* installing *source* package ‘apcluster’ ... ** package ‘apcluster’ 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/apcluster/src' g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 R_init_apcluster.cpp -o R_init_apcluster.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 aggExClusterC.cpp -o aggExClusterC.o aggExClusterC.cpp: In function 'int which_max_NoNA(Rcpp::NumericVector)': aggExClusterC.cpp:74:12: warning: 'index' may be used uninitialized [-Wmaybe-uninitialized] 74 | return index; | ^~~~~ aggExClusterC.cpp:57:9: note: 'index' was declared here 57 | int index; | ^~~~~ g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 apclusterC.cpp -o apclusterC.o apclusterC.cpp: In function 'SEXPREC* apclusterC(SEXP, SEXP, SEXP, SEXP, SEXP)': apclusterC.cpp:69:44: warning: 'yMax' may be used uninitialized [-Wmaybe-uninitialized] 69 | (j == yMax ? max2 : max1)) + lam * oldVal; | ~~~~~~~~~~~^~~~~~~~~~~~~~ apclusterC.cpp:49:17: note: 'yMax' was declared here 49 | int yMax; | ^~~~ g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 apclusterLeveragedC.cpp -o apclusterLeveragedC.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 apclusterSparseC.cpp -o apclusterSparseC.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 distanceL.c -o distanceL.o apclusterLeveragedC.cpp: In function 'SEXPREC* apclusterLeveragedC(SEXP, SEXP, SEXP, SEXP, SEXP)': apclusterLeveragedC.cpp:63:44: warning: 'yMax' may be used uninitialized [-Wmaybe-uninitialized] 63 | (j == yMax ? max2 : max1)) + lam * R(j, ii); | ~~~~~~~~~~~^~~~~~~~~~~~~~ apclusterLeveragedC.cpp:37:17: note: 'yMax' was declared here 37 | int yMax; | ^~~~ g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 preferenceRangeC.cpp -o preferenceRangeC.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 preferenceRangeSparseC.cpp -o preferenceRangeSparseC.o preferenceRangeSparseC.cpp: In function 'SEXPREC* preferenceRangeSparseC(SEXP, SEXP, SEXP, SEXP, SEXP)': preferenceRangeSparseC.cpp:20:12: warning: unused variable 'j' [-Wunused-variable] 20 | int i, j, ii, K, temp1, temp2, length; | ^ preferenceRangeSparseC.cpp:20:15: warning: unused variable 'ii' [-Wunused-variable] 20 | int i, j, ii, K, temp1, temp2, length; | ^~ preferenceRangeSparseC.cpp:20:19: warning: unused variable 'K' [-Wunused-variable] 20 | int i, j, ii, K, temp1, temp2, length; | ^ preferenceRangeSparseC.cpp:20:37: warning: unused variable 'length' [-Wunused-variable] 20 | int i, j, ii, K, temp1, temp2, length; | ^~~~~~ g++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o apcluster.so R_init_apcluster.o aggExClusterC.o apclusterC.o apclusterLeveragedC.o apclusterSparseC.o distanceL.o preferenceRangeC.o preferenceRangeSparseC.o make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/apcluster/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/apcluster/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/apcluster/src' installing to /data/gannet/ripley/R/packages/tests-devel/apcluster.Rcheck/00LOCK-apcluster/00new/apcluster/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘heatmap’ in package ‘apcluster’ Creating a generic function for ‘cutree’ from package ‘stats’ in package ‘apcluster’ ** 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 (apcluster)