downloading reverse dependencies ... downloading dartR.base_0.98.tar.gz ... ok installing dependencies ‘dartR.data’, ‘ggtern’, ‘haplo.stats’, ‘HardyWeinberg’, ‘hierfstat’, ‘iterpc’, ‘leaflet.minicharts’, ‘mmod’, ‘poisbinom’, ‘poppr’, ‘rgl’, ‘SIBER’, ‘SNPassoc’, ‘SNPRelate’, ‘StAMPP’, ‘TxDb.Hsapiens.UCSC.hg19.knownGene’, ‘VariantAnnotation’ also installing the dependencies ‘arsenal’, ‘gdsfmt’, ‘polysat’ begin installing package ‘arsenal’ begin installing package ‘polysat’ begin installing package ‘gdsfmt’ begin installing package ‘poisbinom’ begin installing package ‘VariantAnnotation’ begin installing package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ begin installing package ‘dartR.data’ 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’ begin installing package ‘rgl’ * 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 ‘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 ‘arsenal’ ... ** package ‘arsenal’ 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 ** 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 (arsenal) begin installing package ‘haplo.stats’ * 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) * installing *source* package ‘poisbinom’ ... ** package ‘poisbinom’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpwXcs4F/R.INSTALL33157c8631888/poisbinom/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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 -I"/home/hornik/tmp/R-d-gcc-14/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-d-gcc-14/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-d-gcc-14/lib -Wl,-O1 -o poisbinom.so RcppExports.o init.o poisbinom.o -lfftw3 -lm -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpwXcs4F/R.INSTALL33157c8631888/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) * 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++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmphEu2U6/R.INSTALL3315714de235ae/polysat/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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-d-gcc-14/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-d-gcc-14/lib -Wl,-O1 -o polysat.so RcppExports.o deSilvaFuncs.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmphEu2U6/R.INSTALL3315714de235ae/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 ‘haplo.stats’ ... ** package ‘haplo.stats’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp5Pmzug/R.INSTALL331b154226738c/haplo.stats/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c groupsum.c -o groupsum.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c haplo.stats_init.c -o haplo.stats_init.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c haplo_em_pin.c -o haplo_em_pin.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c louis_info.c -o louis_info.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c seqhap.c -o seqhap.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o haplo.stats.so groupsum.o haplo.stats_init.o haplo_em_pin.o louis_info.o seqhap.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp5Pmzug/R.INSTALL331b154226738c/haplo.stats/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-haplo.stats/00new/haplo.stats/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 (haplo.stats) begin installing package ‘SNPassoc’ * installing *source* package ‘HardyWeinberg’ ... ** package ‘HardyWeinberg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpjmCJ8c/R.INSTALL33158411dac982/HardyWeinberg/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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-d-gcc-14/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-d-gcc-14/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-d-gcc-14/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-d-gcc-14/lib -Wl,-O1 -o HardyWeinberg.so HWxChromosomal.o RcppExports.o SNPHWEX.o support.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpjmCJ8c/R.INSTALL33158411dac982/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 ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ ... ** using staged installation ** R ** 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 (TxDb.Hsapiens.UCSC.hg19.knownGene) * installing *source* package ‘SNPassoc’ ... ** 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 ‘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 *** 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’ ... ** package ‘poppr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmphq2Uv9/R.INSTALL331c6dbc1da99/poppr/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/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 -I"/home/hornik/tmp/R-d-gcc-14/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 -I"/home/hornik/tmp/R-d-gcc-14/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 -I"/home/hornik/tmp/R-d-gcc-14/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 -I"/home/hornik/tmp/R-d-gcc-14/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 -I"/home/hornik/tmp/R-d-gcc-14/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 -I"/home/hornik/tmp/R-d-gcc-14/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 -I"/home/hornik/tmp/R-d-gcc-14/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 -I"/home/hornik/tmp/R-d-gcc-14/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 -shared -L/home/hornik/tmp/R-d-gcc-14/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-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmphq2Uv9/R.INSTALL331c6dbc1da99/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 ‘VariantAnnotation’ ... ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpOj1JLq/R.INSTALL33158750a5b04e/VariantAnnotation/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Biostrings_stubs.c -o Biostrings_stubs.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c IRanges_stubs.c -o IRanges_stubs.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o In file included from vcftype.h:8, from writevcf.h:4, from R_init_VariantAnnotation.c:3: strhash.h:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 8 | khash_t(strhash) *_strhash_new(); | ^~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c XVector_stubs.c -o XVector_stubs.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dna_hash.c -o dna_hash.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rle.c -o rle.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c strhash.c -o strhash.o In file included from strhash.c:2: strhash.h:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 8 | khash_t(strhash) *_strhash_new(); | ^~~~~~~ strhash.c:5:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 5 | khash_t(strhash) *_strhash_new() | ^~~~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c utilities.c -o utilities.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c vcffile.c -o vcffile.o In file included from vcftype.h:8, from vcffile.c:4: strhash.h:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 8 | khash_t(strhash) *_strhash_new(); | ^~~~~~~ vcffile.c:22:27: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 22 | static khash_t(WARNINGS) *vcfwarn_new() | ^~~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c vcftype.c -o vcftype.o In file included from vcftype.h:8, from vcftype.c:1: strhash.h:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 8 | khash_t(strhash) *_strhash_new(); | ^~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c writevcf.c -o writevcf.o In file included from vcftype.h:8, from writevcf.h:4, from writevcf.c:1: strhash.h:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 8 | khash_t(strhash) *_strhash_new(); | ^~~~~~~ gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o VariantAnnotation.so Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o writevcf.o /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpOj1JLq/R.INSTALL33158750a5b04e/VariantAnnotation/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-VariantAnnotation/00new/VariantAnnotation/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘tabulate’ in package ‘VariantAnnotation’ ** 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 (VariantAnnotation) * installing *source* package ‘rgl’ ... ** package ‘rgl’ successfully unpacked and MD5 sums checked ** using staged installation checking for gcc... gcc-14 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc-14 accepts -g... yes checking for gcc-14 option to enable C11 features... none needed checking how to run the C preprocessor... gcc-14 -E checking for gcc... (cached) gcc-14 checking whether the compiler supports GNU C... (cached) yes checking whether gcc-14 accepts -g... (cached) yes checking for gcc-14 option to enable C11 features... (cached) none needed checking for libpng-config... yes configure: using libpng-config configure: using libpng dynamic linkage checking for X... libraries , headers checking for XAllocClassHint... yes checking for GL/gl.h... yes checking for GL/glu.h... yes checking for glEnd in -lGL... yes checking for glEnd... yes checking for gluErrorString in -lGLU... yes checking for gluErrorString... yes checking for pkg-config... yes configure: using Freetype and FTGL configure: creating ./config.status config.status: creating R/noOpenGL.R config.status: creating src/useNULL/Makevars config.status: creating src/Makevars ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp4F1CFW/R.INSTALL33159143155a48/rgl/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c ABCLineSet.cpp -o ABCLineSet.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c BBoxDeco.cpp -o BBoxDeco.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Background.cpp -o Background.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c ClipPlane.cpp -o ClipPlane.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Color.cpp -o Color.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Disposable.cpp -o Disposable.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Light.cpp -o Light.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c LineSet.cpp -o LineSet.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c LineStripSet.cpp -o LineStripSet.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Material.cpp -o Material.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c NULLgui.cpp -o NULLgui.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c PlaneSet.cpp -o PlaneSet.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c PointSet.cpp -o PointSet.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c PrimitiveSet.cpp -o PrimitiveSet.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c R.cpp -o R.