downloading reverse dependencies ... downloading dartR.captive_1.0.2.tar.gz ... ok downloading dartR.popgen_1.0.0.tar.gz ... ok downloading dartR.sexlinked_1.0.5.tar.gz ... ok downloading dartR.sim_0.70.tar.gz ... ok downloading dartR.spatial_0.78.tar.gz ... ok downloading dartRverse_1.0.6.tar.gz ... ok installing dependencies ‘dartR.base’, ‘dartR.captive’, ‘dartR.data’, ‘dartR.popgen’, ‘dartR.sim’, ‘dartR.spatial’, ‘ggtern’, ‘HardyWeinberg’, ‘hierfstat’, ‘iterpc’, ‘leaflet.minicharts’, ‘mmod’, ‘PopGenReport’, ‘poppr’, ‘SIBER’, ‘SNPassoc’, ‘SNPRelate’, ‘StAMPP’ also installing the dependencies ‘poisbinom’, ‘polysat’, ‘genetics’ begin installing package ‘poisbinom’ begin installing package ‘polysat’ begin installing package ‘genetics’ begin installing package ‘dartR.data’ begin installing package ‘SNPRelate’ begin installing package ‘StAMPP’ begin installing package ‘HardyWeinberg’ begin installing package ‘hierfstat’ begin installing package ‘iterpc’ begin installing package ‘leaflet.minicharts’ begin installing package ‘mmod’ begin installing package ‘SIBER’ begin installing package ‘ggtern’ * installing *source* package ‘iterpc’ ... ** this is package ‘iterpc’ version ‘0.4.2’ ** 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’ ... ** this is package ‘leaflet.minicharts’ version ‘0.6.2’ ** 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’ ... ** this is package ‘genetics’ version ‘1.3.8.1.3’ ** 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’ ... ** this is package ‘hierfstat’ version ‘0.5-11’ ** 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’ ... ** this is package ‘SIBER’ version ‘2.1.9’ ** 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 ‘mmod’ ... ** this is package ‘mmod’ version ‘1.3.3’ ** 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’ ... ** this is package ‘StAMPP’ version ‘1.6.3’ ** 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 ‘poisbinom’ ... ** this is package ‘poisbinom’ version ‘1.0.1’ ** package ‘poisbinom’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-16) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-16) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpFVvnzC/R.INSTALL1f98515c3cfb3/poisbinom/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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 gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/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 -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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 poisbinom.cpp -o poisbinom.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o poisbinom.so RcppExports.o init.o poisbinom.o -lfftw3 -lm -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpFVvnzC/R.INSTALL1f98515c3cfb3/poisbinom/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-poisbinom/00new/poisbinom/libs ** R ** 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 (poisbinom) begin installing package ‘SNPassoc’ * installing *source* package ‘ggtern’ ... ** this is package ‘ggtern’ version ‘3.5.0’ ** 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’ ... ** this is package ‘polysat’ version ‘1.7-7’ ** package ‘polysat’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-16) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpThnJlt/R.INSTALL1f993127cfa53/polysat/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o polysat.so RcppExports.o deSilvaFuncs.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpThnJlt/R.INSTALL1f993127cfa53/polysat/src' installing to /home/hornik/tmp/CRAN_recheck/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 ‘SNPassoc’ ... ** this is package ‘SNPassoc’ version ‘2.1-2’ ** package ‘SNPassoc’ 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 (SNPassoc) * installing *source* package ‘HardyWeinberg’ ... ** this is package ‘HardyWeinberg’ version ‘1.7.8’ ** package ‘HardyWeinberg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-16) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpMstryS/R.INSTALL1f98d51988f54/HardyWeinberg/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o HardyWeinberg.so HWxChromosomal.o RcppExports.o SNPHWEX.o support.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpMstryS/R.INSTALL1f98d51988f54/HardyWeinberg/src' installing to /home/hornik/tmp/CRAN_recheck/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 ‘SNPRelate’ ... ** this is package ‘SNPRelate’ version ‘1.41.0’ ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-16) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-16) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpJyWVtD/R.INSTALL1f99a78713fc3/SNPRelate/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c ConvToGDS.cpp -o ConvToGDS.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_SNPRelate.c -o R_SNPRelate.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c SNPRelate.cpp -o SNPRelate.