* installing *source* package ‘ASMap’ ...
** package ‘ASMap’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (GCC) 13.2.0’
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/ASMap/src'
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -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 MSTOpt.cpp -o MSTOpt.o
MSTOpt.cpp: In constructor 'MSTOpt::MSTOpt(const std::vector<std::vector<double> >&, int, int)':
MSTOpt.cpp:20:43: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<std::vector<double> >::size_type' {aka 'long unsigned int'} [-Wformat=]
20 | Rf_error("pair_wise_distances.size() %d != number_of_bins %d\n",
| ~^
| |
| int
| %ld
21 | pair_wise_distances.size(),number_of_bins);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| std::vector<std::vector<double> >::size_type {aka long unsigned int}
MSTOpt.cpp: In member function 'double MSTOpt::new_serialization()':
MSTOpt.cpp:593:49: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wformat=]
593 | Rprintf("the length of the longest path: %d\n", longest_path.size());
| ~^ ~~~~~~~~~~~~~~~~~~~
| | |
| int std::vector<int>::size_type {aka long unsigned int}
| %ld
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -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 genetic_map_DH.cpp -o genetic_map_DH.o
genetic_map_DH.cpp: In member function 'void genetic_map::dump_distance_matrix()':
genetic_map_DH.cpp:191:31: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<std::vector<double> >::size_type' {aka 'long unsigned int'} [-Wformat=]
191 | Rprintf("matrix dimension: %d\n", pair_wise_distances.size());
| ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| int std::vector<std::vector<double> >::size_type {aka long unsigned int}
| %ld
genetic_map_DH.cpp: In member function 'void genetic_map::dump()':
genetic_map_DH.cpp:233:19: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wformat=]
233 | Rprintf("%d,",(connected_components[ii]).size());
| ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| int std::vector<int>::size_type {aka long unsigned int}
| %ld
genetic_map_DH.cpp: In member function 'void genetic_map::write_output(SEXPREC*&)':
genetic_map_DH.cpp:470:17: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wformat=]
470 | Rprintf("%d\t",(connected_components[ii]).size());
| ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| int std::vector<int>::size_type {aka long unsigned int}
| %ld
genetic_map_DH.cpp:477:17: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<std::vector<int> >::size_type' {aka 'long unsigned int'} [-Wformat=]
477 | Rprintf("%d\t",(lg_bins_condensed[ii]).size());
| ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| int std::vector<std::vector<int> >::size_type {aka long unsigned int}
| %ld
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -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 genetic_map_RIL.cpp -o genetic_map_RIL.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c init.c -o init.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -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 is_number.cpp -o is_number.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -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 linkage_group_DH.cpp -o linkage_group_DH.o
linkage_group_DH.cpp: In member function 'void linkage_group::dump_distance_matrix()':
linkage_group_DH.cpp:123:31: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<std::vector<double> >::size_type' {aka 'long unsigned int'} [-Wformat=]
123 | Rprintf("matrix dimension: %d\n", pair_wise_distances.size());
| ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| int std::vector<std::vector<double> >::size_type {aka long unsigned int}
| %ld
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -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 linkage_group_RIL.cpp -o linkage_group_RIL.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -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 mst.cpp -o mst.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -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 sexp.cpp -o sexp.o
g++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o ASMap.so MSTOpt.o genetic_map_DH.o genetic_map_RIL.o init.o is_number.o linkage_group_DH.o linkage_group_RIL.o mst.o sexp.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/ASMap/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/ASMap/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/ASMap/src'
installing to /data/gannet/ripley/R/packages/tests-devel/ASMap.Rcheck/00LOCK-ASMap/00new/ASMap/libs
** R
** data
** 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 (ASMap)