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RenderContext.cpp -o RenderContext.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Shape.cpp -o Shape.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c SphereMesh.cpp -o SphereMesh.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c SphereSet.cpp -o SphereSet.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c SpriteSet.cpp -o SpriteSet.o SpriteSet.cpp: In member function ‘virtual void rgl::SpriteSet::getAttribute(rgl::SceneNode*, rgl::AttribID, int, int, double*)’: SpriteSet.cpp:361:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 361 | for (int i = 0; i < shapelens.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Surface.cpp -o Surface.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c TextSet.cpp -o TextSet.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Texture.cpp -o Texture.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Viewpoint.cpp -o Viewpoint.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c api.cpp -o api.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c assert.cpp -o assert.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c callbacks.cpp -o callbacks.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c device.cpp -o device.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c devicemanager.cpp -o devicemanager.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c fps.cpp -o fps.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c ftgl.cpp -o ftgl.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c geom.cpp -o geom.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c gl.c -o gl.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c gl2ps.c -o gl2ps.o gl2ps.c: In function ‘gl2psBuildBspTree’: gl2ps.c:1619:3: warning: ‘prim’ may be used uninitialized [-Wmaybe-uninitialized] 1619 | gl2psGetPlane(prim, tree->plane); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gl2ps.c:1611:19: note: ‘prim’ declared here 1611 | GL2PSprimitive *prim, *frontprim = NULL, *backprim = NULL; | ^~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c glErrors.cpp -o glErrors.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c glgui.cpp -o glgui.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c gui.cpp -o gui.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c init.cpp -o init.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c par3d.cpp -o par3d.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pixmap.cpp -o pixmap.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c platform.cpp -o platform.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c pretty.c -o pretty.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c render.cpp -o render.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rglmath.cpp -o rglmath.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rglview.cpp -o rglview.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c scene.cpp -o scene.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c select.cpp -o select.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c subscene.cpp -o subscene.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c win32gui.cpp -o win32gui.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c win32lib.cpp -o win32lib.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c x11gui.cpp -o x11gui.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -I/usr/include/libpng16 -DR_NO_REMAP -Iext -Iext/glad/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c x11lib.cpp -o x11lib.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o rgl.so ABCLineSet.o BBoxDeco.o Background.o ClipPlane.o Color.o Disposable.o Light.o LineSet.o LineStripSet.o Material.o NULLgui.o PlaneSet.o PointSet.o PrimitiveSet.o R.o RenderContext.o Shape.o SphereMesh.o SphereSet.o SpriteSet.o Surface.o TextSet.o Texture.o Viewpoint.o api.o assert.o callbacks.o device.o devicemanager.o fps.o ftgl.o geom.o gl.o gl2ps.o glErrors.o glgui.o gui.o init.o par3d.o pixmap.o platform.o pretty.o render.o rglmath.o rglview.o scene.o select.o subscene.o win32gui.o win32lib.o x11gui.o x11lib.o -lGLU -lGL -lpng16 -lX11 -lfreetype -lz -lbz2 -lpng16 -lz -lm -lz -lbrotlidec -lbrotlicommon -L/home/hornik/tmp/R-d-gcc-14/lib -lR cp -Rp OpenGL useNULL && \ cp -p *.c *.h *.cpp useNULL/ && \ cd useNULL && \ /home/hornik/tmp/R-d-gcc-14/bin/R CMD SHLIB -o useNULL.so *.cpp *.c && \ cd .. && \ mkdir -p ../inst/useNULL && \ mv useNULL/useNULL.so ../inst/useNULL/rgl.so && \ rm useNULL/*.cpp useNULL/*.c useNULL/*.h useNULL/OpenGL/* using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[2]: Entering directory '/home/hornik/tmp/scratch/Rtmp4F1CFW/R.INSTALL33159143155a48/rgl/src/useNULL' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c ABCLineSet.cpp -o ABCLineSet.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c BBoxDeco.cpp -o BBoxDeco.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Background.cpp -o Background.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c ClipPlane.cpp -o ClipPlane.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Color.cpp -o Color.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Disposable.cpp -o Disposable.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Light.cpp -o Light.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c LineSet.cpp -o LineSet.