downloading reverse dependencies ... downloading compareGroups_4.8.0.tar.gz ... ok downloading MultiPhen_2.0.3.tar.gz ... ok downloading ToolsForCoDa_1.0.6.tar.gz ... ok downloading dartR_2.9.7.tar.gz ... ok downloading dartR.base_0.65.tar.gz ... ok installing dependencies ‘dartR.data’, ‘ggtern’, ‘HardyWeinberg’, ‘hierfstat’, ‘iterpc’, ‘leaflet.minicharts’, ‘mmod’, ‘PopGenReport’, ‘poppr’, ‘SIBER’, ‘StAMPP’ also installing the dependencies ‘genetics’, ‘polysat’ begin installing package ‘genetics’ begin installing package ‘polysat’ begin installing package ‘HardyWeinberg’ begin installing package ‘dartR.data’ begin installing package ‘StAMPP’ begin installing package ‘ggtern’ begin installing package ‘iterpc’ begin installing package ‘hierfstat’ begin installing package ‘leaflet.minicharts’ begin installing package ‘mmod’ begin installing package ‘SIBER’ * installing *source* package ‘iterpc’ ... ** package ‘iterpc’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (iterpc) * installing *source* package ‘leaflet.minicharts’ ... ** package ‘leaflet.minicharts’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (leaflet.minicharts) * installing *source* package ‘genetics’ ... ** package ‘genetics’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (genetics) * installing *source* package ‘hierfstat’ ... ** package ‘hierfstat’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (hierfstat) * installing *source* package ‘SIBER’ ... ** package ‘SIBER’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SIBER) * installing *source* package ‘dartR.data’ ... ** package ‘dartR.data’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (dartR.data) * installing *source* package ‘mmod’ ... ** package ‘mmod’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (mmod) begin installing package ‘PopGenReport’ * installing *source* package ‘StAMPP’ ... ** package ‘StAMPP’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (StAMPP) * installing *source* package ‘ggtern’ ... ** package ‘ggtern’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** demo ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ggtern) * installing *source* package ‘polysat’ ... ** package ‘polysat’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpec9csU/R.INSTALL15bb6f3e4aaf95/polysat/src' g++-13 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-13/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-13 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-13/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c deSilvaFuncs.cpp -o deSilvaFuncs.o g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-13/lib -Wl,-O1 -o polysat.so RcppExports.o deSilvaFuncs.o -L/home/hornik/tmp/R-d-gcc-13/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpec9csU/R.INSTALL15bb6f3e4aaf95/polysat/src' installing to /home/hornik/tmp/CRAN/Library/00LOCK-polysat/00new/polysat/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 (polysat) begin installing package ‘poppr’ * installing *source* package ‘HardyWeinberg’ ... ** using staged installation ** libs using C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpO2N4VK/R.INSTALL15bb603ef19d7/HardyWeinberg/src' g++-13 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-13/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c HWxChromosomal.cpp -o HWxChromosomal.o g++-13 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-13/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-13 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-13/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c SNPHWEX.cpp -o SNPHWEX.o g++-13 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-13/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c support.cpp -o support.o g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-13/lib -Wl,-O1 -o HardyWeinberg.so HWxChromosomal.o RcppExports.o SNPHWEX.o support.o -L/home/hornik/tmp/R-d-gcc-13/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpO2N4VK/R.INSTALL15bb603ef19d7/HardyWeinberg/src' installing to /home/hornik/tmp/CRAN/Library/00LOCK-HardyWeinberg/00new/HardyWeinberg/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 (HardyWeinberg) * installing *source* package ‘PopGenReport’ ... ** package ‘PopGenReport’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (PopGenReport) * installing *source* package ‘poppr’ ... ** package ‘poppr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-13 (Debian 13.2.0-13) 13.