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c ThreadPool.cpp -o ThreadPool.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c dGenGWAS.cpp -o dGenGWAS.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c dVect.cpp -o dVect.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c genBeta.cpp -o genBeta.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c genEIGMIX.cpp -o genEIGMIX.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c genFst.cpp -o genFst.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c genHWE.cpp -o genHWE.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c genIBD.cpp -o genIBD.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c genIBS.cpp -o genIBS.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c genKING.cpp -o genKING.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c genLD.cpp -o genLD.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c genPCA.cpp -o genPCA.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c genSlideWin.cpp -o genSlideWin.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o SNPRelate.so ConvToGDS.o R_SNPRelate.o SNPRelate.o ThreadPool.o dGenGWAS.o dVect.o genBeta.o genEIGMIX.o genFst.o genHWE.o genIBD.o genIBS.o genKING.o genLD.o genPCA.o genSlideWin.o -lpthread -llapack -L/home/hornik/tmp/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpJyWVtD/R.INSTALL1f99a78713fc3/SNPRelate/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-SNPRelate/00new/SNPRelate/libs ** 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 ** 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 (SNPRelate) * installing *source* package ‘dartR.data’ ... ** this is package ‘dartR.data’ version ‘1.0.8’ ** 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 *** copying figures ** 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) begin installing package ‘dartR.base’ * installing *source* package ‘poppr’ ... ** this is package ‘poppr’ version ‘2.9.6’ ** package ‘poppr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-16) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpmCe8yO/R.INSTALL1fc1c2530ecf0/poppr/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -shared -L/home/hornik/tmp/R/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/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpmCe8yO/R.INSTALL1fc1c2530ecf0/poppr/src' installing to /home/hornik/tmp/CRAN_recheck/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) * installing *source* package ‘PopGenReport’ ... ** this is package ‘PopGenReport’ version ‘3.1’ ** 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 ‘dartR.base’ ... ** this is package ‘dartR.base’ version ‘1.0.5’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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.base) begin installing package ‘dartR.sim’ begin installing package ‘dartR.popgen’ begin installing package ‘dartR.spatial’ * installing *source* package ‘dartR.spatial’ ... ** this is package ‘dartR.spatial’ version ‘0.78’ ** package ‘dartR.spatial’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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.spatial) * installing *source* package ‘dartR.sim’ ... ** this is package ‘dartR.sim’ version ‘0.70’ ** package ‘dartR.sim’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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.sim) begin installing package ‘dartR.captive’ * installing *source* package ‘dartR.popgen’ ... ** this is package ‘dartR.popgen’ version ‘1.0.0’ ** package ‘dartR.popgen’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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.popgen) * installing *source* package ‘dartR.captive’ ... ** this is package ‘dartR.captive’ version ‘1.0.2’ ** package ‘dartR.captive’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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.captive) checking dartR.base_1.0.5.tar.gz ... checking dartR.popgen_1.0.0.tar.gz ... checking dartR.sexlinked_1.0.5.tar.gz ... checking dartR.captive_1.0.2.tar.gz ... checking dartR.sim_0.70.tar.gz ... checking dartR.spatial_0.78.tar.gz ... checking dartRverse_1.0.6.tar.gz ... Depends: Package: dartR.base Depends: R (>= 3.5), adegenet (>= 2.0.0), ggplot2, dplyr, dartR.data Imports: ape,crayon,data.table,foreach,gridExtra,methods,patchwork,plyr, reshape2,SNPRelate,StAMPP,stats,stringr,tidyr,utils,MASS,SNPassoc, snpStats, raster Timings: user system elapsed dartR.base 361.434 18.447 382.663 Results: Check status summary: NOTE OK Source packages 0 1 Reverse depends 2 4 Check results summary: dartR.base ... OK rdepends_dartR.captive ... OK rdepends_dartR.popgen ... OK rdepends_dartR.sexlinked ... OK rdepends_dartR.sim ... NOTE * checking Rd cross-references ... NOTE rdepends_dartR.spatial ... NOTE * checking Rd cross-references ... NOTE rdepends_dartRverse ... OK