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c LineStripSet.cpp -o LineStripSet.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Material.cpp -o Material.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c NULLgui.cpp -o NULLgui.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c PlaneSet.cpp -o PlaneSet.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c PointSet.cpp -o PointSet.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c PrimitiveSet.cpp -o PrimitiveSet.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c R.cpp -o R.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RenderContext.cpp -o RenderContext.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Shape.cpp -o Shape.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c SphereMesh.cpp -o SphereMesh.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c SphereSet.cpp -o SphereSet.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c SpriteSet.cpp -o SpriteSet.o SpriteSet.cpp: In member function ‘virtual void rgl::SpriteSet::getAttribute(rgl::SceneNode*, rgl::AttribID, int, int, double*)’: SpriteSet.cpp:361:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 361 | for (int i = 0; i < shapelens.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Surface.cpp -o Surface.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c TextSet.cpp -o TextSet.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Texture.cpp -o Texture.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Viewpoint.cpp -o Viewpoint.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c api.cpp -o api.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c assert.cpp -o assert.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c callbacks.cpp -o callbacks.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c device.cpp -o device.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c devicemanager.cpp -o devicemanager.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c fps.cpp -o fps.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c ftgl.cpp -o ftgl.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c geom.cpp -o geom.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c glErrors.cpp -o glErrors.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c glgui.cpp -o glgui.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c gui.cpp -o gui.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c init.cpp -o init.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c par3d.cpp -o par3d.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pixmap.cpp -o pixmap.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c platform.cpp -o platform.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c render.cpp -o render.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rglmath.cpp -o rglmath.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rglview.cpp -o rglview.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c scene.cpp -o scene.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c select.cpp -o select.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c subscene.cpp -o subscene.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c win32gui.cpp -o win32gui.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c win32lib.cpp -o win32lib.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c x11gui.cpp -o x11gui.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c x11lib.cpp -o x11lib.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c gl.c -o gl.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c gl2ps.c -o gl2ps.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DHAVE_PNG_H -I/usr/include/libpng16 -DRGL_NO_OPENGL -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c pretty.c -o pretty.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o useNULL.so ABCLineSet.o BBoxDeco.o Background.o ClipPlane.o Color.o Disposable.o Light.o LineSet.o LineStripSet.o Material.o NULLgui.o PlaneSet.o PointSet.o PrimitiveSet.o R.o RenderContext.o Shape.o SphereMesh.o SphereSet.o SpriteSet.o Surface.o TextSet.o Texture.o Viewpoint.o api.o assert.o callbacks.o device.o devicemanager.o fps.o ftgl.o geom.o glErrors.o glgui.o gui.o init.o par3d.o pixmap.o platform.o render.o rglmath.o rglview.o scene.o select.o subscene.o win32gui.o win32lib.o x11gui.o x11lib.o gl.o gl2ps.o pretty.o -lpng16 -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[2]: Leaving directory '/home/hornik/tmp/scratch/Rtmp4F1CFW/R.INSTALL33159143155a48/rgl/src/useNULL' make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp4F1CFW/R.INSTALL33159143155a48/rgl/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-rgl/00new/rgl/libs ** R ** demo ** inst ** byte-compile and prepare package for lazy loading ** 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 (rgl) * installing *source* package ‘gdsfmt’ ... ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpBcuplg/R.INSTALL331577243b7234/gdsfmt/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c R_CoreArray.cpp -o R_CoreArray.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c gdsfmt.cpp -o gdsfmt.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c digest.cpp -o digest.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CoreArray/CoreArray.cpp -o CoreArray/CoreArray.