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpMreWlK/R.INSTALL15bdba48c6bd93/poppr/src' gcc-13 -I"/home/hornik/tmp/R-d-gcc-13/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c adjust_missing.c -o adjust_missing.o gcc-13 -I"/home/hornik/tmp/R-d-gcc-13/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bitwise_distance.c -o bitwise_distance.o bitwise_distance.c: In function ‘association_index_haploid’: bitwise_distance.c:823:7: warning: unused variable ‘only_differences’ [-Wunused-variable] 823 | int only_differences; | ^~~~~~~~~~~~~~~~ bitwise_distance.c:815:7: warning: variable ‘chr_length’ set but not used [-Wunused-but-set-variable] 815 | int chr_length; | ^~~~~~~~~~ bitwise_distance.c:808:8: warning: unused variable ‘R_chr2_1’ [-Wunused-variable] 808 | SEXP R_chr2_1; | ^~~~~~~~ bitwise_distance.c: In function ‘association_index_diploid’: bitwise_distance.c:1190:7: warning: variable ‘chr_length’ set but not used [-Wunused-but-set-variable] 1190 | int chr_length; | ^~~~~~~~~~ bitwise_distance.c:1182:8: warning: unused variable ‘R_chr2_2’ [-Wunused-variable] 1182 | SEXP R_chr2_2; | ^~~~~~~~ bitwise_distance.c:1181:8: warning: unused variable ‘R_chr2_1’ [-Wunused-variable] 1181 | SEXP R_chr2_1; | ^~~~~~~~ gcc-13 -I"/home/hornik/tmp/R-d-gcc-13/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gcc-13 -I"/home/hornik/tmp/R-d-gcc-13/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mlg_clustering.c -o mlg_clustering.o gcc-13 -I"/home/hornik/tmp/R-d-gcc-13/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mlg_counter.c -o mlg_counter.o gcc-13 -I"/home/hornik/tmp/R-d-gcc-13/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c msn.c -o msn.o gcc-13 -I"/home/hornik/tmp/R-d-gcc-13/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c omp_test.c -o omp_test.o gcc-13 -I"/home/hornik/tmp/R-d-gcc-13/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c permut_shuffler.c -o permut_shuffler.o gcc-13 -I"/home/hornik/tmp/R-d-gcc-13/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c poppr_distance.c -o poppr_distance.o poppr_distance.c: In function ‘bruvo_between’: poppr_distance.c:428:13: warning: variable ‘numel’ set but not used [-Wunused-but-set-variable] 428 | int numel; // Number of elements in returned matrix | ^~~~~ gcc-13 -shared -L/home/hornik/tmp/R-d-gcc-13/lib -Wl,-O1 -o poppr.so adjust_missing.o bitwise_distance.o init.o mlg_clustering.o mlg_counter.o msn.o omp_test.o permut_shuffler.o poppr_distance.o -fopenmp -L/home/hornik/tmp/R-d-gcc-13/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpMreWlK/R.INSTALL15bdba48c6bd93/poppr/src' installing to /home/hornik/tmp/CRAN/Library/00LOCK-poppr/00new/poppr/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a generic function from function ‘as.genambig’ in package ‘poppr’ ** help *** installing help indices *** copying figures ** 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 (poppr) checking HardyWeinberg_1.7.7.tar.gz ... checking compareGroups_4.8.0.tar.gz ... checking MultiPhen_2.0.3.tar.gz ... checking ToolsForCoDa_1.0.6.tar.gz ... checking dartR_2.9.7.tar.gz ... checking dartR.base_0.65.tar.gz ... Depends: Package: HardyWeinberg Depends: R (>= 1.8.0), mice, nnet, Rsolnp, shape Imports: Rcpp LinkingTo: Rcpp Timings: user system elapsed HardyWeinberg 148.019 8.865 158.634 Results: Check status summary: NOTE OK Source packages 0 1 Reverse depends 2 3 Check results summary: HardyWeinberg ... OK rdepends_compareGroups ... OK rdepends_dartR.base ... OK rdepends_dartR ... NOTE * checking Rd files ... [1s/1s] NOTE rdepends_MultiPhen ... NOTE * checking Rd files ... [0s/0s] NOTE rdepends_ToolsForCoDa ... OK