* installing *source* package ‘amap’ ...
** package ‘amap’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (GCC) 13.2.0’
using Fortran compiler: ‘GNU Fortran (GCC) 13.2.0’
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/amap/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 acprob.cpp -o acprob.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 burt.c -o burt.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 diss.c -o diss.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 distance.cpp -o distance.o
In file included from distance_T.h:385,
from distance.cpp:3:
distance_T.h.h: In instantiation of 'static void* amap::distance_T<T>::thread_dist(void*) [with T = double]':
distance_T.h.h:755:21: required from 'static void amap::distance_T<T>::distance(double*, int*, int*, T*, int*, int*, int*, int*, int) [with T = double]'
distance.cpp:23:31: required from here
distance_T.h.h:840:30: warning: variable 'ij' set but not used [-Wunused-but-set-variable]
840 | int nbprocess,nr,nc,i,j,dc,ij;
| ^~
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 hclust.cpp -o hclust.o
In file included from distance_T.h:385,
from hclust_T.h.h:6,
from hclust_T.h:45,
from hclust.cpp:49:
distance_T.h.h: In instantiation of 'static void* amap::distance_T<T>::thread_dist(void*) [with T = double]':
distance_T.h.h:755:21: required from 'static void amap::distance_T<T>::distance(double*, int*, int*, T*, int*, int*, int*, int*, int) [with T = double]'
hclust_T.h.h:206:35: required from 'void hclust_T::hclust(int*, double*, int, int, int*, int*, int*, int*, int*, int*, int*, double*, double*, T*, int*) [with T = double]'
hclust.cpp:79:31: required from here
distance_T.h.h:840:30: warning: variable 'ij' set but not used [-Wunused-but-set-variable]
840 | int nbprocess,nr,nc,i,j,dc,ij;
| ^~
distance_T.h.h: In instantiation of 'static void* amap::distance_T<T>::thread_dist(void*) [with T = float]':
distance_T.h.h:755:21: required from 'static void amap::distance_T<T>::distance(double*, int*, int*, T*, int*, int*, int*, int*, int) [with T = float]'
hclust_T.h.h:50:34: required from 'void hclust_T::hcluster(double*, int*, int*, int*, int*, int*, int*, int*, int*, double*, double*, int*, int*) [with T = float]'
hclust.cpp:115:30: required from here
distance_T.h.h:840:30: warning: variable 'ij' set but not used [-Wunused-but-set-variable]
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
hclust_T.h.h: In function 'void hclust_T::hclust(int*, double*, int, int, int*, int*, int*, int*, int*, int*, int*, double*, double*, T*, int*) [with T = double]':
hclust_T.h.h:126:14: warning: 'jm' may be used uninitialized [-Wmaybe-uninitialized]
126 | nn[i]=jm;
hclust_T.h.h:75:12: note: 'jm' was declared here
75 | int im,jm,jj,i,j,ncl,ind,i2,j2,k,ind1,ind2,ind3;
| ^~
distance_T.h.h:54:39: warning: 'im' may be used uninitialized [-Wmaybe-uninitialized]
54 | #define MAX( A , B ) ( ( A ) > ( B ) ? ( A ) : ( B ) )
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
hclust_T.h.h:161:12: note: in expansion of macro 'MAX'
161 | j2=MAX (im,jm);
| ^~~
hclust_T.h.h:75:9: note: 'im' was declared here
75 | int im,jm,jj,i,j,ncl,ind,i2,j2,k,ind1,ind2,ind3;
| ^~
In function 'void hclust_T::hclust(int*, double*, int, int, int*, int*, int*, int*, int*, int*, int*, double*, double*, T*, int*) [with T = float]',
inlined from 'void hclust_T::hcluster(double*, int*, int*, int*, int*, int*, int*, int*, int*, double*, double*, int*, int*) [with T = float]' at hclust_T.h.h:62:24,
inlined from 'void hcluster(double*, int*, int*, int*, int*, int*, int*, int*, int*, double*, double*, int*, int*, int*)' at hclust.cpp:115:30:
hclust_T.h.h:126:14: warning: 'jm' may be used uninitialized [-Wmaybe-uninitialized]
126 | nn[i]=jm;
hclust_T.h.h: In function 'void hcluster(double*, int*, int*, int*, int*, int*, int*, int*, int*, double*, double*, int*, int*, int*)':
hclust_T.h.h:75:12: note: 'jm' was declared here
75 | int im,jm,jj,i,j,ncl,ind,i2,j2,k,ind1,ind2,ind3;
| ^~
In function 'void hclust_T::hclust(int*, double*, int, int, int*, int*, int*, int*, int*, int*, int*, double*, double*, T*, int*) [with T = float]',
inlined from 'void hclust_T::hcluster(double*, int*, int*, int*, int*, int*, int*, int*, int*, double*, double*, int*, int*) [with T = float]' at hclust_T.h.h:62:24,
inlined from 'void hcluster(double*, int*, int*, int*, int*, int*, int*, int*, int*, double*, double*, int*, int*, int*)' at hclust.cpp:115:30:
distance_T.h.h:54:39: warning: 'im' may be used uninitialized [-Wmaybe-uninitialized]
54 | #define MAX( A , B ) ( ( A ) > ( B ) ? ( A ) : ( B ) )
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
hclust_T.h.h:161:12: note: in expansion of macro 'MAX'
161 | j2=MAX (im,jm);
| ^~~
hclust_T.h.h: In function 'void hcluster(double*, int*, int*, int*, int*, int*, int*, int*, int*, double*, double*, int*, int*, int*)':
hclust_T.h.h:75:9: note: 'im' was declared here
75 | int im,jm,jj,i,j,ncl,ind,i2,j2,k,ind1,ind2,ind3;
| ^~
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 kmeans.cpp -o kmeans.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 matrice.cpp -o matrice.o
gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -c pop.f -o pop.o
pop.f:365:35:
365 | CDIF = ABS(COUTS(I2J2)) - ABS(COUTS(I1J1))
| 1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
pop.f:367:39:
367 | CDIF = COUTS(I2J2) - COUTS(I1J1)
| 1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
g++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o amap.so acprob.o burt.o diss.o distance.o hclust.o init.o kmeans.o matrice.o pop.o -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/amap/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/amap/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/amap/src'
installing to /data/gannet/ripley/R/packages/tests-devel/amap.Rcheck/00LOCK-amap/00new/amap/libs
** R
** data
** demo
** exec
** 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 (amap)