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CoreArray/dAllocator.cpp -o CoreArray/dAllocator.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CoreArray/dAny.cpp -o CoreArray/dAny.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CoreArray/dBase.cpp -o CoreArray/dBase.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CoreArray/dBitGDS.cpp -o CoreArray/dBitGDS.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CoreArray/dEndian.cpp -o CoreArray/dEndian.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CoreArray/dFile.cpp -o CoreArray/dFile.o CoreArray/dFile.cpp: In member function ‘void CoreArray::CdObjAttr::Delete(int)’: CoreArray/dFile.cpp:129:17: warning: ignoring return value of ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::at(size_type) [with _Tp = CoreArray::CdObjAttr::TdPair*; _Alloc = std::allocator; reference = CoreArray::CdObjAttr::TdPair*&; size_type = long unsigned int]’, declared with attribute ‘nodiscard’ [-Wunused-result] 129 | fList.at(Index); // check range | ~~~~~~~~^~~~~~~ In file included from /usr/include/c++/14/vector:66, from CoreArray/dPlatform.h:48, from CoreArray/dEndian.h:40, from CoreArray/dBase.h:41, from CoreArray/dFile.h:40, from CoreArray/dFile.cpp:28: /usr/include/c++/14/bits/stl_vector.h:1180:7: note: declared here 1180 | at(size_type __n) | ^~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CoreArray/dParallel.cpp -o CoreArray/dParallel.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c CoreArray/dParallel_Ext.c -o CoreArray/dParallel_Ext.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CoreArray/dPlatform.cpp -o CoreArray/dPlatform.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CoreArray/dRealGDS.cpp -o CoreArray/dRealGDS.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CoreArray/dSerial.cpp -o CoreArray/dSerial.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CoreArray/dStrGDS.cpp -o CoreArray/dStrGDS.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CoreArray/dStream.cpp -o CoreArray/dStream.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CoreArray/dStruct.cpp -o CoreArray/dStruct.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CoreArray/dSparse.cpp -o CoreArray/dSparse.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CoreArray/dVLIntGDS.cpp -o CoreArray/dVLIntGDS.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c -g0 ZLIB/adler32.c -o ZLIB/adler32.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c -g0 ZLIB/compress.c -o ZLIB/compress.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c -g0 ZLIB/crc32.c -o ZLIB/crc32.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c -g0 ZLIB/deflate.c -o ZLIB/deflate.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c -g0 ZLIB/infback.c -o ZLIB/infback.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c -g0 ZLIB/inffast.c -o ZLIB/inffast.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c -g0 ZLIB/inflate.c -o ZLIB/inflate.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c -g0 ZLIB/inftrees.c -o ZLIB/inftrees.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c -g0 ZLIB/trees.c -o ZLIB/trees.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c -g0 ZLIB/uncompr.c -o ZLIB/uncompr.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c -g0 ZLIB/zutil.c -o ZLIB/zutil.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LZ4/lz4.c -o LZ4/lz4.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LZ4/lz4hc.c -o LZ4/lz4hc.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LZ4/lz4frame.c -o LZ4/lz4frame.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LZ4/xxhash.c -o LZ4/xxhash.o cd XZ && tar -xzf xz-5.2.9.tar.gz cd XZ/xz-5.2.9 && \ ./configure CC="gcc-14 " CPP="gcc-14 -E" CXX="g++-14 -std=gnu++17" CXXCPP="" --build="" \ --with-pic --enable-silent-rules --quiet --disable-xz --disable-shared > /dev/null cd XZ/xz-5.2.9/src/liblzma && make make[2]: Entering directory '/home/hornik/tmp/scratch/RtmpBcuplg/R.INSTALL331577243b7234/gdsfmt/src/XZ/xz-5.2.9/src/liblzma' Making all in api make[3]: Entering directory '/home/hornik/tmp/scratch/RtmpBcuplg/R.INSTALL331577243b7234/gdsfmt/src/XZ/xz-5.2.9/src/liblzma/api' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/home/hornik/tmp/scratch/RtmpBcuplg/R.INSTALL331577243b7234/gdsfmt/src/XZ/xz-5.2.9/src/liblzma/api' make[3]: Entering directory '/home/hornik/tmp/scratch/RtmpBcuplg/R.INSTALL331577243b7234/gdsfmt/src/XZ/xz-5.2.9/src/liblzma' CC liblzma_la-tuklib_physmem.lo CC liblzma_la-tuklib_cpucores.lo CC liblzma_la-common.lo CC liblzma_la-block_util.lo CC liblzma_la-easy_preset.lo CC liblzma_la-filter_common.lo CC liblzma_la-hardware_physmem.lo CC liblzma_la-index.lo CC liblzma_la-stream_flags_common.lo CC liblzma_la-vli_size.lo CC liblzma_la-hardware_cputhreads.lo CC liblzma_la-alone_encoder.lo CC liblzma_la-block_buffer_encoder.lo CC liblzma_la-block_encoder.lo CC liblzma_la-block_header_encoder.lo CC liblzma_la-easy_buffer_encoder.lo CC liblzma_la-easy_encoder.lo CC liblzma_la-easy_encoder_memusage.lo CC liblzma_la-filter_buffer_encoder.lo CC liblzma_la-filter_encoder.lo CC liblzma_la-filter_flags_encoder.lo CC liblzma_la-index_encoder.lo CC liblzma_la-stream_buffer_encoder.lo CC liblzma_la-stream_encoder.lo CC liblzma_la-stream_flags_encoder.lo CC liblzma_la-vli_encoder.lo CC liblzma_la-outqueue.lo CC