Install log for 'genepop'

* installing *source* package ‘genepop’ ...
** this is package ‘genepop’ version ‘1.2.11’
** package ‘genepop’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 21.1.1’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/genepop/src'
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DCOMPATIBILITYRCPP  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c CT_tests.cpp -o CT_tests.o
In file included from CT_tests.cpp:40:
./CT_tests.h:115:42: warning: unused variable 'pp' [-Wunused-variable]
  115 |   std::vector<CPopulation *>::iterator p,pp; // CPopulation contient les popName()
      |                                          ^~
./CT_tests.h:116:39: warning: unused variable 'p1' [-Wunused-variable]
  116 |   std::vector<CGenotypes *>::iterator p1,p2; // CGenotypes contient toute l'info sauf les popName()
      |                                       ^~
./CT_tests.h:116:42: warning: unused variable 'p2' [-Wunused-variable]
  116 |   std::vector<CGenotypes *>::iterator p1,p2; // CGenotypes contient toute l'info sauf les popName()
      |                                          ^~
CT_tests.cpp:783:34: warning: unused variable 'p1' [-Wunused-variable]
  783 |   vector<CGenotypes *>::iterator p1,p2; // CGenotypes contient toute l'info sauf les popName()
      |                                  ^~
CT_tests.cpp:783:37: warning: unused variable 'p2' [-Wunused-variable]
  783 |   vector<CGenotypes *>::iterator p1,p2; // CGenotypes contient toute l'info sauf les popName()
      |                                     ^~
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DCOMPATIBILITYRCPP  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c F_est.cpp -o F_est.o
5 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DCOMPATIBILITYRCPP  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c GenepopS.cpp -o GenepopS.o
In file included from GenepopS.cpp:56:
./CT_tests.h:115:42: warning: unused variable 'pp' [-Wunused-variable]
  115 |   std::vector<CPopulation *>::iterator p,pp; // CPopulation contient les popName()
      |                                          ^~
./CT_tests.h:116:39: warning: unused variable 'p1' [-Wunused-variable]
  116 |   std::vector<CGenotypes *>::iterator p1,p2; // CGenotypes contient toute l'info sauf les popName()
      |                                       ^~
./CT_tests.h:116:42: warning: unused variable 'p2' [-Wunused-variable]
  116 |   std::vector<CGenotypes *>::iterator p1,p2; // CGenotypes contient toute l'info sauf les popName()
      |                                          ^~
GenepopS.cpp:1489:16: warning: variable 'popit' set but not used [-Wunused-but-set-variable]
 1489 |         size_t nb_all,popit;
      |                       ^
4 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DCOMPATIBILITYRCPP  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c HW_tests.cpp -o HW_tests.o
HW_tests.cpp:247:23: warning: variable 'necess_mark' set but not used [-Wunused-but-set-variable]
  247 | int possible_exact=0, necess_mark=0;
      |                       ^
HW_tests.cpp:1650:10: warning: variable 'kfi' set but not used [-Wunused-but-set-variable]
 1650 |   size_t kfi,allele, k;
      |          ^
2 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DCOMPATIBILITYRCPP  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c RGenepop.cpp -o RGenepop.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DCOMPATIBILITYRCPP  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c RcppExports.cpp -o RcppExports.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DCOMPATIBILITYRCPP  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c bootstrap.cpp -o bootstrap.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DCOMPATIBILITYRCPP  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c conversions.cpp -o conversions.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DCOMPATIBILITYRCPP  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c genepop.cpp -o genepop.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DCOMPATIBILITYRCPP  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c multimig.cpp -o multimig.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DCOMPATIBILITYRCPP  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c proba.cpp -o proba.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DCOMPATIBILITYRCPP  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c settings.cpp -o settings.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DCOMPATIBILITYRCPP  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c tools.cpp -o tools.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang21/lib -L/usr/local/clang21/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -L/usr/local/clang21/lib/clang/21/lib/x86_64-unknown-linux-gnu -o genepop.so CT_tests.o F_est.o GenepopS.o HW_tests.o RGenepop.o RcppExports.o bootstrap.o conversions.o genepop.o multimig.o proba.o settings.o tools.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/genepop/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/genepop/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/genepop/src'
installing to /data/gannet/ripley/R/packages/tests-clang/genepop.Rcheck/00LOCK-genepop/00new/genepop/libs
** R
** 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 (genepop)