downloading reverse dependencies ... downloading tricolore_1.2.4.tar.gz ... ok downloading dartR_2.9.9.5.tar.gz ... ok downloading dartR.base_1.0.7.tar.gz ... ok downloading vdar_0.1.3-2.tar.gz ... ok installing dependencies ‘dartR.data’, ‘ggtern’, ‘HardyWeinberg’, ‘hierfstat’, ‘iterpc’, ‘leaflet.minicharts’, ‘mmod’, ‘PopGenReport’, ‘poppr’, ‘SIBER’, ‘SNPassoc’, ‘StAMPP’ also installing the dependencies ‘genetics’, ‘polysat’, ‘poisbinom’ begin installing package ‘genetics’ begin installing package ‘polysat’ begin installing package ‘poisbinom’ begin installing package ‘ggtern’ begin installing package ‘dartR.data’ begin installing package ‘StAMPP’ begin installing package ‘HardyWeinberg’ begin installing package ‘iterpc’ begin installing package ‘hierfstat’ begin installing package ‘leaflet.minicharts’ begin installing package ‘SIBER’ begin installing package ‘mmod’ * 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 ‘0.6.3’ ** 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 ‘poisbinom’ ... ** this is package ‘poisbinom’ version ‘1.0.2’ ** package ‘poisbinom’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-7) 15.2.0’ using C++ compiler: ‘g++-15 (Debian 15.2.0-7) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpOcMxCh/R.INSTALL1443f077e2b620/poisbinom/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/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-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/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++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/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++-15 -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/RtmpOcMxCh/R.INSTALL1443f077e2b620/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 ‘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 ‘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++-15 (Debian 15.2.0-7) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpKNxZwb/R.INSTALL1443ea3e4483b8/polysat/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/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++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/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++-15 -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/RtmpKNxZwb/R.INSTALL1443ea3e4483b8/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 ‘ggtern’ ... ** this is package ‘ggtern’ version ‘4.0.0’ ** 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 ‘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 ‘1.7.9’ ** package ‘HardyWeinberg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-7) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpXn9k19/R.INSTALL1443f851c35079/HardyWeinberg/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/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++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/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++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/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++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/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++-15 -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/RtmpXn9k19/R.INSTALL1443f851c35079/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 ‘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) * installing *source* package ‘poppr’ ... ** this is package ‘poppr’ version ‘2.9.8’ ** package ‘poppr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-7) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpmJD8pK/R.INSTALL1446ad33f38074/poppr/src' gcc-15 -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-15 -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-15 -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-15 -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-15 -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-15 -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-15 -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-15 -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-15 -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-15 -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/RtmpmJD8pK/R.INSTALL1446ad33f38074/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 ‘3.1.3’ ** 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) checking ggtern_4.0.0.tar.gz ... checking tricolore_1.2.4.tar.gz ... checking dartR_2.9.9.5.tar.gz ... checking dartR.base_1.0.7.tar.gz ... checking vdar_0.1.3-2.tar.gz ... Depends: Package: ggtern Depends: R (>= 4.0), ggplot2 (>= 4.0.0) Imports: compositions (>= 2.0-2), grid, gridExtra (>= 2.3), gtable (>= 0.1.2), latex2exp (>= 0.5), MASS, plyr (>= 1.8.3), scales (>= 1.3.0), stats, proto (>= 1.0), utils, lattice, hexbin (>= 1.28.2), methods, rlang (>= 1.1.0) Timings: user system elapsed ggtern 110.539 6.024 118.21 Results: Check status summary: ERROR NOTE OK Source packages 0 1 0 Reverse depends 1 0 3 Check results summary: ggtern ... NOTE * checking CRAN incoming feasibility ... [6s/7s] NOTE rdepends_dartR.base ... OK rdepends_dartR ... OK rdepends_tricolore ... ERROR * checking tests ... [3s/3s] ERROR rdepends_vdar ... OK Check results changes: Package: tricolore Check: package dependencies Old result: ERROR New result: OK Package: tricolore Check: tests New result: ERROR Package: vdar Check: CRAN incoming feasibility Old result: NOTE