liblzma_la-stream_encoder_mt.lo CC liblzma_la-alone_decoder.lo CC liblzma_la-auto_decoder.lo CC liblzma_la-block_buffer_decoder.lo CC liblzma_la-block_decoder.lo CC liblzma_la-block_header_decoder.lo CC liblzma_la-easy_decoder_memusage.lo CC liblzma_la-filter_buffer_decoder.lo CC liblzma_la-filter_decoder.lo CC liblzma_la-filter_flags_decoder.lo CC liblzma_la-index_decoder.lo CC liblzma_la-index_hash.lo CC liblzma_la-stream_buffer_decoder.lo CC liblzma_la-stream_decoder.lo CC liblzma_la-stream_flags_decoder.lo CC liblzma_la-vli_decoder.lo CC liblzma_la-check.lo CC liblzma_la-crc32_table.lo CC liblzma_la-crc32_fast.lo CC liblzma_la-crc64_table.lo CC liblzma_la-crc64_fast.lo CC liblzma_la-sha256.lo CC liblzma_la-lz_encoder.lo CC liblzma_la-lz_encoder_mf.lo CC liblzma_la-lz_decoder.lo CC liblzma_la-lzma_encoder_presets.lo CC liblzma_la-lzma_encoder.lo CC liblzma_la-lzma_encoder_optimum_fast.lo CC liblzma_la-lzma_encoder_optimum_normal.lo CC liblzma_la-fastpos_table.lo CC liblzma_la-lzma_decoder.lo CC liblzma_la-lzma2_encoder.lo CC liblzma_la-lzma2_decoder.lo CC liblzma_la-price_table.lo CC liblzma_la-delta_common.lo CC liblzma_la-delta_encoder.lo CC liblzma_la-delta_decoder.lo CC liblzma_la-simple_coder.lo CC liblzma_la-simple_encoder.lo CC liblzma_la-simple_decoder.lo CC liblzma_la-x86.lo CC liblzma_la-powerpc.lo CC liblzma_la-ia64.lo CC liblzma_la-arm.lo CC liblzma_la-armthumb.lo CC liblzma_la-sparc.lo CCLD liblzma.la PC liblzma.pc make[3]: Leaving directory '/home/hornik/tmp/scratch/RtmpBcuplg/R.INSTALL331577243b7234/gdsfmt/src/XZ/xz-5.2.9/src/liblzma' make[2]: Leaving directory '/home/hornik/tmp/scratch/RtmpBcuplg/R.INSTALL331577243b7234/gdsfmt/src/XZ/xz-5.2.9/src/liblzma' cp XZ/xz-5.2.9/src/liblzma/.libs/liblzma.a . rm -rf XZ/xz-5.2.9/dos rm -rf XZ/xz-5.2.9/po g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o gdsfmt.so R_CoreArray.o gdsfmt.o digest.o CoreArray/CoreArray.o CoreArray/dAllocator.o CoreArray/dAny.o CoreArray/dBase.o CoreArray/dBitGDS.o CoreArray/dEndian.o CoreArray/dFile.o CoreArray/dParallel.o CoreArray/dParallel_Ext.o CoreArray/dPlatform.o CoreArray/dRealGDS.o CoreArray/dSerial.o CoreArray/dStrGDS.o CoreArray/dStream.o CoreArray/dStruct.o CoreArray/dSparse.o CoreArray/dVLIntGDS.o ZLIB/adler32.o ZLIB/compress.o ZLIB/crc32.o ZLIB/deflate.o ZLIB/infback.o ZLIB/inffast.o ZLIB/inflate.o ZLIB/inftrees.o ZLIB/trees.o ZLIB/uncompr.o ZLIB/zutil.o LZ4/lz4.o LZ4/lz4hc.o LZ4/lz4frame.o LZ4/xxhash.o ./liblzma.a -lpthread -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpBcuplg/R.INSTALL331577243b7234/gdsfmt/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-gdsfmt/00new/gdsfmt/libs ** 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 ** 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 (gdsfmt) begin installing package ‘SNPRelate’ * installing *source* package ‘SNPRelate’ ... ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpWTYCgO/R.INSTALL333a2c2385e2fb/SNPRelate/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/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 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/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-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/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-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/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-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/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-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/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-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/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-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/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-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/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-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/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-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/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-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/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-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/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-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/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-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/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-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/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-d-gcc-14/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-d-gcc-14/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpWTYCgO/R.INSTALL333a2c2385e2fb/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) checking SNPassoc_2.1-2.tar.gz ... checking dartR.base_0.98.tar.gz ... Depends: Package: SNPassoc Depends: R (>= 4.0.0) Imports: haplo.stats, mvtnorm, parallel, survival, tidyr, plyr, ggplot2, poisbinom Timings: user system elapsed SNPassoc 127.525 12.798 134.663 Results: Check status summary: OK Source packages 1 Reverse depends 1 Check results summary: SNPassoc ... OK rdepends_dartR.base ... OK