3.7/Rcpp/include' -I'/data/gannet/ripley/R/test-3.7/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection  -c helloWorld.cpp -o helloWorld.o
g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I../inst/include -I'/data/gannet/ripley/R/test-3.7/Rcpp/include' -I'/data/gannet/ripley/R/test-3.7/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection  -c loc2U.cpp -o loc2U.o
g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I../inst/include -I'/data/gannet/ripley/R/test-3.7/Rcpp/include' -I'/data/gannet/ripley/R/test-3.7/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection  -c runMCMCBP.cpp -o runMCMCBP.o
g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I../inst/include -I'/data/gannet/ripley/R/test-3.7/Rcpp/include' -I'/data/gannet/ripley/R/test-3.7/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection  -c runMCMCfunc.cpp -o runMCMCfunc.o
g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I../inst/include -I'/data/gannet/ripley/R/test-3.7/Rcpp/include' -I'/data/gannet/ripley/R/test-3.7/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection  -c runMCMCpartialPois.cpp -o runMCMCpartialPois.o
runMCMCfunc.cpp: In function ‘double logft_Pois_max(arma::mat, arma::mat, arma::mat)’:
runMCMCfunc.cpp:38:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   38 |     for(int i=0; i<lam.n_rows; i++)
      |                  ~^~~~~~~~~~~
runMCMCfunc.cpp:40:40: warning: left operand of comma operator has no effect [-Wunused-value]
   40 |         Pt *= gsl_cdf_poisson_P(t, lam[i,0]);
      |                                        ^
runMCMCfunc.cpp:41:43: warning: left operand of comma operator has no effect [-Wunused-value]
   41 |         Pt1 *= gsl_cdf_poisson_P(t-1, lam[i,0]);
      |                                           ^
runMCMCfunc.cpp: In function ‘double logft_Pois_min(arma::mat, arma::mat, arma::mat)’:
runMCMCfunc.cpp:53:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   53 |     for(int i=0; i<lam.n_rows; i++)
      |                  ~^~~~~~~~~~~
runMCMCfunc.cpp:55:42: warning: left operand of comma operator has no effect [-Wunused-value]
   55 |         Pt *= 1-gsl_cdf_poisson_P(t, lam[i,0]);
      |                                          ^
runMCMCfunc.cpp:56:45: warning: left operand of comma operator has no effect [-Wunused-value]
   56 |         Pt1 *= 1-gsl_cdf_poisson_P(t-1, lam[i,0]);
      |                                             ^
runMCMCfunc.cpp: In function ‘arma::mat rhoSph(arma::mat, double, double)’:
runMCMCfunc.cpp:100:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  100 |  for(int i=0; i < T.n_rows; i++)
      |               ~~^~~~~~~~~~
runMCMCfunc.cpp:102:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  102 |   for(int j=0; j < T.n_cols; j++)
      |                ~~^~~~~~~~~~
runMCMCfunc.cpp: In function ‘arma::mat rhoMatern(arma::mat, double, double)’:
runMCMCfunc.cpp:119:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  119 |  for(int i=0; i < T.n_rows; i++)
      |               ~~^~~~~~~~~~
runMCMCfunc.cpp:121:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  121 |   for(int j=0; j < T.n_cols; j++)
      |                ~~^~~~~~~~~~
g++ -std=gnu++11 -shared -L/usr/local/lib64 -o geoCount.so helloWorld.o loc2U.o runMCMCBP.o runMCMCfunc.o runMCMCpartialPois.o -L/data/gannet/ripley/R/R-devel/lib -lRlapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath -lgsl -lgslcblas -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/geoCount/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/geoCount/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/geoCount/src'
installing to /data/gannet/ripley/R/packages/tests-devel/geoCount.Rcheck/00LOCK-geoCount/00new/geoCount/libs
** R
** data
** inst
** 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 (geoCount)